Subset (5)

F1000Journal · 8.11k rows

Split (1)

data · 8.11k rows

link stringlengths 41 45	date stringlengths 9 9	paper dict	reviews listlengths 1 6	version int64 1 5	main stringlengths 38 42
https://f1000research.com/articles/13-406/v1	26 Apr 24	{ "type": "Case Report", "title": "Case Report: Pre- and post-natal evolution of Kabuki Syndrome due to a novel genetic mutation", "authors": [ "Nesrine Souayeh", "Asma MARZOUK", "Nour Jelalia", "Ikhlas BEN AYED", "Alaa Ziadi", "Madiha TRABELSI", "Asma Bouaziz", "Najeh Hsayaoui", "Asma MARZOUK", "Nour Jelalia", "Ikhlas BEN AYED", "Alaa Ziadi", "Madiha TRABELSI", "Asma Bouaziz", "Najeh Hsayaoui" ], "abstract": "Kabuki syndrome is a rare condition characterized by intellectual disability, poly-malformative syndrome, and distinctive facial dysmorphia. It also exhibits clinical and biological heterogeneity, with rare and diverse symptoms. Genetic analysis plays a significant role in both positive diagnosis and prognosis. Recently, whole exome sequencing has identified several genes responsible for the disease, notably KMT2D and KDM6A. Studying new mutations in this disease will contribute to understanding the role of these genes in the pathogenesis of Kabuki syndrome. We report a case of a 9-and-a-half-year-old boy, born to non-consanguineous parents, diagnosed with Kabuki syndrome. This article describes the prenatal diagnosis process and the postnatal progression. Genetic analysis revealed a novel missense point mutation in the KMT2D gene, classified as a class 4 missense mutation, responsible for Kabuki syndrome.", "keywords": [ "Kabuki syndrome", "mutation", "exome", "genetic study", "intellectual disability", "case report" ], "content": "Introduction\n\nKabuki syndrome is a rare poly-malformative syndrome associated with variable degrees of intellectual disability and specific facial dysmorphology. It was first described by Niikawa et al.1 and Kuroki et al.2 in Japan in 1981. Kabuki syndrome is defined by five essential diagnostic criteria: specific craniofacial dysmorphology, growth retardation, intellectual disability, skeletal manifestations, and dermatoglyphic anomalies. Other clinical symptoms may also be present but are not always observed. The prevalence of Kabuki syndrome is estimated to be around 1 in 32,000 births.1 There are two genes responsible for this condition: primarily, germline heterozygous loss of function mutations in KMT2D gene, also known as lysine methyltransferase 2D (MLL2), which encodes a methyltransferase, and secondarily, the lysine demethylase 6A (KDM6A) gene, the second gene identified in this disorder, which codes for a histone demethylase. The number of individuals with mutations in this gene is currently low. In this case report, we present a case of Kabuki syndrome suspected in the prenatal period and confirmed by genetic analysis, revealing a novel mutation with a favorable prognosis, particularly regarding intellectual function. The objective of our report was to further elucidate the clinical and biological manifestations of this condition and highlight the importance of early genetic diagnosis.\n\n\nCase report\n\nWe present the case of a nine-and-a-half-year-old boy who has been followed since birth for Kabuki syndrome. His mother has no significant medical history, and no similar cases have been reported in the family.\n\nThe mother was twenty-nine years old, Para 0, Gravida 1, with no familial history of genetic abnormalities or intellectual defect. She was referred by a private gynecologist to the Department of Gynecology and Obstetrics at Ben Arous Regional Hospital following the discovery at 26 weeks’ gestation of ventriculomegaly with bilateral pyelectasis. The pregnancy follow-up was irregular, and the mother didn’t undergo first-trimester combined screening for chromosome abnormalities.\n\nUltrasound performed at our department showed bilateral colpocephaly associated with an enlarged cavum pellucidum (Figure 1). Furthermore, biometric measurements did not reveal intrauterine fetal growth restriction. All tests for common infectious diseases such as Toxoplasmosis, syphilis, varicella-zoster virus, parvovirus B19, Rubella, Cytomegalovirus, and Herpes simplex virus come back negative.\n\nA fetal Magnetic Resonance Imaging (MRI) was performed at 28 weeks’ gestation, confirming the diagnosis of agenesis of the corpus callosum associated with ventriculomegaly, without other associated malformations, particularly no other abnormalities to the brain (Figure 2).\n\nAn amniocentesis was performed after parental consent to obtain standard karyotype, which showed a normal male 46, XY chromosomal formula.\n\nA meeting was organized with the parents, involving gynecologists and pediatricians, to discuss the possible origins of the anomalies and their associated prognosis. The parents decided to continue the pregnancy to term without any further investigations.\n\nThe patient was born vaginally at 37 weeks’ gestation with good adaptation to extrauterine life. Upon initial examination, he was eutrophic with a weight of 3050 g, length of 49 cm, and head circumference of 34 cm. He exhibited facial dysmorphology, including a flat occiput, prominence of the metopic suture, an oval-shaped face with a narrow forehead, large almond-shaped eyes, and intermittent convergent strabismus of the left eye. Examination of the limbs revealed flat feet, without any other musculoskeletal malformations. However, upon examination of the external genitalia, no gonads could be palpated.\n\nHe was initially hospitalized for transient respiratory distress, which resolved within 48 hours. A grade 3 murmur was also detected upon cardiac auscultation at the aortic area. Upon examination of the external genitalia, gonads were not palpable. The neurological examination was unremarkable.\n\nThe patient’s facial dysmorphology became more evident at the age of 4 years and 9 months. It was characterized by a flattening of the occiput, marked microcephaly at (-2) standard deviations (SD) with prominence of the metopic suture, and an oval-shaped face with a narrow forehead. The eyes showed sparse outer halves of both eyebrows, increased eye size with heavy eyeliner, intermittent convergent strabismus of the left eye, inversion, or eversion of the lower eyelids on both sides, forward-tilted nostrils, a mildly marked philtrum with notable depression at the root and tip of the nose (Figure 3). The ears were wide and protruding, with outwardly turned earlobes. In the oral cavity, there was a high-arched palate, a small mouth with a thin upper lip, and micrognathia (Figure 3). In the limbs, bilateral brachydactyly of the hands was observed (Figure 4a) but radiological examination did not provide evidence supporting this finding (Figure 5). Hypoplastic nails of the 5th fingers and toes, bilateral persistence of fetal fingerprints, and ligamentous hyperlaxity with loose skin were also noted (Figure 4 a,b).\n\na: Bilateral brachydactyly of the hands; b: Hypoplastic nails of the 5th fingers and toes, bilateral persistence of fetal fingerprints, and ligamentous hyperlaxity with loose skin.\n\nIn terms of psychomotor development, there was a slight delay in achieving a sitting position at nine months and walking at eighteen months. Speech therapy evaluation revealed nasal speech with a slight delay in language acquisition, with the patient starting to form short phrases at the age of three.\n\nNeurological investigations showed agenesis of the corpus callosum on transfontanellar ultrasound performed on day 32 of life. Given these lesions and the flat occiput, the diagnosis of Crouzon syndrome was suspected, which also remains a differential diagnosis of Kabuki syndrome. A subsequent brain CT-scan revealed a complete agenesis of the corpus callosum, associated with dilation and enlargement of the occipital horns of the lateral ventricles, colpocephaly, distortion of the frontal horns of the lateral ventricles resembling the appearance of bull horns, and ascent of the roof of the third ventricle. Partial filling and hypoplasia of the maxillary sinuses and agenesis of the frontal sinuses were also observed, with no signs of craniofacial dysostosis. A brain Magnetic Resonance Imaging confirmed the total agenesis of the corpus callosum, with an eccentric appearance of the lateral ventricles and bilateral dilations of the occipital and temporal horns.\n\nRegarding neurosensory evaluations, an ophthalmological examination performed under general anesthesia revealed visual acuity of 5/10 with correction in the right eye and 7/10 in the left eye, along with convergent strabismus in the left eye. Auditory-evoked potentials were found to be normal.\n\nOn the therapeutic level, speech therapy intervention was carried out, and the following results were observed after rehabilitation: Currently, the patient presents with logorrhea, some pronunciation difficulties, and a normal IQ. He presents a significant improvement in communication, good comprehension of simple instructions, good acquisition of oral and written language, and no contraindications for school inclusion. The recommended approach and therapeutic plan included parental initiation and guidance, referral to a specialized center or other specialties for school integration, continued speech therapy, and recommended consultations with child psychiatry.\n\nIn terms of growth and weight, the patient experienced stature growth retardation with a deviation from the growth curve at the age of 5 years (Figure 6). Bone age evaluation performed at the chronological age of 5 years revealed a 2-year lag compared to the chronological age, suggesting a possible endocrine cause. Blood tests showed Thyroid-stimulating hormone (TSH) at 1.88 μIU/ml (0.35-4.94 μIU/ml), Thyroxin (FT4) at 13.97 pmol/l (9-19 pmol/l), cortisol level at 140 ng/ml (100-240 ng/ml), Adrenocorticotropic hormone (ACTH) at 28.6 ng/l (7.2-63.3 ng/l), Insulin Growth factor 1 (IGF1) at 87.53 ng/ml (associated with normal liver function), insulin stimulation test for Growth hormone (GH) secretion at 4.63 ng/ml (>20 ng/ml). The diagnosis of growth hormone deficiency was established. A Magnetic Resonance Imaging (MRI) of the hypothalamus-pituitary region showed no abnormalities. The patient was started on injectable growth hormone therapy at a dose of 0.030 mg/kg/day subcutaneously, with good progress (average height gain of 7.5 cm per year) (Figure 6).\n\nRegarding the respiratory tract, the patient had recurrent episodes of bronchiolitis associated with pneumonia, with a frequency of two infections per year. The latest episode was at the age of eight years old. An initial immunodeficiency workup returned normal.\n\nRegarding the cardiac aspect, the cardiac ultrasound performed at birth revealed a restrictive subaortic ventricular septal defect without significant impact on the heart. Subsequent echocardiographic evaluations showed the same aspect of the ventricular septal defect (VSD), and periodic monitoring was recommended without the need for surgical intervention. Currently, he presents with a small VSD without any significant impact.\n\nThe anomalies identified during the prenatal ultrasound have been confirmed. An abdominal ultrasound performed at the age of one month revealed left renal megacalycosis. A follow-up ultrasound at the age of one year showed left pyelectasis with anterior-posterior pyelic diameter (APPD) of 16mm, without visible obstruction, consistent with pyelo-ureteral junction syndrome. A renal scintigraphy performed at the age of 4 years showed left pyelectasis with satisfactory non-obstructive drainage and symmetrical renal function. The right kidney showed early perfusion and uptake with delayed drainage, responding fully to Lasix injection, with an estimated relative function of 48%. The left kidney showed normal perfusion and uptake, with pyelectasis and delayed drainage responding to Lasix injection, with an estimated relative function of 52%. A retrograde uretero-cystography was performed, and showed no abnormalities, particularly no passive or active vesicoureteral reflux. The patient is currently being followed up in pediatric surgery. He did not experience urinary tract infections.\n\nAdditionally, in the presence of empty scrotum, testicular ultrasound revealed two inguinal testicles. He underwent surgery without any complications.\n\nAs part of the genetic investigation, a postnatal karyotype was performed, resulting in 46, XY normal formula. To confirm the diagnosis, DNA extraction was carried out and high-throughput sequencing using the MiSeq sequencer was performed, thanks to a custom panel containing genes implicated in Kabuki syndrome as described in the literature. Subsequently, bioinformatic analysis was completed for variant annotation, filtration, and classification. A variant in the KMT2D gene (NM_003482.4): c.11782C>T (p.Gln3928Ter) was identified, representing a likely pathogenic class 4 missense point mutation according to the recommendations of the American College of Medical Genetics and Genomics (ACMG) (Figure 7).\n\n\nDiscussion\n\nKabuki syndrome presents a high interindividual clinical variability.3 The initial clinical presentation varies from person to person.4 Growth retardation is almost always present. In our patient, stature growth retardation was observed from the age of six months, but there was no weight retardation. Auditory abnormalities are observed in 20 to 30% of cases5 but were not observed in our patient. These abnormalities can be due to conductive, sensorineural, or mixed hearing loss. Ophthalmological abnormalities such as strabismus, ptosis, and corneal anomalies can impact vision.5 In our study, our patient presented with convergent strabismus and myopia. Hypotonia is an important sign in Kabuki syndrome, often noted from birth and persisting for several years,6 often associated with swallowing difficulties due to hypotonia. In our patient, hypotonia and swallowing difficulties were absent. The most common musculoskeletal abnormalities in Kabuki syndrome are brachydactyly, brachymesophalangy, clinodactyly of the 5th finger, scoliosis, hypermobility, or dislocation of certain joints.7 Musculoskeletal abnormalities were mostly consistent with the literature, except for scoliosis, which was not present in our patient.\n\nCardiac involvement is found in 50% of patients.8 The most common malformations are atrial or ventricular septal defects and aortic coarctation. In our observation, a restrictive ventricular septal defect was noted, but without cardiac impairment. Renal abnormalities have been observed in 25% of Kabuki syndrome patients.8 These abnormalities include hydronephrosis, abnormal kidney position, and renal dysplasia. In our observation, the patient had malformative uropathy in the form of pyeloureteral junction syndrome without involvement of the upper urinary tract. In the literature, the association of pyeloureteral junction syndrome with Kabuki syndrome has not been reported. Growth hormone (GH) deficiency or hyperinsulinism have been described in 15 to 25% of cases.4,7 In our case, the patient suffered from GH deficiency and was successfully treated with hormone replacement therapy. Gastrointestinal and hepatic abnormalities are described in only 5% of Kabuki syndrome patients. These can include intestinal malrotation, anorectal anomalies, ano-vestibular fistulas, biliary atresia, and hepatic fibrosis.6 In our case, no gastrointestinal or hepatic abnormalities were noted. Sixty percent of patients develop infections, mainly chronic otitis media, upper respiratory tract infections, and pneumonia. This increased susceptibility to infections could be due to anatomical or immunological abnormalities.8 There is an associated immune deficiency with IgA deficiency and hypogammaglobulinemia.9 Our patient suffered from recurrent acute bronchiolitis before the age of two, with signs of maxillary sinusitis on brain CT scan. An immune assessment was performed on our patient and showed no abnormalities.\n\nThe diagnosis of Kabuki syndrome is usually suspected based on clinical presentation but confirmed through genetic testing. The majority of affected patients are sporadic cases, but there are some cases in the literature with autosomal dominant transmission.9,10 The KMT2D or MLL2 gene, also known as ALR (ALL1-related gene), is the most well-known gene responsible for Kabuki syndrome. It is located on chromosome 12. The encoded protein is a histone-3-lysine-4-methyltransferase. The clinical heterogeneity found in this disease can be explained by the pleiotropic effect of KMT2D and its variable expression.11,12 A 2010 exome sequencing study of 10 patients with Kabuki syndrome identified the KMT2D gene as a major cause.13 According to several studies, a mutation in the KMT2D gene is found in 56 to 75% of cases,13,14 thus determining Kabuki syndrome type 1.9 Nonsense mutations are the most frequent. Furthermore, there are rare cases of mosaic mutations that are identified during Kabuki syndrome.15 The second gene responsible for Kabuki syndrome is KDM6A (or UTX), located on the X chromosome, that codes for the KDM6A protein, responsible for Kabuki syndrome type 2.9 There is an interaction between the two proteins KDM6A and KMT2D.16 Facial dysmorphia is more pronounced in type 1, while cardiovascular abnormalities are more frequent in type 2. The diagnostic approach in cases of Kabuki syndrome requires initial screening for mutations in the KMT2D gene since it is the most frequent. If the clinical presentation strongly suggests it, further screening for mutations in the KDM6A gene or large DNA rearrangements may be necessary if no mutations are found in the KMT2D gene. In our case, we identified the KMT2D variant (NM_003482.4): c.11782C>T (p.Gln3928Ter), which is a point mutation by substitution in the KMT2D gene, a likely pathogenic nonsense mutation of class 4 according to the recommendations of the American College of Medical Genetics and Genomics “ACMG,” and not reported in the “Clinvar” database (Figure 7). Finally, Sanger sequencing was performed to confirm the mutation. This genetic mutation determined a phenotype characterized by the absence of neonatal hypotonia or swallowing disorders,9 the absence of frequent immune deficiency seen in other phenotypes, the absence of digestive abnormalities, the presence of facial dysmorphia typical of type 1 associated with a more frequent cardiac malformation in type 2,9 the presence of an endocrinopathy such as GH deficiency, which responds to usual doses of replacement hormones unlike other genetic abnormalities such as Turner syndrome,17 and an average intellectual level as described in the literature.17 Furthermore, there are several differential diagnoses that can delay the positive diagnosis, such as CHARGE syndrome characterized by a cleft palate, which may be present in Kabuki syndrome but absent in our case.18 Another possibility is 22q11 deletion syndrome characterized by urinary tract malformations but presenting different facial features.18 There is also Crouzon syndrome characterized by ventriculomegaly, similar to our case, but with facial dysmorphia characterized by a prominent forehead and hypoplastic nasal bone. Therefore, genetic testing is essential for a definitive diagnosis.19\n\nFinally, this case report’s strength resides in the coherence of the diagnostic process and the long-term surveillance enabling us to describe all the clinical abnormalities’ evolution in time.\n\n\nConclusions\n\nThe diagnosis of Kabuki syndrome is clinical. However, confirmation through genetic testing is necessary to optimize patient management, establish a rapid screening strategy, and especially to address the multiple complications associated with the syndrome. Kabuki syndrome is characterized by phenotypic heterogeneity due to the various mutations described. The syndrome is inherited in an autosomal dominant manner, highlighting the importance of genetic counseling. Prenatal diagnosis is increasingly recommended, even though the risk of recurrence of this condition is low.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient’s legal guardian on the 10th July 2023.\n\n\nAuthor’s contribution\n\nAll authors contributed to the exploration and/or therapeutic management of the case report. Nesrine Souayeh and Asma Marzouk: drafted and revised the manuscript. All authors contributed to the study design approved the final manuscript.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nHarvard Dataverse: CARE checklist for ‘Pre- and Post-natal evolution of Kabuki Syndrome due to a novel genetic mutation’. https://doi.org/10.7910/DVN/WXEZW1\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nNiikawa N, Matsuura N, Fukushima Y, et al.: Kabuki make-up syndrome: a syndrome of mental retardation, unusual facies, large and protruding ears, and postnatal growth deficiency. J. Pediatr. 1981 Oct; 99(4): 565–569. PubMed Abstract \| Publisher Full Text\n\nKuroki Y, Suzuki Y, Chyo H, et al.: A new malformation syndrome of long palpebral fissures, large ears, depressed nasal tip, and skeletal anomalies associated with postnatal dwarfism and mental retardation. J. Pediatr. 1981 Oct; 99(4): 570–573. PubMed Abstract \| Publisher Full Text\n\nKokitsu-Nakata NM, Petrin AL, Heard JP, et al.: Analysis of MLL2 gene in the first Brazilian family with Kabuki syndrome. Am. J. Med. Genet. A. 2012 Aug; 158A(8): 2003–2008. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBögershausen N, Wollnik B: Unmasking Kabuki syndrome. Clin. Genet. 2013 Mar; 83(3): 201–211. PubMed Abstract \| Publisher Full Text\n\nBokinni Y: Kabuki syndrome revisited. J. Hum. Genet. 2012 Apr; 57(4): 223–227. PubMed Abstract \| Publisher Full Text\n\nMichot C, Corsini C, Sanlaville D, et al.: Finger creases lend a hand in Kabuki syndrome. Eur. J. Med. Genet. 2013 Oct; 56(10): 556–560. PubMed Abstract \| Publisher Full Text\n\nAdam MP, Hudgins L: Kabuki syndrome: a review. Clin. Genet. 2005 Mar; 67(3): 209–219. Publisher Full Text\n\nCourcet JB, Faivre L, Michot C, et al.: Clinical and molecular spectrum of renal malformations in Kabuki syndrome. J. Pediatr. 2013 Sep; 163(3): 742–746. PubMed Abstract \| Publisher Full Text\n\nBarry KK, Tsaparlis M, Hoffman D, et al.: From Genotype to Phenotype—A Review of Kabuki Syndrome. Genes. 2022 Sep 29; 13(10): 1761. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCourtens W, Rassart A, Stene JJ, et al.: Further evidence for autosomal dominant inheritance and ectodermal abnormalities in Kabuki syndrome. Am. J. Med. Genet. 2000 Jul 31; 93(3): 244–249. PubMed Abstract \| Publisher Full Text\n\nAnsari KI, Mandal SS: Mixed lineage leukemia: roles in gene expression, hormone signaling and mRNA processing. FEBS J. 2010 Apr; 277(8): 1790–1804. PubMed Abstract \| Publisher Full Text\n\nAnsari KI, Kasiri S, Hussain I, et al.: Mixed lineage leukemia histone methylases play critical roles in estrogen-mediated regulation of HOXC13. FEBS J. 2009; 276(24): 7400–7411. PubMed Abstract \| Publisher Full Text\n\nPaulussen ADC, Stegmann APA, Blok MJ, et al.: MLL2 mutation spectrum in 45 patients with Kabuki syndrome. Hum. Mutat. 2011 Feb; 32(2): E2018–E2025. PubMed Abstract \| Publisher Full Text\n\nMiyake N, Koshimizu E, Okamoto N, et al.: MLL2 and KDM6A mutations in patients with Kabuki syndrome. Am. J. Med. Genet. A. 2013 Sep; 161A(9): 2234–2243. PubMed Abstract \| Publisher Full Text\n\nPriolo M, Micale L, Augello B, et al.: Absence of deletion and duplication of MLL2 and KDM6A genes in a large cohort of patients with Kabuki syndrome. Mol. Genet. Metab. 2012 Nov; 107(3): 627–629. PubMed Abstract \| Publisher Full Text\n\nLederer D, Grisart B, Digilio MC, et al.: Deletion of KDM6A, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome. Am. J. Hum. Genet. 2012; 90(1): 119–124. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCaciolo C, Alfieri P, Piccini G, et al.: Neurobehavioral features in individuals with Kabuki syndrome. Mol. Genet. Genomic Med. 2018 Mar 13; 6(3): 322–331. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSamri I: Kabuki syndrome: first Moroccan series [dissertation]. Morocco: 2018.\n\nAdam MP, Banka S, Bjornsson HT, et al.: Kabuki syndrome: international consensus diagnostic criteria. J. Med. Genet. 2019 Feb; 56(2): 89–95. PubMed Abstract \| Publisher Full Text" }	[ { "id": "301560", "date": "17 Jul 2024", "name": "Hans van Bokhoven", "expertise": [ "Reviewer Expertise Neurogenetics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case report describes a young boy with clinical features reminiscent of Kabuki syndrome. The clinical diagnosis was supported by the identification of a nonsense variant in the KMT2D gene in the boy.\nThis case report adds to the phenotypic and genotypic variability known for Kabuki syndrome and in that respect the novelty of this report is limited; i.e. a confirmatory finding. While not spectacular, for a case report this would be acceptable. The report could be improved by several adaptations.\nMost importantly, it is never stated whether the nonsense variant is de novo or inherited. If the latter would be the case, a more in depth clinical report of the parent carrying the variant would be required. In addition, in that case one would be curious to know whether this parent is mosaic for the variant. If the variant id de novo, it should be explicitly stated in this case report. Figure 7 is confusing. Please provide a figure that clearly shows the variant, preferably in the same orientation as the reading frame of the gene. The Sanger sequences of the variant in the patient and in a control 9a parent) would be a lot more informative. The clinical images are not very informative. Images in figure 1 and 2 should clearly depict the anomalies (by arrows and other indicators) that can be discerned. In figure 3, the main features that would point to Kabuki syndrome cannot be seen. Figures 4 and 5 could be combined in one figure. In addition to that. It would have been nice to have another figure 5 that presents the CT- and/or MRI brain scans that reveled several important brain structural anomalies as mentioned in the text. In the introduction it is said that the identified variant has a favorable prognosis. What is the rationale of this claim. In the introduction it would be helpful to provide the OMIM links to both types of KS. Please provide comparative values of growth values (weight, length, head circumference) for the geographical comparators (e.g. P<50%).\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] }, { "id": "306044", "date": "12 Aug 2024", "name": "Kazuhiko Nakabayashi", "expertise": [], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSouayeh et al. reported a case of a 9-and-a-half-year-old boy who was suspected for Kabuki syndrome since the prenatal period. The authors conducted a custom panel sequencing, and identified a likely pathogenic variant in the KMT2D gene. Although the authors did not specify when this genetic testing was conducted, the result seemed to allow the authors to determine the diagnosis of this patient as Kabuki syndrome.\nI suggest the authors report the likely pathogenic KMT2D variant in ClinVar.\nIn the current manuscript, it is hard to figure out which of the known major and minor Kabuki syndrome phenotypes the patient exhibits or exhibited. I suggest the authors refer to the clinical findings from 80 Kabuki syndrome patients described by Faundes et al 2021,Table 1 (Ref 1), and describe whether their patient exhibits each of the clinical features or not in a table format.\nThe authors need to present their sequencing data showing the presence of the likely pathogenic variant (c.11782C>T): either the result of the custom panel sequencing visualized using a genome browser such as IGV or the Sanger sequencing result.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-406
https://f1000research.com/articles/13-405/v1	26 Apr 24	{ "type": "Systematic Review", "title": "Patient education for individuals with Interstitial Lung Disease: A scoping review.", "authors": [ "Revati Amin", "K. Vaishali", "G. Arun Maiya", "Aswini Kumar Mohapatra", "Mukesh Kumar Sinha", "Anup Bhat", "Tulasiram Bommasamudram", "Vishak Acharya", "Shweta Gore", "Revati Amin", "G. Arun Maiya", "Aswini Kumar Mohapatra", "Mukesh Kumar Sinha", "Anup Bhat", "Tulasiram Bommasamudram", "Vishak Acharya", "Shweta Gore" ], "abstract": "Objectives Interstitial Lung Disease (ILD) is a severe and rapidly progressing disease with a high fatality rate. Patient education (PE) has been demonstrated to promote long-term adherence to exercise and lifestyle improvements by assisting patients in developing self-management techniques. Our scoping review's goal was to chart out the prevailing level of research about the content, processes, and effectiveness of PE for patients with ILD.\n\nMethods The relevant databases were searched using the rules provided by Arksey and O'Malley in 2005 and the Joanna Briggs Institute reviewers' manual 2015: an approach for JBI scoping reviews. Individuals with ILD, published in English between the years of inception and 2020, and describing PE administered by various healthcare practitioners were among the 355 studies found and reviewed. Thirteen studies met these criteria.\n\nResults PE delivery process, delivery techniques, quality of life assessments, common PE themes, and healthcare professional participation were all recognized and cataloged.\n\nConclusion Despite the fact that healthcare professionals (physicians, nurses, and physiotherapists) provide PE to patients with ILD regularly, the PE provided varies greatly (contents of PE, process of delivery and delivery techniques). During the scoping review, a significant variation in the themes was addressed. They could not provide any evidence-based specific recommendations for all healthcare practitioners due to the studies' heterogeneity and lack of effectiveness measures.", "keywords": [ "educational contents", "effectiveness", "interstitial lung disease", "patient education", "process of delivery", "pulmonary rehabilitation", "scoping review" ], "content": "1. Introduction\n\nInterstitial lung disease (ILD) is a condition that leads to an incremental inability to maintain normal levels of blood oxygen due to impaired gas exchange through the alveolar-capillary membrane.1 ILD is frequently associated with poor health outcomes including exercise limitation, exercise-induced breathlessness, decreased physical activity, poor quality of life, increased health service utilization, and death.2–6 The experience with ILD is that of a long way to diagnosis, intense symptomatic burden, insufficient information of the disease and anxiety.5\n\nPulmonary rehabilitation (PR) is a fundamental mode of treatment to improve exercise tolerance and minimize symptoms in patients with chronic lung disease.7,8 Evidence supports the effectiveness of PR in ILD and guidelines for the management of ILD have adopted PR as a priority intervention. PR encompasses a range of interventions focussed on the individual needs of the patient. One important component of PR is Patient Education (PE).\n\nPE helps patients develop self-management strategies and has shown to improve long-term adherence to exercise and lifestyle changes. PE offers insight into the knowledge that patients need for the best possible treatment for chronic diseases.9 The educational programs seek to strengthen disease management10–15 and enhance self-efficacy.16,17 Various guidelines generated by national and international advisory committees emphasize the value of PE in chronic lung disease.18–21 The instructional content should be readily available and strategically focused on providing efficient, cost-effective, and high-quality health education. Quality education in health seeks to enhance the lives of individuals through the encouragement of improvement in attitudes, values, awareness, skills, and behaviour.22 Oxygen therapy, exacerbation control, energy conservation, symptom management, mood disorders, medications, lung transplants, and end-of-life care are all topics covered in educational programs for ILD patients.23\n\nPE can be broken down into five distinct phases. The patient's prior knowledge, misconceptions, learning abilities, cognition, comprehension, attitudes, and motivation are all assessed in the first stage. Following the assessment, the patient's approaches, problems, and learning needs will be diagnosed. The third phase is to work with the patient to organize education, set goals, and choose educational interventions. It is critical to discuss the type of education, the frequency, who will offer the education, and when and how it will be addressed during the planning process.\n\nScoping reviews analyze the scope and depth of available data on a particular topic, as well as the nature of published studies, in order to provide a comprehensive overview of broad, varied literature. Scoping reviews also allow researchers to go further into specific research topics in order to conduct more thorough systematic reviews. When time is restricted and there is no clear information or knowledge about a topic to start a systematic review, a scoping review is undertaken.\n\nA continuing assessment of patient needs and priorities provides the framework for further education. Since PR was developed and designated for patients with chronic obstructive pulmonary disease (COPD), which has a disease mechanism and symptoms that are fundamentally different from ILD. PE issues defined for patients with COPD, such as the physiological basis for exercise limitation, symptoms, treatment, disease severity, and outcomes, may not be relevant or significant for patients with other pulmonary disorders, such as ILD. Although healthcare practitioners routinely deliver PE verbally to patients with ILD, little is known about the actual content and mechanisms of this provision, as well as its overall efficacy. There is a need to map the available research because there is a lack of evidence about the administration and content of PE delivered in ILD patients. Therefore, the goal of this scoping review was to define and map the current information of the content, processes, and efficiency of PE provided for patients with ILD.\n\n\n2. Materials and methods\n\nThe methodology framework used in this study was initially outlined by Arksey and O’Malley24 and revised Joanna Briggs Institute reviewers' manual 2015: methodology for JBI scoping reviews.25 The scoping review is reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement for reporting scoping reviews (PRISMA-ScR).26 The framework was divided into five independent phases: formulating the research question; locating relevant studies; identifying studies; organizing and extracting data; and, at last, summarizing and presenting the results.\n\nThe specific research questions were as follows:\n\n1. What are the contents (topics) of the PE provided for patients living with ILD?\n\n2. What processes or methods were used when providing PE to patients living with ILD?\n\nWe undertook a comprehensive PubMed and Scopus literature search to identify studies describing the PE provided for patients with ILD. Inclusion criteria consisted of studies including patients with ILD (aged > 18 years) referred for PR in any health care setting. The PR sessions have to be inclusive of PE administration using either booklets, leaflets, websites, mobile applications or verbal/practical demonstration. Articles published in English from inception to 2020. The content of the PE (topics addressed, different processes of the PE intervention, location of delivery, mode, who delivered PE, and technique of delivery), provided through a pulmonary rehabilitation program. Types of sources: Any type of research design, such as quantitative, qualitative, or mixed methods were included in the study. Articles written in languages other than English, editorials and commentaries were excluded.\n\nSearch strategy: Initially, a PubMed and Scopus search was undertaken, followed by a screening of the titles and abstracts of retrieved papers, as well as the search terms utilized to describe them. A thorough search was then conducted across all of the involved databases utilizing all identified keywords and index terms. In order to locate more pertinent sources, the reference lists of the included papers and reports were examined as well. Grey literature from databases and conference proceedings was also investigated, and duplicate publications were found and eliminated. The titles and abstracts of articles were examined to determine whether they met the inclusion criteria. If an article satisfied the criteria or needed further review before being excluded, its full text was retrieved. A third reviewer (AM) resolved any differences between the two independent reviewers' (RA and VK) assessments of whether the full-text paper fulfilled the inclusion criteria. Using specific terms for each database, the search on PubMed and Scopus concentrated on the three main ideas of ILD, physiotherapy, and patient education (PE).\n\n“Idiopathic pulmonary fibrosis” OR “IPF” OR “pulmonary fibrosis” OR “fibrosis” OR “ILD” OR “interstitial lung disease” OR “lung disease” OR “pulmonary disease” AND “physiotherapy” OR “physical therapy” OR “physical training” OR “physical rehabilitation” OR “pulmonary rehabilitation” OR “pulmonary rehabilitation training” AND “health education” OR “patient care” OR “self-management” OR “health communication” OR “health behaviour” OR “PE” OR “booklets” OR “pamphlets” OR “leaflets” OR “brochures” OR “handout” OR “flyer” OR “electronic educational materials” OR “web-based education” OR “tele-rehabilitation” OR “telerehabilitation” OR “telehealth” OR “telerehab” OR “mHealth” OR “telecare”.\n\nFollowing the initial screening, 14,727 articles were evaluated through assessing their titles and abstracts against established inclusion and exclusion criteria. When one reviewer (RA) was unsure whether to include or exclude an article, it was independently reviewed by another reviewer (VK). 355 articles were subsequently found to be eligible for full-article review. The 355 papers were then evenly allocated alphabetically between the two reviewers (RA and VK). Each full text article was thoroughly reviewed against the inclusion and exclusion criteria implementing the PRISMA extension for Scoping Reviews (PRISMA ScR) flow approach.27 (Figure 1)\n\nOrganising and extracting data: To organize the data collected systematically, a data extraction form was developed. This form consisted of a table with predefined categories that corresponded to the scoping review's objectives and research questions. These categories included information about the author, year of publication, country, study design, sample size, the content of the PE, processes of delivery, effectiveness (outcomes). The data from each article was documented in these specific categories for a thorough analysis. (Table 1–3)\n\n\n\n1. Accessing home care and support for both patients and carers\n\n2. End of life care and advance directives\n\n3. Managing co-existing medical conditions\n\n4. Managing medications and side effects\n\n\n3. Results\n\nThe information was collected and summarised for extraction and the results were recorded in the same framework we developed for analysis.\n\nA total of 13 articles were included in the scoping review. (Table 1–3) There was 1 single group intervention pre-post pilot study design,28 2 systematic reviews,29,30 1 non-RCT (prospective study),31 5 qualitative observational studies,32–36 4 review articles.37–40 (Figure 2)\n\nAll the studies described multiple PE topics. The most commonly discussed educational topics included: pathophysiology of ILD (1),35 clinical tests (1),35 managing breathlessness/dyspnoea (3),33,35,36 managing cough (3),33,35,36 managing fatigue (3),33,35,36 managing flare-ups (2),33,36 prognosis (1),35 managing anxiety, panic and depression (2),33,36 using supplemental oxygen (3),33,35,36 using ambulatory oxygen (1),36 using nocturnal oxygen (1),36 regular vaccination (2),33,36 managing medications and side-effects (3),33,35,36 good nutrition (1),33 managing co-existing medical condition (1),33 accessing home care and support for both patients and caretakers (3),33,35,36 smoking cessation (1),33 symptoms of gastroesophageal reflux disorder,29 adherence,29 end-of-life acre and advanced directives (4),33,35,36,40 valued education regarding pulmonary rehabilitation (3),32,33,34 importance of exercises (3),32,33,34 discussion over ILD specific topics (1),36 autonomy (1).36 (Figure 3)\n\n5 studies identified the involvement of health practitioners such as nurses (2)34,35 pulmonologists (3),32,33,36 kinesiologists (1),34 respiratory physicians (2),32,36 physiotherapists (4),29–32 and rheumatologists (2),32,36 in delivering PE to patients with ILD. A few studies (3) also mentioned the need for involvement of bystanders and caregivers in the PE sessions along with patients with ILD.28–30 (Figure 4)\n\nProcess of delivery:\n\nPE was found to be implemented in a variety of settings including outpatient settings, outpatient supervised PR programs, inpatient PR programs, primary healthcare centers, and acute care units.29–31 However, none of the studies mentioned use of PE as a part of the treatment program for ILD patients.29–31\n\nQualitative findings:\n\nThe majority of the articles included in the scoping review were qualitative study designs.32–36 These study designs aimed at highlighting the core topics and themes required for the development of educational booklets concerning the patient point of view.32,33 These studies describe the interests of the patients, their understanding about the disease and brought to light their expectations from the physicians and healthcare professionals with respect to the disease by qualitatively analyzing their perspectives via focused groups and in-depth interviews.32–35\n\nMost of the qualitative studies were conducted either by a face-to-face communication,32–35 via a telephonic interview,33,34 website surveys,36 questionnaire prescription34 to design the components of PE in ILD for patient centred approach. Interviews were conducted with patients to collect sociodemographic information; this information included their management of ILD (e.g., drug therapy, specialist input, acute ILD exacerbations), satisfaction with the overall handling of their disease, medication profile, and travel costs.32–36 Holland AE et al., in a qualitative review enlisting core topics essential for inclusion in the PE program for ILD patients stating the need for ILD specific PE packages for patients.33\n\nDelivery technique:\n\nA few studies mentioned prescribing PE orally as a part of the rehabilitation or treatment program, although content was not disclosed.30,31 A few mentioned the use of websites such as Pulmonary Fibrosis Foundation (www.pulmonaryfibrosis.org), (https://www.ofev.com/support/open-doors; https://www.esbriethcp.com/ipf-patient-assistance/patient-education-inspiration.html), web-based information booklet28 for delivering PE among ILD patients and caregivers specifically.37\n\nEffectiveness (Outcome measures):\n\nNone of the articles used PE-specific outcome measures. But for their overall study objectives, they used different outcomes measures.28,29,30,34\n\nQuality of life:\n\nNiemitz M et al., (2019) used self-reported scales to rate self-efficacy, scales for patients and caregivers to rate health-related quality of life (chILD-QOL), satisfaction with PE.28 The majority of the studies used disease-specific, health-related quality of life tools as an outcome measure. Scales such as St. George Respiratory Questionnaire (SGRQ),29,30 Chronic Respiratory Disease Questionnaire (CRQ),29,30 Short Form- 36 (SF-36),29,30 King’s brief Interstitial Lung Disease questionnaire (K-BILD),35 University of California, Shortness of Breath Questionnaire (UCSD SOBQ),35 International Physical Activity Questionnaire (IPAQ),30 A Tool to Assess Quality of Life in Idiopathic Pulmonary Fibrosis (ATAQ IPF) scores,30 Idiopathic Pulmonary Fibrosis (IPF) specific SGRQ scores.30\n\nPhysical status, dyspnoea, lung function:\n\nAuthors have used indicators such as 6 MWD to determine ILD patients' physical status.30 For dyspnea stages, Beck’s Depression Inventory (BDI),30 and Modified Borg Scale (MBS)31 were used. For the assessment of performance indicators, spirometric indicators like Forced Vital Capacity (FVC), Forced Expiratory Reserved Volume in 1 Second (FEV1) and diffusing capacity of lung of carbon monoxide (DLCO) were used.30\n\nIn patients with ILD, PE is an integral component of care. Before beginning, a physiotherapist has an overall objective or goal for PE. The learning objectives for knowledge acquisition, solving problems, learning skills and behavioural change can be helpful. The method used could be visual and realistic, including demonstrations.29,30 The physiotherapist would evaluate when and where to incorporate PE during rehabilitation.32,34–36\n\n\n4. Discussion\n\nIn line with the research questions laid down by us in our review, the first question focuses on the contents (topics) of PE provided for patients living with ILD. Patients require healthcare professionals to devote time with them after diagnosis, as highlighted by the studies included in this scoping review.29,30,40 The patients with ILD should be given with a brief introduction regarding the disease and its course. They should be provided with an insight of what happens to the lungs because of the disease, various triggers, irritants and causes of ILD. They should be given a brief knowledge about the signs and symptoms, situations during exacerbations and how to manage them.29,30,32,40\n\nA multidisciplinary approach towards treating ILD patients is of utmost importance concerning managing the disease course. This involves the participation of the healthcare team, the patient themselves, and their caregivers.28,29,36,39 PE must include awareness regarding the medications prescribed their effects on the body systems. Reactive oxygen species are responsible for tissue damage in ILDs, despite the fact that oxygen deficiency also occurs in these circumstances. Recognizing the significance of reactive oxygen species offers novel opportunities for therapeutic intervention.\n\nReference 41 Supplemental oxygen is one such component the patient should be made aware about. Since patients frequently receive oxygen therapy at home, the findings in this review recommend that patients should obtain PE regarding oxygen dosage and concentration during exacerbations and before engaging in strenuous activities. A large subgroup of people with ILD are normoxic at rest but rapidly desaturate on exertion. This can limit exercise capacity and worsen dyspnoea. When mobilizing or doing other tasks, using ambulatory or short-burst oxygen may help enhance exercise capacity and relieve dyspnoea.43 Including a discussion of these concepts within the PE approaches both via face-to-face discussions by the pulmonologist, rheumatologist, immunologist, physiotherapist, and the staff nurses and reiterated in a written form using booklets or flyers is essential. Oxidative stress, which results from exposure to oxidizing agents including cigarette smoke, air pollution, and infections, has been linked to a variety of lung conditions. Therefore, the onset or advancement of these diseases has been linked to dietary components and nutrients that may have protective effects against oxidative processes and inflammatory reactions.\n\nA dietician should be involved for discussion regarding the various areas the patients can reach out to and maintain and help establish an individualized diet plan for better living.\n\nExercise intolerance is an essential feature of ILD associated with poor quality of life and closely linked to mortality. Given the well-documented short-term effects of PR on lung function, quality of life, and improvements in activities of daily living, PE resources must emphasize the necessity of assessment and the advantages of exercise throughout the disease's course. Dysnoea and fatigue are key debilitating factors experienced by patients with ILD. The physiotherapist should spend time with the patients in educating them about the evaluation of the factors causing dyspnoea and fatigue and the non-pharmacological solutions to those problems which eventually affect the ADL’s and functional abilities of ILD patients.32,34,35,36 In the studies included in this review, there must be a possible overlap between PR providers, which is likely to lack specificity.\n\nThere is lack of clarity regarding the contents of PE delivered to the patients with ILD by the physiotherapists. Individual perception of the patients, such as dyspnea, depression, and health-related quality of life (HRQoL), is more strongly interrelated. Consequently, the management of dyspnea and depressive symptoms could be an essential tool for optimizing the HRQoL of patients with ILD. Self-care is one such component that needs to be addressed to overcome exacerbations. Patients need to be briefed about the various techniques that can be used to self-manage their symptoms when in times of need.11 There is no clear perspective in the current literature regarding the management of mental health among ILD patients. There is a lack of evidence and clarity regarding who provided the PE to the ILD patients and the duration spent doing the same in literature. Also, the effect of PE post-intervention on follow-up has not been addressed in any of the available literature. Outcome assessment tools need to be established for PE in ILD to know the knowledge of PE retained by the patients and its effects on their quality of life during follow-up.\n\nProcess of delivery:\n\nIn line with the research questions laid down by this review, the second question focuses on processes or methods used when providing PE to patients living with ILD. According to the content gathered from literature, various modalities of PE delivery to ILD patients can be used. There is lack of clarity regarding the process of PE delivery among ILD patients.\n\nAs of other chronic respiratory diseases, PE in ILD can be delivered verbally by the multidisciplinary healthcare team during their follow-up visits.30,31,44,45 PE delivery through cutting-edge technology such as telerehabilitation allows the entire multidisciplinary team to collaborate and discuss the patient's whereabouts and caregiver involvement.46\n\nIn contrast to other chronic respiratory disorders, PE can be delivered in ILD using a web-based platform that employs an innovative and digital design.28,37 To communicate the contents of PE, healthcare practitioners can use instructional manuals, brochures, handouts, and other materials.29,30 This can make the process easier as it becomes convenient for the patients and refer to the contents whenever possible. Educational booklets and handouts can also be a fantastic resource for disseminating PE knowledge in a diverse country like India, where there is a shortage of social-based platforms and smartphone use among individuals living in rural and remote sections of the country where internet penetration is very low. Educational booklets can be made exciting and understandable to the local population with the optimal use of illustrations, making it self-explanatory. By include progress/log charts in the booklet, we can keep track of adherence. Booklets can be a source to track, evaluate, and grade the performance for further progression.\n\nDuring this scoping review, we identified significant diversity in the themes. The systematic reviews were unable to address the complexities of PE, limiting their capacity to give meaningful, evidence-based recommendations for PE. Also, a systematic review on educational programs in ILD management did not address PE topics with ILD patients.30 While existing recommendations recognize crucial educational topics such as chronic pulmonary disease, dyspnea treatment, fatigue, oxygen therapy, and smoking cessation, none of these themes have been investigated in PE intervention clinical trials.29,30,40 The study's limitations also included specific PE topics that were often not recognized clearly by a physiotherapist. According to this scoping review, the healthcare team, including pulmonologists, physiotherapists, psychologists, nurses, rheumatologists, and nutritionists, was all involved in delivering PE to ILD patients.30,32–36 None of the studies gave details about the type of training obtained by physiotherapists and other healthcare professionals to provide effective PE. Whether health practitioners had been trained in PE and the study authors chose not to provide this knowledge in the paper or whether the clinicians had been trained in PE is unknown. Holland AE has enlisted the physician-centered perspective regarding core topics for PE prescription in her review.32 The review discusses in detail the opinions of the patients and physicians regarding PE among ILD patients. She concluded that ILD patients appreciate the ability to undergo PR training, but they identify specific topics that do not currently cover their needs. Patients and clinicians did not agree upon the most important topics for inclusion. The construction of a comprehensive ILD PR curriculum should consider utilizing patients' knowledge and clinician approaches.32\n\nA couple of studies involved family members and caregivers with the patients themselves during the PE sessions.28 Caregivers must be included in PE sessions to better grasp the disease process and help their loved ones emotionally.28,29,36,40\n\nThe scoping review revealed that none of the studies addressed the location of PE delivery and follow-up periods for the educational sessions. The lack of recommendations on where and when to deliver PE for patients with ILD leads to this disparity. This is another significant gap in the literature.\n\nThe goals and priorities defined in the scoping review included PE but was not the primary intervention in the included studies.30 The important findings were the cost-effectiveness of using healthcare facilities, exercise tolerance, quality of life,29,30 and coping mechanisms.33 The majority of research have classified PE as a self-management program,30 however because the authors have not defined PE, explaining it as a self-management program is regrettably unclear. Self-management can imply different things to different people, and it's rarely defined in the literature. Some consider it synonymous with PE; others see PE as part of self-management.\n\nThe authors used a variety of PE delivery techniques and procedures, which can be divided into two categories: verbal and written approaches.30,31 The authors have addressed education topic with ILD patients, who are by far the most common recipients of PE.30 None of the studies mentioned the PE delivery mechanism or methodology. Healthcare practitioners, especially physiotherapists, employ various treatment strategies in PE, including the method of teaching that is undecisive.32,33,34 Depending on the goals of PE, additional verbal methods can be further suited to adopt a team - based approach or a counselling approach.47\n\nAnother common form of PE was giving patients booklets,31 which were typically given in addition to discussion. However, they did not provide specific information on the contents of the booklet. This is also an efficacious method of PE delivery but must be easily understood irrespective of the level of literacy of the patient.48–55 Few studies addressed the use for patients and caregivers of ILD-specific PE based on the web.28 In future research, the emphasis should be on developing a patient disclosure guideline by ensuring that the print content is designed in plain language and simple design, ensuring consistency in PE.\n\nThe studies mainly used measures such as health-related quality of life questionnaires28–30 and physiological performance measures as likely markers of PE efficacy. None of the studies have used outcomes measures explicitly to determine the effectiveness of PE. None concentrated on the influence of the PE alone. In addition, there are a limited range of valid PE instruments for patients with chronic diseases, while other methods are valid, reproducible, and sensitive to determine health status, quality of life28–30 and physiological function and are well-established. One study discussed using self-reported scales to assess self-efficacy, quality of life and patient satisfaction for children with ILD.28 Due to the heavy dependency on verbal contact in health care meetings, clear verbal communication, especially in PE, is essential for all health professionals. A 'Teach Back' informal approach for assessing the efficacy of PE ensures patients understand the directions. Future research could concentrate on those relevant methods that a health provider and a patient both settled on, for assessment of the efficacy of PE intervention with a PE specific goal, for example, information development, acquisition of skills, or behavioural change.41,42\n\nNone of the studies have recorded disease and mortality, time for the first admission, number of hospital admissions and readmissions, reason for admission and overall hospital stays of days, appointments with the general practitioner and doctor visits, and prescription dispensations.\n\n\n5. Conclusion\n\nThe aim of this scoping review was to examine and summarize the most recent information about the content, methods, and overall efficacy of patient education (PE) given to individuals with ILD. Our review revealed that providing PE as part of ILD care requires physiotherapists alongside other medical professionals. However, there is insufficient details about the precise material and procedures used by these professionals. Precise explanations of the educational subjects addressed, the environment, goals, and techniques for PE delivery for individuals with ILD are lacking in the literature. The absence of consistent, evidence-based recommendations on educational materials specifically designed for patients with ILD may be the cause of this ambiguity, given the variability of the studies that have been observed.\n\nAlso, the duration of PE provided or outcome measures to determine the PE's effectiveness is not specified. Further studies are needed to identify best practices for both the content and the processes of PE interventions and thereby optimize the quality of life of ILD patients.\n\n\n6. Relevance to clinical practice\n\nThis scoping study will enable researchers to develop a patient-centered education manual/website that may be an instructional guide for delivering PE to ILD patients. Patients can get personalized help and better understand their disease, diagnosis, signs and symptoms, medications, coping methods, and pulmonary recovery (exercises and progression). The pulmonary rehabilitation education manual will act as a source of reinforcement and will assist in maintaining pulmonary rehabilitation compliance.\n\n\nEthical approval\n\nEthical approval is not required for the study.\n\n\nConsent\n\nNot applicable.\n\n\nAuthor contributions\n\nK.V: Conceptualization and design of the study, acquisition of data, analysis and interpretation of data; R.A: Drafting the article, design of the study, acquisition of data, analysis and interpretation of data; G.A.M, A.K.M, M.K.S, A. B, T. B, V. A and S.G: Revising the manuscript critically for important intellectual content and provided final approval of the version to be submitted.", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\nThe author(s) own the figures attached below accompanying this manuscript. The author(s) declare that all the figures are their original work and not been adopted/reused from any other article.\n\nHarvard Dataverse: Figure for < Figure 1 Consort flow diagram>, https://doi.org/10.7910/DVN/MSNWBL. 56\n\nHarvard Dataverse: Figure for < Figure 2 Demographic characteristics for study designs>, https://doi.org/10.7910/DVN/AW9AGO. 57\n\nHarvard Dataverse: Figure for < Figure 3 Components for patient education identified in literature for individuals with ILD>, https://doi.org/10.7910/DVN/SGHSH5. 58\n\nHarvard Dataverse: Figure for < Figure 4 Involvement of healthcare professionals identified in PE programs for Individuals with ILD>, https://doi.org/10.7910/DVN/TOJYWC. 59\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication). 10/DVN/TOJYWC.\n\nHarvard Dataverse: Checklist for < Reporting Guidelines: Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) Checklist>, https://doi.org/10.7910/DVN/RXDIMN\n\n\nReferences\n\nRaghu G: Interstitial lung disease: a diagnostic approach. Am. J. Respir. Crit. Care Med. 1995; 151: 909–914. PubMed Abstract \| Publisher Full Text\n\nRyu JH, Daniels CE, Hartman TE, Eunhee SY: Diagnosis of interstitial lung diseases. Mayo Clinic Proceedings. Elsevier; 2007; Vol. 82(8): pp. 976–986. Publisher Full Text\n\nAntoniou KM, Margaritopoulos GA, Tomassetti S, et al.: Interstitial lung disease. Eur. Respir. Rev. 2014; 23(131): 40–54. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChang JA, Curtis JR, Patrick DL, et al.: Assessment of health-related quality of life in patients with interstitial lung disease. Chest. 1999; 116(5): 1175–1182. Publisher Full Text\n\nHolland AE: Exercise limitation in interstitial lung disease-mechanisms, significance and therapeutic options. Chron. Respir. Dis. 2010; 7(2): 101–101, 111. PubMed Abstract \| Publisher Full Text\n\nSchoenheit G, Becattelli I, Cohen AH: Living with idiopathic pulmonary fibrosis: an in-depth qualitative survey of European patients. Chron. Respir. Dis. 2011; 8(4): 225–231. Publisher Full Text\n\nRaghu G, Collard HR, Egan JJ, et al.: An official ATS/ERS/JRS/ALAT statement: idiopathic pulmonary fibrosis: evidence-based guidelines for diagnosis and management. Am. J. Respir. Crit. Care Med. 2011; 183(6): 788–824. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpruit MA, Singh SJ, Garvey C, et al.: An official American Thoracic Society/European Respiratory Society statement: key concepts and advances in pulmonary rehabilitation. Am. J. Respir. Crit. Care Med. 2013; 188(8): e13–e64. PubMed Abstract \| Publisher Full Text\n\nLelorain S, Bachelet A, Bertin N, et al.: French healthcare professionals' perceived barriers to and motivation for therapeutic patient education: A qualitative study. Nurs. Health Sci. 2017; 19(3): 331–339. PubMed Abstract \| Publisher Full Text\n\nBartholomew LK, Czyzewski DI, Parcel GS, et al.: Self-management of cystic fibrosis: short-term outcomes of the Cystic Fibrosis Family Education Program. Health Educ. Behav. 1997; 24(5): 652–666. PubMed Abstract \| Publisher Full Text\n\nZwerink M, Brusse-Keizer M, van der Valk PD , et al.: Self management for patients with chronic obstructive pulmonary disease. Cochrane Database Syst. Rev. 2014; 3. Publisher Full Text\n\nSavage E, Beirne PV, Chroinin MN, et al.: Self-management education for cystic fibrosis. Cochrane Database Syst. Rev. 2011; 7. Publisher Full Text\n\nWolf F, Guevara JP, Grum CM, et al.: Educational interventions for asthma in children. Cochrane Database Syst. Rev. 1996; 2010(1). Publisher Full Text\n\nGallefoss F, Bakke PS: Impact of patient education and self-management on morbidity in asthmatics and patients with chronic obstructive pulmonary disease. Respir. Med. 2000; 94(3): 279–287. PubMed Abstract \| Publisher Full Text\n\nDevine EC, Pearcy J: Meta-analysis of the effects of psychoeducational care in adults with chronic obstructive pulmonary disease. Patient Educ. Couns. 1996; 29(2): 167–178. PubMed Abstract \| Publisher Full Text\n\nJönsson T, Ekvall Hansson E, Thorstensson CA, et al.: The effect of education and supervised exercise on physical activity, pain, quality of life and self-efficacy-an intervention study with a reference group. BMC Musculoskelet. Disord. 2018; 19: 1–1.\n\nChen SY, Sheu S, Chang CS, et al.: The effects of the self-efficacy method on adult asthmatic patient self-care behavior. J. Nurs. Res. 2010; 18(4): 266–274. Publisher Full Text\n\nBlackstock F, Webster KE: Disease-specific health education for COPD: a systematic review of changes in health outcomes. Health Educ. Res. 2007; 22(5): 703–717. PubMed Abstract\n\nBateman ED, Hurd SS, Barnes PJ, et al.: Global strategy for asthma management and prevention: GINA executive summary. Eur. Respir. J. 2008; 31(1): 143–178. PubMed Abstract \| Publisher Full Text\n\nGibson PG, Powell H, Wilson A, et al.: Self-management education and regular practitioner review for adults with asthma. Cochrane Database Syst. Rev. 1996; 2010(1).\n\nKlein JJ, Van der Palen J, Uil SM, et al.: Benefit from the inclusion of self-treatment guidelines to a self-management programme for adults with asthma. Eur. Respir. J. 2001; 17(3): 386–394. PubMed Abstract \| Publisher Full Text\n\nMcDougal J, Gettys A, Hagood JS: ChILD family education. Pediatr. Allergy Immunol. Pulmonol. 2010; 23(1): 87–90. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKing J, Tessier S, Charette MJ, et al.: Patient education provided by physiotherapists for patients with chronic obstructive pulmonary disease: Results of a scoping review. Physiother. Can. 2018; 70(2): 141–151. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArksey H, O'Malley L: Scoping studies: towards a methodological framework. Int. J. Soc. Res. Methodol. 2005; 8(1): 19–32. Publisher Full Text\n\nPeters M, Godfrey C, McInerney P, et al.: The Joanna Briggs Institute reviewers' manual 2015: methodology for JBI scoping reviews.\n\nTricco AC, Lillie E, Zarin W, et al.: PRISMA extension for scoping reviews (PRISMA-ScR): checklist and explanation. Ann. Intern. Med. 2018; 169(7): 467–473. PubMed Abstract \| Publisher Full Text\n\nPage MJ, Moher D: Evaluations of the uptake and impact of the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) Statement and extensions: a scoping review. Syst. Rev. 2017; 6: 1–4.\n\nNiemitz M, Schrader M, Carlens J, et al.: Patient education for children with interstitial lung diseases and their caregivers: a pilot study. Patient Educ. Couns. 2019; 102(6): 1131–1139. PubMed Abstract \| Publisher Full Text\n\nGarvey C: Interstitial lung disease and pulmonary rehabilitation. J. Cardiopulm. Rehabil. Prev. 2010; 30(3): 141–146. Publisher Full Text\n\nYu X, Li X, Wang L, et al.: Pulmonary rehabilitation for exercise tolerance and quality of life in IPF patients: a systematic review and meta-analysis. Biomed. Res. Int. 2019; 2019: 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOzalevli S, Karaali HK, Ilgin D, et al.: Effect of home-based pulmonary rehabilitation in patients with idiopathic pulmonary fibrosis. Multidiscip. Respir. Med. 2010; 5(1): 1–7.\n\nHolland AE, Fiore JF Jr, Goh N, et al.: Be honest and help me prepare for the future: what people with interstitial lung disease want from education in pulmonary rehabilitation. Chron. Respir. Dis. 2015; 12(2): 93–101. PubMed Abstract \| Publisher Full Text\n\nHolland AE, Watson A, Glaspole I: Comprehensive pulmonary rehabilitation for interstitial lung disease: a consensus approach to identify core education topics. Patient Educ. Couns. 2019; 102(6): 1125–1130. PubMed Abstract \| Publisher Full Text\n\nMorisset J, Dube BP, Garvey C, et al.: The unmet educational needs of patients with interstitial lung disease. Setting the stage for tailored pulmonary rehabilitation. Ann. Am. Thorac. Soc. 2016; 13(7): 1026–1033. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcLean AE, Webster SE, Fry M, et al.: Priorities and expectations of patients attending a multidisciplinary interstitial lung disease clinic. Respirology. 2021; 26(1): 80–86. PubMed Abstract \| Publisher Full Text\n\nRamadurai D, Corder S, Churney T, et al.: Idiopathic pulmonary fibrosis: educational needs of health-care providers, patients, and caregivers. Chron. Respir. Dis. 2019; 16: 1479973119858961.\n\nQuinn C, Wisse A, Manns ST: Clinical course and management of idiopathic pulmonary fibrosis. Multidiscip. Respir. Med. 2019; 14(1): 35. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWijsenbeek MS, Holland AE, Swigris JJ, et al.: Comprehensive supportive care for patients with fibrosing interstitial lung disease. Am. J. Respir. Crit. Care Med. 2019; 200(2): 152–159. Publisher Full Text\n\nWuyts WA, Peccatori FA, Russell AM: Patient-centred management in idiopathic pulmonary fibrosis: similar themes in three communication models. Eur. Respir. Rev. 2014; 23(132): 231–238. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRaghu G, Richeldi L: Current approaches to the management of idiopathic pulmonary fibrosis. Respir. Med. 2017; 129: 24–30. PubMed Abstract \| Publisher Full Text\n\nSchillinger D, Piette J, Grumbach K, et al.: Closing the loop: physician communication with diabetic patients who have low health literacy. Arch. Intern. Med. 2003; 163(1): 83–90. Publisher Full Text\n\nSchillinger D, Grumbach K, Piette J, et al.: Association of health literacy with diabetes outcomes. JAMA. 2002; 288(4): 475–482. Publisher Full Text\n\nBell EC, Cox NS, Goh N, et al.: Oxygen therapy for interstitial lung disease: a systematic review. Eur. Respir. Rev. 2017; 26(143): 160080. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVisca D, Montgomery A, De Lauretis A, et al.: Ambulatory oxygen in interstitial lung disease. Eur. Respir. J. 2011; 38(4): 987–990. Publisher Full Text\n\nKara M, Türkinaz AŞ: Effect of education on self-efficacy of Turkish patients with chronic obstructive pulmonary disease. Patient Educ. Couns. 2004; 55(1): 114–120. PubMed Abstract \| Publisher Full Text\n\nFriedman AJ, Cosby R, Boyko S, et al.: Effective teaching strategies and methods of delivery for patient education: a systematic review and practice guideline recommendations. J. Cancer Educ. 2011; 26: 12–21. PubMed Abstract \| Publisher Full Text\n\nElder JP, Ayala GX, Harris S: Theories and intervention approaches to health-behavior change in primary care. Am. J. Prev. Med. 1999; 17(4): 275–284. Publisher Full Text\n\nEffing TW, Bourbeau J, Vercoulen J, et al.: Self-management programmes for COPD: moving forward. Chron. Respir. Dis. 2012; 9(1): 27–35. Publisher Full Text\n\nRoberts NJ, Ghiassi R, Partridge MR: Health literacy in COPD. Int. J. Chron. Obstruct. Pulmon. Dis. 2008; 3(4): 499–507. PubMed Abstract\n\nGazmararian JA, Baker DW, Williams MV, et al.: Health literacy among Medicare enrollees in a managed care organization. JAMA. 1999; 281(6): 545–551. PubMed Abstract \| Publisher Full Text\n\nWolf MS, Gazmararian JA, Baker DW: Health literacy and functional health status among older adults. Arch. Intern. Med. 2005; 165(17): 1946–1952. Publisher Full Text\n\nSadeghi S, Brooks D, Goldstein RS: Patients’ and providers’ perceptions of the impact of health literacy on communication in pulmonary rehabilitation. Chron. Respir. Dis. 2013; 10(2): 65–76. PubMed Abstract \| Publisher Full Text\n\nBorge CR, Larsen MH, Osborne RH, et al.: Exploring patients’ and health professionals’ perspectives on health literacy needs in the context of chronic obstructive pulmonary disease. Chronic Illn. 2022; 18(3): 549–561. PubMed Abstract \| Publisher Full Text\n\nKing J, Taylor M: Adults living with limited literacy and chronic illness: Patient education experiences. Adult Basic Education and Literacy Journal. 2010; 4(1): 24–33.\n\nPaasche-Orlow MK, Riekert KA, Bilderback A, et al.: Tailored education may reduce health literacy disparities in asthma self-management. Am. J. Respir. Crit. Care Med. 2005; 172(8): 980–986. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmin R: Replication Data for: Figure 1 Consort flow diagram. Harvard Dataverse. 2024; V1. Publisher Full Text\n\nAmin R: Replication Data for: Figure 2 Demographic characteristics for study designs. Harvard Dataverse. 2024; V1. Publisher Full Text\n\nAmin R: Replication Data for: Figure 3 Components for patient education identified in literature for individuals with ILD. Harvard Dataverse. 2024; V1. Publisher Full Text\n\nAmin R: Replication Data for: Figure 4 Involvement of healthcare professionals identified in PE programs for Individuals with ILD. Harvard Dataverse. 2024; V1. Publisher Full Text" }	[ { "id": "274664", "date": "10 May 2024", "name": "Jaya Shanker Tedla", "expertise": [ "Reviewer Expertise Rehabilitation", "Physical Therapy", "Physiotherapy", "Patient education", "and Student teaching." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The introduction explains the justification for performing a scoping review to map the existing knowledge gaps in PE for patients with ILD. You could explain why previous studies on PE for ILD patients are insufficient or inadequate, emphasizing the necessity for additional studies.\n2. The methodology includes a thorough explanation of the search strategy, including terms utilized and the search procedure. You could discuss any steps to reduce bias in the search strategy, including consulting with a librarian or examining gray literature sources.\n3. The methodology could explain how the data extraction forms categories were identified and whether they evolved due to initial analysis or pilot testing.\n4. You could have sections like \"Contents of Patient Education,\" Management Strategies, Process of Delivery, Limitations, etc. In the discussion.\n5. One of the main limitations is the lack of recorded data on hospital admissions, disease and mortality, etc. However, future research should address the consequences of this paucity of data on the interpretation of PE effectiveness, as well as the the necessity for more extensive outcome assessment.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "274658", "date": "21 May 2024", "name": "Saima Zaki", "expertise": [ "Reviewer Expertise Interstitial Lung Disease", "Pulmonary Rehabilitation", "Cardiac Autonomic Modulation", "Cardiorespiratory fitness and Training", "Metabolic Disorders", "Lifestyle Disorders", "Sports Rehabilitation", "Clinical Research", "Patient Education and Counseling", "Quality of Life" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nTitle In your eligibility criteria, you have mentioned that Patient Education (PE) considered during Pulmonary Rehabilitation (PR) is being taken into account. Therefore, to accurately reflect the focus of your study, the title should explicitly indicate that it pertains to Patient Education during Pulmonary Rehabilitation. The current title, \"Patient education for individuals with Interstitial Lung Disease: A scoping review,\" can be misleading as it suggests that PE was delivered during various interventions, not specifically PR.\nSuggested Title Revision: \"Patient Education during Pulmonary Rehabilitation for Individuals with Interstitial Lung Disease: A Scoping Review\"\nAbstract Comment 1: In the abstract, the authors define Interstitial Lung Disease (ILD) as \"a severe and rapidly progressing disease with a high fatality rate.\" While this definition captures the severity of some forms of ILD, it is important to note that ILD encompasses a diverse group of lung disorders, each with varying degrees of severity and rates of progression.\nI recommend refining the definition to better reflect this diversity. A more accurate definition would acknowledge that while some types of ILD, such as Idiopathic Pulmonary Fibrosis (IPF), are indeed rapidly progressing and have a high fatality rate, other forms may progress more slowly and have different prognoses.\nSuggested revision: \"Interstitial Lung Disease (ILD) refers to a group of lung disorders characterized by inflammation and scarring of the lung tissue, leading to impaired gas exchange. The progression and severity of ILD vary widely depending on the specific type, with some forms, such as Idiopathic Pulmonary Fibrosis (IPF), being rapidly progressive and associated with a high fatality rate, while others may progress more slowly.\"\nComment 2: In method, it is suggested that to mention name of searched databases.\nComment 3: In the second paragraph of the introduction, the transition to Pulmonary Rehabilitation (PR) is abrupt and disrupts the flow of the narrative.\nComment 4: In the last three paragraphs of the introduction, there are several significant statements made without any references to support them. Providing references for these statements is crucial to establish credibility and allow readers to verify the information. Here are the specific areas where references are needed: Pulmonary Rehabilitation (PR) and Chronic Obstructive Pulmonary Disease (COPD): \"Since PR was developed and designated for patients with chronic obstructive pulmonary disease (COPD), which has a disease mechanism and symptoms that are fundamentally different from ILD.\" Reference needed to support the historical context and the distinction between COPD and ILD. PE Issues Defined for COPD Patients: \"PE issues defined for patients with COPD, such as the physiological basis for exercise limitation, symptoms, treatment, disease severity, and outcomes, may not be relevant or significant for patients with other pulmonary disorders, such as ILD.\" References needed to support the differences in educational needs and issues between COPD and ILD patients. Content and Mechanisms of PE Provision: \"Although healthcare practitioners routinely deliver PE verbally to patients with ILD, little is known about the actual content and mechanisms of this provision, as well as its overall efficacy.\" References needed to support the claim about the lack of knowledge regarding the content and mechanisms of PE provision for ILD patients. Need for Mapping Available Research: \"There is a need to map the available research because there is a lack of evidence about the administration and content of PE delivered in ILD patients.\" References needed to justify the need for the scoping review based on the current gaps in the literature. To enhance the credibility and robustness of your manuscript, I strongly recommend including appropriate references to support these statements. This will not only strengthen your argument but also provide readers with sources for further reading.\nResults Comment 5: There appears to be a major discrepancy in your study's reporting. In the PRISMA flowchart, it is stated that 12,642 articles were included in the scoping review. However, in the results section, it is mentioned that a total of 13 articles were included in the review. This inconsistency needs to be addressed and clarified to maintain the credibility and accuracy of your study.\nComment 6: There is a significant and unacceptable discrepancy between the narrative description of the study selection process and the PRISMA flowchart in your manuscript. In the narrative, it is mentioned that 355 articles were selected for full-text review. However, the PRISMA flowchart states that 12,642 articles were included in the scoping review. This is a major inconsistency that undermines the credibility and integrity of your scientific writing. Such a blunder in reporting the methodology is not acceptable in scientific literature and must be corrected immediately. Accurate and consistent reporting of the study selection process is crucial for the transparency and reproducibility of your research.\nDiscussion Comment 7: The discussion section lacks a brief summary of the main findings of your review in the first paragraph. This summary is crucial as it provides readers with an immediate understanding of the key outcomes of your study. Furthermore, there is no mention of Patient Education (PE) during Pulmonary Rehabilitation (PR) throughout the discussion, which is a significant oversight given the focus of your review. In the management section, the text begins appropriately with a discussion on the multidisciplinary approach but abruptly shifts to discussing reactive oxygen species without proper context or references. This sudden transition disrupts the flow and coherence of the section. Additionally, the statements about reactive oxygen species are not supported by any references, which is a significant omission in a scientific manuscript.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) No", "responses": [] }, { "id": "274667", "date": "17 Jun 2024", "name": "Sanjay Tejraj Parmar", "expertise": [], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe justification for performing a scoping review to map the existing knowledge gaps in PE for patients with ILD is explained in the introduction. You could explain on why previous studies on PE for ILD patients is insufficient or inadequate, emphasizing the necessity for additional study.\n\nThe introduction discusses the lack of studies on the content, delivery, and efficacy of PE for ILD patients. To highlight the need of filling this knowledge gap, you could briefly discuss how it might affect clinical practice or patient outcomes.\n\nThere is discussion of a transparent method for selecting and screening articles, which includes independent evaluation by multiple reviewers. You could discuss any steps performed, such inter-rater reliability tests or calibration exercises, to guarantee consistency and reliability amongst reviewers.\n\nThe study emphasizes critical elements such medication management, oxygen therapy, nutrition, and exercise and acknowledges the significance of a multidisciplinary approach in the management of ILD. You may be more specific about how each member of the healthcare team contributes to patient education and care coordination.\n\nSome terms or concepts mentioned, such as \"reactive oxygen species\" and \"telerehabilitation\" may need further explanation.\n\nThe conclusions and implications of the review should include combining the major themes that were covered throughout, such as the importance of outcome measures, the lack of standardized approaches to PE delivery.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-405
https://f1000research.com/articles/13-404/v1	26 Apr 24	{ "type": "Research Article", "title": "Co-administration of a Hepatitis B vaccine with CpG-ODN 2395 induces stronger immune response in BALB/c mice", "authors": [ "Titilayo Kemi Sophia Nelly ADEDJOBI", "Daniel Kariuki", "James Kimotho", "Daniel Kariuki", "James Kimotho" ], "abstract": "Background Proof of effects of Cytosine Phosphoguanine Oligodeoxynucleotides (CpG ODNs), adjuvanted Hepatitis B Virus (HBV) vaccine on immune response is limited. This study aimed to assess the effect of five CpG ODNs in HBV Vaccine-immunized BALB/c mice and to identify the most effective CpG ODN adjuvant.\n\nMethods This laboratory-based experimental study was conducted using a total of 36 female BALB/c mice, which were clustered into 12 groups and immunized intramuscularly. Group 1 was immunized with CpG ODN 18281-1 alone, group 2 with vaccine plus CpG ODN 18281-1, group 3 with CpG ODN 18281-2 alone, group 4 with CpG ODN 18281-2 plus vaccine, group 5 CpG ODN 18289 alone, group 6 with CpG ODN 18289 plus vaccine, group 7 CpG ODN 1826 S alone, group 8 with CpG ODN 1826 S plus vaccine, group 9 CpG ODN 2395 alone, group 10 with CpG ODN 2395 plus vaccine, group 11 with vaccine alone and group 12 with Phosphate Buffer Saline (PBS). All the groups were observed for 14 and 28 days after immunization.\n\nResults In the vaccinated groups, those receiving supplementation with CpG 2395 exhibited a significant 4.4-fold elevation, resulting in a signal-to-noise ratio (S/N) value of 14.1 compared to the vaccine group only (S/N = 3.22) by day 28 (p-value < 0.0001). For mice immunized with the vaccine plus CpG ODNs, cytokine profiling using real-time quantitative polymerase chain reaction revealed increased IL-6 expression levels and decreased TNF-α levels compared to the untreated group, normalized with the housekeeping gene HPRT 1. However, the expression of IL-6 and TNF-α was not statistically significant between the treated groups (p-value ≥ 0.2). Parameters for toxicity were within the normal range in all treatment groups.\n\nConclusion Based on these results the co-administration of the HBV vaccine with CpG ODN 2395 induces high immune responses in comparison to HBV vaccine alone.", "keywords": [ "Hepatitis B virus (HBV)", "vaccine", "adjuvants", "CpG ODNs" ], "content": "1. Introduction\n\nInfectious diseases pose a significant threat to human health.1 The etiological agent of both acute and chronic hepatitis B virus infections in humans is the Hepatitis B Virus (HBV), a partly double-stranded hepatotropic DNA virus. After six months of infection, serum Hepatitis B Surface Antigen (HBsAg; the viral glycoprotein) indicates a chronic HBV infection.2 Currently, about 250 million people have chronic HBV infection globally, and every year, almost 800,000 people die from liver illnesses linked to HBV.3 African regions have the highest prevalence of chronic HBV infection.2 According to a dashboard from the World Health Organization, over 91 million Africans have Hepatitis B or C infections and almost 70% of all HBV infections occur there (WHO Africa, 2021). Although antiviral medications have advanced, primary prevention by immunization remains the most effective and cost-efficient public health intervention.4 The introduction of immunization has greatly reduced the prevalence and death rate of infectious diseases.1 Therefore, the best method to prevent HBV infection is vaccination.\n\nThere are certain drawbacks to the current HBV vaccine. The delivery of recombinant HBV vaccines to nations where infection is widespread is a challenge because of the high cost of vaccine production and a small percentage of vaccine recipients are not developing protective immunity even after receiving more than the recommended three doses of the vaccine.5 Also, in the five years following immunization, 8-42% of those who had protective antibodies lost immunity.6\n\nAdjuvants are added to vaccines to stabilize and increase the potential of triggering a strong immune response.7 They have been shown to reduce the amount of antigen needed to trigger a particular degree of immunological response.8 For example, MF59 increased the effectiveness of the flu vaccine by 5-8 times.9 Based on their characteristics, adjuvants can be divided into several groups, such as those that are based on aluminum salts, oil emulsions, or toll-like receptor (TLR) agonists.8 Synthetic CpG Oligodeoxynucleotides (ODNs) show promise as adjuvants in vaccines.10 Typically, they are single-stranded DNA molecules synthesized with specific sequence settings, notably containing unmethylated CpG dinucleotides, known as CpG motifs.11 They can trigger an innate immune response in cells expressing TLR9, such as human plasmacytoid dendritic cells and B cells, resulting in the production of T helper 1 cells and proinflammatory cytokines.12 In addition to being potent vaccine adjuvants, synthetic CpG oligodeoxynucleotides (CpG ODNs) are TLR9 agonists and mimic the function of naturally occurring CpG motifs found in bacterial DNA.8 Alongside boosting the function of proficient antigen-presenting cells like B cells, macrophages, dendritic cells, T cells, and natural killer cells, the simultaneous administration of CpG ODNs with vaccines facilitates the augmentation of both humoral and cellular immune responses targeted towards the vaccine. Furthermore, it enhances the efficacy of specialized antigen-presenting cells.13 Recent studies have consistently shown that CpG ODN serves as a more potent Th1-like adjuvant in comparison to the “gold standard,” complete Freund’s adjuvant (CFA). This superiority is evident in its ability to enhance the development of cytotoxic T lymphocytes (CTL) and T cells that secrete interferon (IFN). Furthermore, other research has indicated that CpG ODN can achieve heightened levels of antigen-specific activation without eliciting the severe local inflammatory reactions associated with CFA.14\n\nThis study established the effects of CpG ODNs adjuvanted HBV vaccine on immunological response in BALB/c mice.\n\n\n2. Methods\n\nEthical clearance was granted by the Mount Kenya University Review Committee (Approval number 2196 on 16th of September 2023) and approval to carry out this study was obtained from KEMRI- Animal Care and Use Committee (KEMRI-ACUC/03.07.2023 on 28th of July 2023). All animal experimentation adhered to the national and international standards as approved by the KEMRI-Animal Care and Use Committee and as specified in the above protocol number. The Engerix B vaccine was solely utilized for research purposes in this study and was neither altered nor commercialized.\n\nFemale BALB/c mice, weighing 20 ± 2 grams each, were purchased from the Institute of Primate Research (IPR) in Kenya. The mice acclimated for seven (7) days in a standard facility at KEMRI, during which they were provided with commercial pellets for food and had unrestricted access to water. Every effort was made to adhere to the principles of the 3Rs (replacement, reduction, and refinement) to minimize their injury and suffering.15\n\nThis study was conducted at KEMRI, Innovation & Technology Transfer Division (ITTD) and followed a laboratory-based experimental study. The sample size was determined using the “resource equation (E)”.16 A total of 36 female BALB/c mice were used in this study. Mice for the experiments were clustered into 12 groups and immunized intramuscularly. Group 1 was immunized with 0.67 μM of CpG ODN 18281-1 alone, group 2 with 1 μg of Engerix B vaccine plus 0.67 μM CpG ODN 18281-1, group 3 with 0.67 μM of CpG ODN 18281-2 alone, group 4 with 0.67 μM of CpG ODN 18281-2 plus 1 μg of Engerix B vaccine, group 5 with 0.67 μM of CpG ODN 18289 alone, group 6 with 0.67 μM of CpG ODN 18289 plus 1 μg of Engerix B vaccine, group 7 with 0.67 μM of CpG ODN 1826 S alone, group 8 with 0.67 μM of CpG ODN 1826 S plus 1 μg of Engerix B vaccine, group 9 with 0.67 μM of CpG ODN 2395 alone, group 10 with 0.67 μM of CpG ODN 2395 plus 1 μg of Engerix B vaccine, group 11 with 1 μg of Engerix B vaccine (GlaxoSmithKline, Version number: GDS015/IPI11) and group 12 with 50 μL of PBS (Thermo Fisher Scientific, Lot n°178050) as negative control. Each treatment group of mice received a booster dose on day 14, consisting of 1μg of the Engerix B vaccine and 0.67 μM of CpG ODNs (supplied by Macrogen Europe, Lot n°230620-002-C3-C7) (Table 1).\n\n* Modified phosphorothioate.\n\nMice were blood-sampled on days 14 and 28 post-vaccination. The collected blood underwent processing to obtain plasma or remained as whole blood. Tail bleeding was used for plasma collection, while cardiac puncture was employed for obtaining whole blood. Tail blood was mixed with 50 μL of heparin (Kilitch Drugs India Ltd. Batch No: KLRC1004) in a 1.25 mL cryovial tube, and then centrifuged at 4000 rpm for 20 minutes to collect the supernatant. Before collecting whole blood, mice were euthanized with CO2, and approximately 700 μL was drawn into 1.5 mL Ethylenediaminetetraacetic acid (EDTA)-containing tubes. Plasma was stored at -20°C, while whole blood was stored at -80°C. Spleen tissues were dissected from the mice and placed in sterile 1.5 mL Eppendorf tubes on ice. These spleen samples were stored at -80°C until they were utilized for total RNA extraction and subsequent experiments.\n\nAssessment of humoral immune responses to the vaccine involved utilizing the Enzyme-Linked Immunosorbent Assay (ELISA) to measure HBV antibody levels. The Mouse HBV Surface Antibody (HBsAb) Qualitative Test Kit ELISA, along with its protocol, was employed for this purpose (manufactured by Solarbio Science & Technology Co., Ltd, China). ELISA plates were analyzed at a wavelength of 450nm using the ELISA Microplate Reader (manufactured in California, USA). Samples from each group were tested in triplicate, and the average Optical Density (OD) value was utilized to determine antibody levels.\n\n2.6.1 Preparation of total RNA from spleen tissues and cDNA synthesis\n\nSpleen tissue samples were processed to extract total RNA employing the Total RNA Extraction Kit (manufactured by Solarbio Science & Technology Co., Ltd, China), following the provided instructions. The concentration and purity of the RNA were evaluated using the spectrophotometer (manufactured by Thermo Fisher Scientific, Waltham, Massachusetts, USA) at absorbance 260/280. The samples were then stored at -80°C for subsequent experiments. Subsequently, cDNA synthesis from the extracted total RNA samples was performed utilizing the Universal RT-PCR Kit and its associated protocol (manufactured by Solarbio Science & Technology, Beijing, China).\n\n2.6.2 Quantitative Polymerase Chain Reaction (qPCR)\n\nA 2X SYBR Green quantitative PCR Mastermix (manufactured by Solarbio Science & Technology Co., Ltd, China) was utilized in a total reaction volume of 25μL. Amplification was carried out on the Applied Biosystems Quant Studio 5 qPCR platform (manufactured by PE Applied Biosystems, USA) using the PCR thermal profile detailed in Table 2. The primers employed for amplifying TNF-α, Il-6, and the housekeeping gene are listed in Table 3. The relative quantification of gene expression was determined using the delta-delta threshold cycle (∆∆Ct) formula, ∆Ct = Ct (gene of interest) – Ct (housekeeping gene), by Medrano et al.17\n\nAnalysis of the complete blood count in whole blood was conducted utilizing the HumaCount 30TS hematology analyzer machine (manufactured by Human Diagnostics Worldwide, Germany) by the provided protocol. Additionally, the serum levels of Aspartate Transaminase (AST), Alanine Transferase (ALT), Creatinine, and Urea were assessed using the Reflotron colorimetric test strips (manufactured by Woodley Equipment Company, England) following the prescribed protocols.\n\nThe Signal-to-noise ratio values (OD at 450 nm/PBS) calculated from the ELISA optical densities and the quantification cycle (Ct) values were recorded and analyzed in Microsoft Excel (2016). Relative mRNA expression levels of the target genes were normalized to HPRT 1 using the 2-ΔΔCt method. The data obtained for the hematological and biochemical parameters were expressed as mean values using Microsoft excel (2016). Statistical significance of differences was determined through One-way ANOVA and Student’s t-tests, with a p-value <0.05 being considered as statistically significant for all performed tests.\n\n\n3. Results\n\nAfter the first immunization with the Engerix B vaccine supplemented with CpG-ODNs, the presence of antibodies in the plasma of all the immunized mice was observed. At day 14, it was shown that there was a statistically significant difference (p < 0.0001) in Signal Noise ratio (S/N) values among the vaccinated groups supplemented with CpGs (Figure 1).19 Moreover, the findings demonstrated that the CpG 18281-1, CpG 18281-2, CpG 18289, and CpG 1826 supplemented groups exhibited 1.2, 1.8, 1.1, and 1.6-fold increases respectively with signal-to-noise ratio values (2.5, 3.8, 2.2 and 3.3 respectively) compared to vaccine group only (S/N = 2.1).\n\nKey: CpG 18281-1Vac = CpG ODN 18281-1+Vaccine. CpG 18281-2Vac = CpG ODN 18281-2+Vaccine. CpG 18289Vac = CpG ODN 18289+Vaccine. CpG 1826SVac = CpG ODN 1826S+Vaccine. CpG 2395Vac = CpG ODN 2395+Vaccine. PBS = Negative control ( p < 0.01; p < 0.0001).\n\nOn the 28th day, the signal-to-noise (S/N) ratio values were markedly elevated in all treated groups compared to those on day 14 (p < 0.0001). Notably, the groups supplemented with CpG 2395 showed a substantial 4.4-fold increase, reaching a signal-to-noise ratio value of 14.1 compared to the vaccine group only (S/N = 3.22). This was notably higher than the corresponding values for other CpG ODNs combined with the vaccine (Figure 2). Specifically, CpG 18281-1, CpG 18281-2, CpG 18289, and CpG 1826 supplemented groups exhibited increases of 1.6, 2, 1.2, and 3.6-fold, respectively, with signal-to-noise ratio values of 5.1, 6.4, 3.9, and 11.7, respectively. These findings underscore that CpG ODN 2395 demonstrated the most significant effectiveness when combined with the Engerix B vaccine.\n\nKey: CpG 18281-1Vac = CpG ODN 18281-1+Vaccine. CpG 18281-2Vac = CpG ODN 18281-2+Vaccine. CpG 18289Vac = CpG ODN 18289+Vaccine. CpG 1826SVac = CpG ODN 1826S+Vaccine. CpG 2395Vac = CpG ODN 2395+Vaccine. PBS = Negative control ( p < 0.0001).\n\nThe groups of mice that received CpG ODNs-only exhibited lower levels of IL-6 compared to the expression level observed for the group treated with 1μg of vaccine. The Fold Change in Transcription (FCT) for CpG 18281-1 was 0.41, for CpG 18281-2 was 0.34, for CpG 18289 was 0.40, for CpG 1826 S was 0.35, and for CpG 2395 was 0.28 against 0.96 (Figure 3A). However, the levels of IL-6 expressed in mice immunized with CpG ODNs plus vaccine are higher compared to the group of mice given the vaccine alone. The FCT for the CpG ODN 18281-1 + Vaccine group was 2.57, for the CpG ODN 18281-2 + Vaccine group was 2.16, for the CpG ODN 18289 + Vaccine group was 1.20, for the CpG ODN 1826 S + Vaccine group was 1.31, for the CpG ODN 2395 + Vaccine group was 2.77, and for the vaccine alone was 0.96 (Figure 3A).\n\nKey: Vacc alone: Vaccine alone. CpG 18281-1+Vacc = CpG ODN 18281-1+Vaccine. CpG 18281-2+Vacc = CpG ODN 18281-2+Vaccine. CpG 18289+Vacc = CpG ODN 18289+Vaccine. CpG 1826+Vacc = CpG ODN 1826S+Vaccine. CpG 2395+Vacc = CpG ODN 2395+Vaccine. PBS = Negative control. (A) IL-6 gene expression, (B) TNF-α gene expression.\n\nRegarding TNF-α expression, mice treated with CpGs-only and CpG 18281-1 + Vaccine, CpG 18281-2 + Vaccine, CpG 2395 + Vaccine, and vaccine group-only exhibited lower levels of TNF-α (FCT < 1.00) compared to the non-treated PBS group (FCT=1.00). Only the groups that received vaccine + CpG 18289 and CpG 1826 expressed a high level of TNF-α, with FCT values of 2.29 and 4.96, respectively (Figure 3B).\n\nThe hematological characteristics of female BALB/c mice inoculated with 1 μg of vaccine alongside CpG ODN 2395 and PBS alone are presented in Table 4. The Neutrophil counts in the group of vaccine supplemented with CpG ODN 2395 and vaccine alone were lower than the untreated group (PBS). All the parameters for White Blood Cells, Lymphocytes, Monocytes, Eosinophils, Basophils, Red Blood Cells, HB, HCT, MCV, and Platelets were within the normal range. Higher MCHC counts were found in all treated and untreated groups. Also, higher MCH was observed in the vaccine group.\n\nThe comprehensive analysis revealed no statistically significant difference (p ≥ 0.33) between the mice receiving treatment and those not receiving treatment.\n\nBiochemical analysis of female BALB/c mice immunized with 1μg of vaccine plus CpG ODN 2395 and PBS alone are presented in Figure 4. Results for ALT, AST, Creatinine, and urea showed no statistical difference between treated and non-treated groups (p ≥ 0.85).\n\nKey: ALT = Alanine transaminase (U/L); AST = Aspartate aminotransferase (U/L); Creatinine (mg/dl); Urea (mg/dl).\n\n\n4. Discussion\n\nThis study has demonstrated that including CpG ODN 2395 in the HBV vaccine increases the immune-potentiating effect of the vaccine. CpG ODN 2395 is a class C CpG that combines the characteristics of both CpG-A and CpG-B ODNs. The CpG-A ODNs cause pDCs to produce high levels of IFN-α and TNF-α. They weakly stimulate TLR9 and IL-6 production. The CpG-B ODNs increase B-cell activation, maturation, and proliferation. They also induce IL-6, IFN-α, and TNF-α production.20 Strong immune-boosting effects of CpG-C ODNs have been demonstrated; nevertheless, certain sequence characteristics are required.20 For example, ODN 2395 includes two key features in its sequence that could be contributing to its adjuvant character. First, a palindromic sequence with several CpG motifs at the 3′-end of the ODN, followed by one or more TCG elements at the 5′-end of the ODN. It has been shown that the hexameric motif 5′ GTCGTT in ODN 2395 is the ideal sequence for CpG-C ODN activities.20\n\nOther studies have demonstrated that the addition of CpG ODN to the HBV vaccine increased the titers of antibodies against HBsAg (anti-HBs).21,22 Due to its immunostimulatory properties, many studies support the use of CpG DNA-based trials for immunotherapy against infectious disorders.23 In this study, groups of mice treated with 1 μg of Engerix B vaccine plus CpG ODNs showed substantial levels of S/N ratio values compared to groups treated with vaccine alone after 14 and 28 days of vaccination (** p ˂ 0.0001). This supports the study conducted by Jurk et al24 who showed that CpG ODNs are potent inducers of the innate immune system. Our findings also confirm those of25 who showed that J&J vaccination against SARS-CoV-2 at low and high doses in combination with CpG ODN 18281-1, CpG ODN 18281-2, and CpG ODN 18289 generated higher levels of specific IgG than the vaccine alone. On the other hand,26 demonstrated that the majority of antibodies were IgG2a in mice injected with HBsAg containing CpG ODN (1826), indicating a potent Th1-type response. Surprisingly, the CpG ODN 1826 generated substantially more IgG2a than IgG1 even when paired with alum, showing that the effects of CpG ODN 1826 dominate over those of alum about T-cell help.26 The findings of,27 show that CpG ODN 1826 can induce ten times more anti-HBs titers in an alum-adjuvanted HBsAg vaccination compared to vaccine plus alum only. In addition, following immunization with the combined adjuvant rather than alum alone, elevated antibody titers manifest at a significantly earlier time point and are more Th1-biased.27 His study concludes that ODNs with cytosine guanine dinucleotides are immunomodulatory and stimulate both professional B cells and Antigen antigen-presenting cells.\n\nThe CpG-ODNs upregulate MHC II and other co-stimulatory molecules. They cause the secretion of cytokines such as TNF-α, and IL-6 and the production of immunoglobulins by B cells.27 The IL-6 molecule is a pleiotropic cytokine predominantly expressed in activated monocytes or macrophages, but also fibroblasts or activated endothelial cells of inflamed tissues. IL-6 is inducible by LPS, TNF-α, and some interferons. Regarding the biological effects, IL-6 not only induces acute inflammation but also elicits anti-inflammatory effects. Furthermore, IL-6 induces terminal differentiation of B cells to plasma cells, which led to the descriptive name B-cell differentiation factor.15 This study showed that all groups treated with vaccine plus CpG ODNs expressed Il-6 except the group treated with vaccine only (FCT = 0.96). This study observed no statistical difference in levels of IL-6 between treated and untreated groups (p ≥ 0.2). This finding agrees with that of28 who showed that both untreated and HBV vaccine-only treated groups produced less IL-6 at 0.603- and 1.469-fold changes in transcription (FCT) respectively.\n\nTNF-α is a non-glycosylated 17-kDa protein that is mostly produced by macrophages, CD4+, CD8+, activated NK cells, neutrophils, and CD8+ T cells.15 In this study, TNF-α levels in the untreated group (FCT: 1.00) were higher compared to treated groups. Although these differences were not statistically significant (p ≥ 0.2), except for the treated groups of vaccine plus CpG 18289 and CpG 1826, which expressed TNF-α at FCT values of 2,29 and 4.96 respectively. This finding does not agree with the study by Ref. 28 which showed that mice treated with the HBV vaccine expressed higher levels of TNF-α than the untreated group at 28.84 – and 1.00 FCT respectively. These results showed that CpG ODNs enhance the secretion of Il-6, and only CpG 18289 and CpG 1826 had effect on the expression of TNF-α (Figure 3).\n\nThe body weight, behavior, and body features were normal in mice treated with CpG ODN 2395. There was also no evidence of toxicity. Results of the hematological study showed that values were normal in all parameters analyzed in both treated and untreated groups. As observed by Ref. 29 RBC, Hemoglobin, MCV, monocyte, eosinophil, basophil, platelet, and lymphocyte levels were within the normal range. Though value differences were observed between treated groups regarding Neutrophils and HCT in the CpG ODN 2395 group, MCHC in all groups, and MCH in the HBV vaccine-only group, differences were not significant (p ≥ 0.05) (Table 4).\n\nBlood biochemical profiles are a useful diagnostic tool since they show the animal’s physiological condition.25 Urea and creatinine levels were determined to check kidney function and, ALT and AST levels were also determined to check liver function in mice immunized with the vaccine + CpG ODN 2395. This study observed no significant difference in values of these parameters between the treated groups and the untreated group (p ≥ 0.05) (Figure 4).\n\nAs a result, the findings indicated that the ALT, AST, urea, and creatinine parameters were within normal ranges.\n\n\nConclusion\n\nBased on the results, we conclude that the HBV vaccine with CpG ODN 2395 has a higher potential of inducing body antibody and IL-6-based protection against HBV infection and is not toxic.\n\n\nInstitutional review board statement\n\nEthical clearance has been obtained by the Mount Kenya University Review Committee (Approval number 2196 on 16/09/2023).\n\n\nAuthor roles\n\nTitilayo Kemi Sophia Nelly Adedjobi: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Resources, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Daniel Kariuki: Conceptualization, Formal Analysis, Supervision, Writing – Review & Editing; James Kimotho: Conceptualization, Formal Analysis, Supervision, Writing – Review & Editing.\n\n\nEthics and consent\n\nMount Kenya University Review Committee (Approval number 2196 on 16th of September 2023) and approval to carry out this study was obtained from KEMRI - Animal Care and Use Committee (KEMRI-ACUC/03.07.2023 on 28th of July 2023).", "appendix": "Data availability\n\nFigshare: ‘Co-administration of a Hepatitis B vaccine with CpG-ODN 2395 induces a stronger immune response in BALB/c mice.’ https://doi.org/10.6084/m9.figshare.24745470.v2. 19\n\nThis project contains the following underlying data:\n\n• Biochemical results.png (results from biochemical analysis of the whole blood from the mice)\n\n• Hematology results.png (results from hematological analysis of the whole blood from the mice)\n\n• qPCR results.png (results from the real-time PCR for the target genes; IL-6, TNF-α and housekeeping gene, HPRT 1)\n\n• Signal-to-noise ratio values calculated from Elisa Optical Densities.png (obtained from the different treatments)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\nFigshare: Arrive checklist for ‘Co-administration of a Hepatitis B vaccine with CpG-ODN 2395 induces a stronger immune response in BALB/c mice.’ https://doi.org/10.6084/m9.figshare.24745470.v2. 19\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nAcknowledgments\n\nThe African Union; Pan African University Institute for Basic Sciences, Technology and Innovation (PAUISTI); and Kenya Medical Research Institute (KEMRI).\n\n\nReferences\n\nShi S, Zhu H, Xia X, et al.: Vaccine adjuvants: Understanding the structure and mechanism of adjuvanticity. Vaccine. May 27, 2019; 37(24): 3167–3178. Elsevier Ltd. PubMed Abstract \| Publisher Full Text\n\nYuen MF, et al.: Hepatitis B virus infection. Nat. Rev. Dis. Prim. Jun. 07, 2018; 4. Nature Publishing Group. Publisher Full Text\n\nTaherkhani R, Farshadpour F: Prevalence, genotype distribution and mutations of hepatitis B virus and the associated risk factors among pregnant women residing in the northern shores of Persian Gulf, Iran. PLoS One. Mar. 2022; 17(3 March): e0265063. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeireles LC, Marinho RT, Van Damme P: Three decades of hepatitis B control with vaccination. World J. Hepatol. 2015; 7(18): 2127–2132. Baishideng Publishing Group Co. Publisher Full Text\n\nQiu Y, et al.: DNA-based vaccination against hepatitis B virus using dissolving microneedle arrays adjuvanted by cationic liposomes and CpG ODN. Drug Deliv. Sep. 2016; 23(7): 2391–2398. PubMed Abstract \| Publisher Full Text\n\nZannoIli R, Morgese G, Jli RZ, et al.: Therapeutic Controversies HEPATITIS B VACCINE: CURRENT ISSUES The opinions of the European.\n\nYu P, et al.: A CpG oligodeoxynucleotide enhances the immune response to rabies vaccination in mice. Virol. J. Nov. 2018; 15(1): 174. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKuo TY, et al.: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. Sci. Rep. Dec. 2020; 10(1): 20085. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOu H, et al.: Longevity of protective immune responses induced by a split influenza A (H7N9) vaccine mixed with MF59 adjuvant in BALB/c mice.2017.\n\nChu CY, et al.: Cytosine-phosphate-guanine oligodeoxynucleotides containing GACGTT motifs enhance the immune responses elicited by keyhole limpet hemocyanin antigen in dairy cattle. Nucleic Acid Ther. Oct. 2011; 21(5): 323–332. PubMed Abstract \| Publisher Full Text\n\nOu H, et al.: Longevity of protective immune responses induced by a split influenza A (H7N9) vaccine mixed with MF59 adjuvant in BALB/c mice.2017.\n\nSuriano CM, Verpeut JL, Kumar N, et al.: AAV Decreases Dendritic Complexity Adeno-associated virus (AAV) reduces cortical dendritic complexity in a TLR9-dependent manner.2021. Publisher Full Text\n\nJohns JR: CPG-B ODN AND E7-PEPTIDE FUNCTIONALIZED PAMAM DENDRIMERS FOR CO-DELIVERY OF HPV-16 CANCERS THERAPUETIC VACCINE.\n\nVaccine Adjuvants.\n\nMöller B, Villiger PM: Inhibition of IL-1, IL-6, and TNF-α in immune-mediated inflammatory diseases. Springer Semin. Immunopathol. Jun. 2006; 27(4): 391–408. PubMed Abstract \| Publisher Full Text\n\nCharan J, Kantharia N: How to calculate sample size in animal studies? J. Pharmacol. Pharmacother. Oct. 2013; 4(4): 303–306. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMedrano G, Guan P, Barlow-Anacker AJ, et al.: Comprehensive selection of reference genes for quantitative RT-PCR analysis of murine extramedullary hematopoiesis during development. PLoS One. Jul. 2017; 12(7): e0181881. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOdukoya OA, Ajjan R, Lim K, et al.: The pattern of cytokine mRNA expression in ovarian endometriomata.1997.\n\nAdedjobi TKSN, Kariuki D, Kimotho J: Co-administration of a Hepatitis B vaccine with CpG-ODN 2395 induces a stronger immune response in BALB/c mice. [Dataset]. Figshare. 2024. Publisher Full Text\n\nLi T, et al.: A novel C type CpG oligodeoxynucleotide exhibits immunostimulatory activity in vitro and enhances antitumor effect in vivo. Front. Pharmacol. 2020; 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCooper CL, et al.: HBV Vaccine in Healthy Adults: A Double-Blind Phase I/II Study.2004.\n\nDavis HL, et al.: CpG DNA overcomes hyporesponsiveness to hepatitis B vaccine in orangutans.Reference Source\n\nZhu B, Wang T, Wei X, et al.: CpG DNA-triggered upregulation of TLR9 expression affects apoptosis and immune responses in human plasmacytoid dendritic cells isolated from chronic hepatitis B patients. Arch. Physiol. Biochem. 2023; 129(2): 330–337. PubMed Abstract \| Publisher Full Text\n\nJurk M, et al.: C-Class CpG ODN: Sequence requirements and characterization of immunostimulatory activities on mRNA level. Immunobiology. 2004; 209(1–2): 141–154. PubMed Abstract \| Publisher Full Text\n\nCelise DA, Kimotho J, Kimani JW, et al.: Increase in the Immune Response in Balb/c Mice after the Co-Administration of a Vector-Based COVID-19 Vaccine with Cytosine Phosphoguanine Oligodeoxynucleotide. Vaccines (Basel). Dec. 2022; 11(1): 53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDavis HL, Weeranta R, Waldschmidt TJ, et al.; CpG DNA Is a Potent Enhancer of Specific Immunity in Mice Immunized with Recombinant Hepatitis B Surface Antigen 1.1998. Reference Source\n\nSpecial Feature.\n\nNdung’u F, Nyanjom S, Omari S, et al.: Preliminary assessment of adjuvant activities of Glycine Max (L.) Merr saponin extract in BALB/c mice immunized with hepatitis B virus vaccine. F1000Res. Sep. 2023; 12: 1145. Publisher Full Text\n\nSilva-Santana G, et al.: Clinical hematological and biochemical parameters in Swiss, BALB/c, C57BL/6 and B6D2F1 Mus musculus. Animal Model Exp. Med. Dec. 2020; 3(4): 304–315. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "292789", "date": "05 Jul 2024", "name": "Wolfram H Gerlich", "expertise": [ "Reviewer Expertise Medical Virology", "Hepatitis B vaccines and diagnostics" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comment\nThe subject of this paper is principally interesting. The immunogenicity of current hepatitis B vaccines is not optimal and insufficient for recipients with impaired immune system. While the composition of the HBV surface antigen in the vaccines is virtually unchanged for 40 years, some new adjuvants have been introduced for problematic recipients, e.g., an CpG ODN for the vaccine Heplisav-B. This paper does not deal directly with development of a vaccine for use in human recipients and does not discuss this aspect in the introduction or discussion. Instead, a search for an optimally active CpG ODN as adjuvant for the conventional hepatitis B vaccine Engerix B from GSK was undertaken using mice for immunization. The experiments could have been potentially useful, but, unfortunately, the study design and the assays for the immune response, i.e. antiHBs and the cytokines, are inadequate as pointed out below.\nSpecific comments\nThe abbrev. KEMRI should be once explained: Kenya Medical Research Institute. At least once the composition of Engerix B should be explained: 20 microgram HBsAg /ml expressed in yeast and 0.5 mg Al-Ions as aluminumhydroxide. Is injection of the CpG alone an immunization? CpGs are not antigens! The authors used a qualitative assay for the antiHBs level without any standardized reference sample. State of the art is to measure and report antiHBs levels in mIU/mL using calibrated assays. The antiHBs assay is problematic and possibly nonspecific.\nSince calibration in mIU/mL antiHBs is missing, at least a curve between the OD and increasing dilutions of an arbitrary antiHBs standard should have been done as in ref. 26. Are data on the limit of detection and the range of semi-quantitation of this Mouse HBV Surface Antibody (HBsAb) Qualitative test kit ELISA assay available? Does this assay detect only mouse antiHBs? How are positive and negative results distinguished if no cutoff is mentioned in the results? See also point 8. Does the assay detect all immunoglobulin classes (IgG and IgM)?\n\nThe quantification of the RNA encoding TNF-alpha, IL-6 and HPRT1 is suboptimal and not calibrated with quantitative standard samples. Results. This sentence contains an error: Moreover, the findings demonstrated that the CpG 18281-1, CpG 18281-2, CpG 18289, and CpG 1826 supplemented groups exhibited 1.2, 1.8, 1.1, and 1.6-fold increases respectively with signal-to-noise ratio values (2.5, 3.8, 2.2 and 3.3 respectively) compared to vaccine group only (S/N = 2.1).Ã¢ÂÂ It should be 2.2 : 2.1 = 1.047, i.e., 1.0 and not 1.1. Irrespectively, both the ratio of 1.1 or 1.047 are not at all a notable increase.\nIn contrast, following this sentence, it should be mentioned that the S/N for CpG2395Vac was significantly lower than for the vaccine alone. Here, this ODN seems to inhibit the antiHBs response.\n\nFigure 1 and 2. Which S/N value corresponds to a cutoff between positive and negative?\nThe PBS control obviously does not provide a valid control because the two CpGs in fig. 1 without vaccine generate higher S/N signals than the vaccine alone. In fig. 2 CpG 18281-2 alone generates an as high S/N of ca. 3 as the vaccine alone. Obviously, an S/N of 3 does not indicate specific antiHBs antibody since an adjuvant without antigen cannot induce a specific antibody. It should also be noted that the obviously nonspecific S/N signals for the CpGs alone between 1- 3 did not change much from the first to the second blood sampling.\n\n9. Ref. 19 from the authors of this manuscript, Adedjobi TKSN, Kariuki D, Kimotho J, contains exactly the same data as here. Is this compatible to this submission? 10. Refs. 21 and 22 cannot be found without additional data. 11. The authors should have followed the experimental approach described 26 years ago in J Immunol. (ref. 26).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "297823", "date": "16 Jul 2024", "name": "Fengmin Lu", "expertise": [ "Reviewer Expertise Microbiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nADEDJOBI et.al found the co-administration of the HBV vaccine with CpG ODN 2395 induces high immune responses compared to the HBV vaccine alone. This is interesting research, but I have some questions may need to be addressed and suggestions to the authors.\nThe sample size of mice in each group is too few for the current study. Please explicitly state the number of independent experimental replicates used to generate the data in all relevant figures. Why mice immunized with CpG ODNs alone generated HBsAb? Does the vaccine with CpG-ODN provide better protection? Why is there a decrease in neutrophils in the peripheral blood of the vaccine group？ How do you determine the dosage of 0.67μM to administer? There are studies have reported that the immune cells of male and female react differently to pathogens, do male mice produce the same results?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "271988", "date": "10 Sep 2024", "name": "Brandi Tranae' Johnson-Weaver", "expertise": [ "Reviewer Expertise Vaccines", "immunology", "adjuvants", "allergy" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors compare antigen-specific antibody responses in BALB/c mice after intramuscular immunization with the HepB vaccine Engerix alone, with various CpG sequences alone, or the combination of the vaccine containing various CpG sequences as an adjuvant. The authors described vaccine-induced antibody responses as a signal to noise ratio normalized to antibody responses from mice immunized with a PBS control. The authors also report vaccine-induced fold-change in key cytokines, including IL-6 and TNFa, and assessed whole blood samples for cell composition and blood chemistries to monitor for abnormal responses. The authors identify CpG 2395 as a potent adjuvant that does not induce abnormal blood counts or chemistries after immunization.\nAlthough CpG 2395 appears to be the superior CpG adjuvant tested in the described studies, several key elements limit the enthusiasm of the results.\nThe authors evaluate 12 vaccine conditions using 3 mice per group. Statistical analyses are reported to be tested by ANOVA or t-test; however, it is not clear which assay used which test to determine statistical differences. More clarification and transparency is required to demonstrate the statistical differences reported in this manuscript. Please provide power calculations to identify the statistical power required to observe differences across 12 immunization groups.\n\nFigures 1 and 2 also appear to compare responses across multiple groups; however, the authors do not discuss if multiple comparison analyses or corrections were performed. Similarly, the methods do not provide sufficient detail to understand the ELISA results. For example, what is the serum/plasma dilution for testing the samples in the assay? Also, does biological replicates and technical replicates combine to determine the S/N ratio for each group.\nFigure 3 does not appear to have any statistical analyses performed.\nWhile the blood cell count and biochemistry data are interesting, there does not appear to be any statistical comparisons between readouts.\nOne benefit of vaccine adjuvants is the ability to modulate the type of antigen-specific immune response, this manuscript lacks a thorough characterization of vaccine-induced immunity despite the authors referencing other literature reports that described vaccine-induced antibody isotypes and T cell cytokine responses.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-404
https://f1000research.com/articles/13-403/v1	26 Apr 24	{ "type": "Study Protocol", "title": "Comparison of Neutrophil Lymphocyte Ratio combined SOFA versus APACHE IV in assessing the Prognosis of Sepsis Patients admitted to Medical Intensive Care Unit", "authors": [ "Venkat Reddy", "Sunil Kumar", "Sunil Kumar" ], "abstract": "Background Sepsis poses a significant threat in the Medical Intensive Care Unit (MICU), with high morbidity and mortality rates. Accurate prognostic tools are essential for guiding patient management. This study aims to compare the effectiveness of Neutrophil–Lymphocyte Ratio with Sequential Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation IV (APACHE IV) in predicting sepsis outcomes. A prospective cross-sectional design will enrol septic MICU patients, collecting baseline data and scoring systems. Patient outcomes, including mortality and length of MICU stay, will be analyzed using correlation and ROC curve analyses. This study addresses the current gap in direct comparisons of these tools.\n\nResults The results of this study are anticipated to reveal significant correlations between the Neutrophil Lymphocyte Ratio combined with SOFA and APACHE IV scores and patient outcomes. Specifically, we expected to observe strong associations between the combined scoring system and mortality rates, length of MICU stay, and the need for organ support. Furthermore, we anticipate that the Neutrophil Lymphocyte Ratio combined with SOFA will demonstrate higher predictive accuracy than APACHE IV to assess prognosis in sepsis patients admitted to the MICU.\n\nConclusion Based on the results obtained from this prospective cross-sectional study, we can draw conclusions regarding the comparative effectiveness of NLR (Neutrophil Lymphocyte Ratio) combined with SOFA and APACHE IV in assessing the prognosis of sepsis in the MICU. We anticipate that the combined scoring system will provide a more accurate prognostic assessment and enable healthcare professionals to make well-informed choices regarding patient care and the distribution of resources. These findings will contribute to building evidence on sepsis and may have implications for improving patient outcomes in the MICU setting.", "keywords": [ "Neutrophil Lymphocyte Ratio", "SOFA", "APACHE IV", "critical ill patient", "sepsis" ], "content": "Introduction\n\nSepsis, a potentially fatal illness, is a severe organic malfunction caused by an uncontrolled response to infection in the body. If ignored, it can develop into septic shock, which is characterized by serious metabolic and circulatory problems and is often fatal.1\n\nInflammation and immunological response are crucial factors in many chronic illnesses. An indicator of the balance between two components of the defense mechanism, including acute and chronic inflammation (expressed by means of neutrophil count) and adaptive immunity (expressed by means of lymphocyte count), is (theeutrophil-to-lymphocyte ratio NLR, a biomarker found in the blood (peripheral).\n\nNLR, an inflammatory biomarker computed by dividing the total count of neutrophils by the total count of lymphocytes, is a marker of systemic inflammation. This measure does not increase the price of standard full blood count testing routinely conducted in hospital settings. NLR has been studied as a prognostic indicator in various conditions, including sepsis, community-acquired pneumonia, and various forms of cancer.2\n\nNLR is a widely utilized marker to assess the severity of bacterial infection and to predict the prognosis of patients with tumor pneumonia.3 NLR serves as a straightforward parameter for evaluating an individual’s inflammatory status and has demonstrated its utility in predicting the mortality of significant cardiac diseases, as well as being a robust prognostic factor for various cancer types.4,5\n\nThe SOFA is a straightforward and objective scoring system that assesses the severity and number of multi-organ dysfunctions across six organ systems: respiratory, liver, urology, cardiovascular, coagulation, and neurological. This score gauges dysfunction in individual organs or provides an overall assessment of organ dysfunction.6 A higher SOFA score indicates a greater likelihood of mortality.\n\n\n\n• To Compare Neutrophil Lymphocyte Ratio combined with SOFA versus APACHE (Acute Physiology And Chronic Health Evaluation) IV in assessing the Prognosis of Sepsis Patients admitted to the Medical Intensive Care Unit.\n\n\n\n• To estimate the combined SOFA and Neutophil Lymphocyte Ratio score in sepsis patients\n\n• To estimate APACHE IV Score in sepsis patients\n\n• To compare the neutrophil lymphocyte ratio combined sofa with APACHE IV in predicting outcomes in terms of mortality, ICU (Intensive Care Unit) stay, and mechanical ventilation in patientswith sepsis\n\n\nMethods\n\nResearch design: Prospective, Cross sectional study.\n\nSetting: All patients visiting the Department of General Medicine (Acharya VinobhaBhave Rural Hospital, Datta Meghe Institute of Medical Sciences, Sawangi (Meghe), Wardha) who met the criteria for sepsis.\n\nAfter obtaining written informed consent, all patients who satisfied the inclusion and exclusion criteria were included in the study.\n\nDuration for study: 2022 to 2024.\n\nInclusion criteria:\n\n• Patients older than 18 years of age\n\n• The patient satisfied diagnosis and diagnostic criteria of sepsis on the SOFA, and their survival time after admission is ≥24 hours.\n\nThe following exclusion criteria must be met:\n\n• Patients with an emergency room survival time of fewer than twenty-four hours;\n\nCardiac or Respiratory Arrest\n\n• Pregnancy;\n\n• Immune system disorders;\n\n• Malignant tumors; and\n\n• Haematological disorders.\n\nOutcomes:\n\n1. Mortality (within a specified time frame): The primary outcome measure indicated whether the patient died within a specified time period.\n\n2. Length of MICU stay - The duration will be measured in hours or days.\n\n3. Requirement for organ support: The need for specific interventions or therapies to support organ function, such as mechanical ventilation or vasopressors.\n\nExposures:\n\n1. Neutrophil Lymphocyte Ratio - A calculated by dividing the neutrophil count by the lymphocyte count from a patient’s blood sample, reflecting the balance between anti-inflammatory neutrophils and pro-inflammatory lymphocytes.\n\n2. SOFA score: A scoring system that evaluates the degree of organ malfunction in six major organ systems: circulatory, neurological, hepatic, renal, respiratory, and coagulation.\n\n3. APACHE IV score: A comprehensive scoring system that evaluates the severity of acute conditions, incorporating physiological parameters, chronic illness, and age.\n\nPredictors:\n\n1. Comorbidities: pre-existing illnesses that could affect the patient’s prognosis, such as diabetes, hypertension, or chronic kidney disease.\n\n2. Source of infection: The primary site or origin of the infection causing sepsis (e.g., respiratory, urinary, and abdominal).\n\n3. Microbiological culture results: Laboratory results identifying the specific causative organism responsible for the infection.\n\n4. Laboratory parameters: Results of blood tests, including white blood cell count and lactate levels, may indicate the severity of infection and organ dysfunction.\n\nPotential confounders:\n\n1. Presence of septic shock: The occurrence of sepsis-induced circulatory and cellular/metabolic abnormalities results in a higher risk of mortality.\n\n2. Severity of illness: The overall severity and complexity of the patient’s acute illness, which may affect prognosis.\n\n3. Use of specific treatments or interventions: The administration of specific therapies or interventions such as antibiotics or fluid resuscitation can influence patient outcomes.\n\nEffect modifiers:\n\n1. Age: Patient age may modify the relationship between exposure and outcomes.\n\n2. Sex: The biological sex of the patient may interact with exposure to influence outcomes.\n\n3. Presence of comorbidities: Pre-existing medical conditions may modify the effects of exposure on outcomes.\n\n4. Source of infection: The specific site or origin of the infection may interact with the exposure to affect outcomes.\n\n5. Specific type of organ dysfunction: The presence of specific organ dysfunction may modify the effects of exposure on outcomes.\n\nCollection of Blood Sample\n\nTo begin the blood collection process, the skin above the median cubital vein was prepared by applying spirit to the cubital fossa area. Additionally, a tourniquet was placed proximal to the fossa. Subsequently, a sterile venipuncture needle, the standard in its design, was used to collect the blood. blood was drawn into a bulb containing potassium ethylenediamine tetra acetate for sample collection and complete blood cell count analysis. Importantly, blood sample analysis was carried out within a 15-minute timeframe from the time of collection.\n\nConfidentiality\n\nThe collected data will be kept confidential. The data were coded and entered into a password-protected digital form. The names and other personal details of the patients will not be revealed.\n\nProcedure\n\nBlood samples will be taken under strict aseptic precautions.\n\nMeasurement of Blood Pressure\n\nAccording to the guidelines set forth by the American Heart Association (AHA), readings of 130 mmHg or higher for systolic blood pressure (SBP) or 80 mmHg or higher for diastolic blood pressure (DBP) are indicative of elevated blood pressure. The blood pressure of each patient was measured according to the protocol recommended by the AHA.\n\nA comprehensive clinical examination will be conducted and all observed findings will be recorded. A thorough patient history and examinations will be performed. Relevant historical information, including smoking and alcohol consumption as well as medication use, will be documented. We will also assess any pre-existing medical conditions in the patients, inquiring about a history of hypertension, diabetes, malignancy, and chronic kidney and liver disease. Physical examination will include pulse rate, blood pressure, Glassgow coma scale score, and complete blood count.\n\nThe SOFA score, referred to as the sepsis-related organ failure assessment score previously, is employed to monitor an individual’s condition during their ICU stay. It is used to assess the degree of organ function or rate of organ failure in a person (Table 1)\n\nThe parameters for assessment include:\n\n1. Age (years)\n\n2. Body Temperature (°C)\n\n3. Mean Arterial Pressure (MAP, mmHg)\n\n4. Heart Rate (HR, beats per minute)\n\n5. Respiratory Rate (RR, breaths per minute)\n\n6. Mechanical Ventilation (Yes/No)\n\n7. Fraction of Inspired Oxygen (FiO2, %)\n\n8. Partial Pressure of Oxygen (pO2, mmHg)\n\n9. Partial Pressure of Carbon Dioxide (pCO2, mmHg)\n\n10. Arterial pH\n\n11. Sodium (Na+, mEq/L)\n\n12. Urine Output (mL per 24 hours)\n\n13. Creatinine (mg/dL)\n\n14. Urea (mEq/L)\n\n15. Blood Sugar Level (BSL, mg/dL)\n\n16. Albumin (g/L)\n\n17. Bilirubin (mg/dL)\n\n18. Hematocrit (Ht, %)\n\n19. White Blood Cell Count (x1000/mm3)\n\n20. Glasgow Coma Scale (GCS) with subcomponents:\n\n- Eye Response\n\n- Verbal Response\n\n- Motor Response\n\n21. Chronic Health Conditions:\n\n- Chronic Renal Failure (CRF) or hemodialysis (HD)\n\n- Cirrhosis\n\n- Hepatic Failure\n\n- Metastatic Carcinoma\n\n- Lymphoma\n\n- Leukemia or Myeloma\n\n- Immunosuppression\n\n- Acquired Immunodeficiency Syndrome (AIDS)\n\nContinuous variables will be expressed as mean ± Standard Deviation and compared across groups using unpaired t-test or ANOVA.\n\nCategorical variables will be expressed as the number and percentage of patients and compared across groups. All the data will be entered in Microsoft Excel 2013, and the statistical software R studio Version 4.3.1 will be used for the analysis. An alpha level of 5% will be considered, that is, if any p-value is less than 0.05, it will be considered significant. Means between two different groups will be assessed using an unpaired t-test. Correlations will be done using Spearman’s or Pearson’s correlations.\n\n\n\n1. Selection Bias: Non-random or non-representative participant selection.\n\n2. Information Bias: Errors or inconsistencies in measurement or data recording.\n\n3. Confounding Bias: Distortion of association due to an extraneous variable.\n\n4. Reporting Bias: Publication bias favoring significant or positive results.\n\n5. Observer Bias: Biased interpretation or reporting by researchers or clinicians.\n\n6. Lead-time Bias: Differences in outcome assessment timing affecting results.\n\nApplying Krejcie and Morgan Formula for the estimation of the sample size\n\nχ2 is the chisquare tabulated value for 1 Degree of Freedom at 95% confidence interval\n\nN is the total number of patients\n\nP is the 50% proportion\n\nc is the Error of Margin at 5%\n\nSubstituting the appropriate values for the statistical estimation in equation 1 leads to\n\nThis study aimed to assess the prognosis of sepsis patients in the MICU by comparing the neutrophil-lymphocyte ratio combined with the SOFA score versus the APACHE IV score. The expected outcomes included a comparative analysis of the predictive performance of these scoring systems in predicting mortality, length of MICU stay, and requirement for organ support. Additionally, the association between Neutrophil Lymphocyte Ratio, SOFA score, APACHE IV score, and outcomes will be examined. This study will evaluate the accuracy and discriminatory power of the scoring systems, identify potential effect modifiers, and explore the clinical implications of using these tools in assessing sepsis prognosis. These findings will contribute to the understanding of prognostic assessment in sepsis and may have implications for patient management and decision-making in the MICU.\n\nThe study will be distributed in index journal.\n\n\nDiscussion\n\nA critical clinical state known as sepsis is characterised by dysregulated response of host to infections & frequently develops as consequence of severe infection.8 Cardinal symptoms of inflammation, such as vasodilation, leukocyte buildup, and increased vascular permeability, are part of this response and can manifest in tissues far from the infection site. High death rates are associated with sepsis, especially in patients who require treatment in the ICU. Early and precise diagnosis is essential to improve the prognosis of patients with sepsis.9\n\nIn critically ill patients, sepsis diagnosis is a formidable challenge, necessitating a multifaceted approach. In addition to obtaining a comprehensive medical history and conducting thorough physical examination, laboratory markers of infection and inflammation are vital components of the diagnostic process. These markers include White Blood Cell (WBC), C-reactive protein (CRP), procalcitonin (PCT), neutrophil, and lymphocyte counts. Among these indicators, neutrophil-to-lymphocyte ratio (NLR) has emerged as a valuable biomarker for sepsis diagnosis.\n\nNLR is a straightforward and cost-effective parameter derived from complete blood count (CBC). It offers insights into the balance between neutrophils, which are indicative of inflammation, and lymphocytes, which reflects the immune response. Significantly, in sepsis, a higher NLR is associated with a worse outcome. The natural reaction of the immune system to infection and other stressful situations is an increase in neutrophil counts and a decrease in lymphocyte counts. While lymphocyte numbers decrease when activated cells travel to inflammatory tissues and incur greater apoptosis, neutrophil counts increase as a result of reduced apoptosis and rapid mobilization of neutrophils from the bone marrow.8\n\nThe neutrophil-lymphocyte count ratio (NLCR), first described in 2001, is a simple, quick, and economical metric for evaluating stress and inflammation in critically ill patients. Zahorec et al. conducted a prospective study. involving ninty patients in the ICU, revealing that NLR had the capability to forecast the severity and future outcomes in patients with sepsis.10 Recent research has demonstrated the predictive utility of NLCR in patients presenting to the Emergency Department (ED) with suspected bacteremia, as well as its correlation with the short- and long-term outcomes of patients in critical conditions.11\n\nHeffernan et al. observed that trauma patients and those meeting the criteria for systemic inflammatory response syndrome (SIRS) exhibited a concurrent condition characterized by both low lymphocyte counts and high neutrophil counts.12 In contrast, Bermejo-Martín et al. found a link between reduced circulating neutrophil counts and an increased risk of mortality.13 This raises the possibility that sepsis patients with low circulating neutrophil counts may find it difficult to generate a potent innate immune response. Furthermore, sepsis syndrome may cause neutrophils to adhere to the vascular endothelium more strongly, which would lower the number of circulating neutrophils. Endothelial injury is a common consequence of sepsis.12\n\nThe SOFA scoring system is a widely utilized tool for gauging the severity of organ dysfunction in critically ill patients, including those with sepsis. The SOFA examines the condition in six distinct organ systems: cardiovascular, neurological, hepatic, renal, respiratory, and coagulation. Each system was assigned a score ranging from zero, representing normal function, to four, denoting severe dysfunction or failure). A score of 3 or 4 in any particular system indicated a high likelihood of organ failure within that specific system. The SOFA assigns a numerical value to each system, providing healthcare providers with a measurable indicator of dysfunction across various organs.13\n\nIn a study conducted by Shimoyama et al., it was noted that SOFA scores were correlated with higher estimated risk levels than NLR. Furthermore, this study disclosed that the likelihood of mortality increased by 13 % %with every increase of 1 unit in the SOFA scores. This phenomenon can be explained by the fact that SOFA scores are confined to a limited numerical range between 0 and 20, whereas the NLR lacks an upper numerical limit, permitting a wider spectrum of values.13,14\n\nBoth NLR and platelet-to-lymphocyte ratio (PLR) were identified as straightforward, cost-efficient, and expeditious indicators of mortality when juxtaposed with more intricate scoring systems, such as APACHE II and SOFA scores. The amalgamation of these biomarkers, such as SOFA scores and NLR, has the potential to increase the accuracy of mortality predictions. This unified approach capitalizes on the strengths of both systems and offers a more comprehensive evaluation of a patient’s condition. Consequently, the integration of SOFA scores and NLR can empower healthcare providers to make better informed decisions regarding the prognosis and treatment of critically ill patients, particularly those with sepsis in the intensive care unit (ICU).13\n\nNotably, when measuring the neutrophil-to-lymphocyte ratio (NLR) upon admission to the Intensive Care Unit (ICU), researchers have found associations with both short-term and long-term mortality in critically ill adult patients. This suggests that NLR could serve as a valuable indicator of the inflammatory response in critically ill adults. In the context of sepsis management in the ICU, the NLR and NLCR can serve as valuable tools for risk stratification and prognostication. These biomarkers provide clinicians with additional insights into patients’ inflammatory and immune responses, helping to guide early intervention and treatment decisions. The APACHE IV is an enhanced and modernized model designed to forecast the mortality rate of groups of critically ill patients, while the previously revised equation is used to predict mortality rates in hospitals following coronary artery bypass graft (CABG) surgery.\n\nThe APACHE IV is a scoring system and predictive model utilized in medical settings to assess the severity of illness and predict the risk of mortality.15 It includes the following components:\n\n1. Acute Physiology Score (APS): This component assesses the physiological status of a patient upon admission to the ICU. It considers vital signs, laboratory values, and other clinical parameters to measure the severity of an acute illness.\n\n2. Age: The patient’s age is a factor in the APACHE IV model, as older age can be associated with increased mortality risk.\n\n3. Chronic Health Points (CHP): This component considers a patient’s pre-existing health conditions and comorbidities. It assigns points based on the presence and severity of chronic illness.\n\n4. Glasgow Coma Scale (GCS): The patient’s degree of consciousness and neurological function are evaluated using the GCS.\n\n5. Admission Source: This component considers where the patient was admitted, such as the emergency department, operating room, or other locations within the hospital.\n\n6. Admission Type: It categorizes the patient’s admission as either scheduled (elective) or unscheduled (emergency).\n\n7. Diagnostic Category: This component classifies the patient into one of several diagnostic categories, which helps to group patients with similar conditions for risk prediction.\n\n8. Chronic Health Conditions: APACHE IV includes specific chronic health conditions and comorbidities as risk factors.\n\n9. Organ Support: It considers whether the patient requires mechanical ventilation, renal replacement therapy, or other forms of organ support.\n\n10. Surgical Status: APACHE IV accounts for surgical patients and their post-operative status, including elective or emergency surgery.\n\nThese components were used to calculate the predicted risk of mortality for each ICU patient. The APACHE IV score provides valuable information for clinicians and researchers to assess illness severity and make informed decisions regarding patient care. It is a widely used tool in critical care medicine for risk stratification and quality improvement. Keep in mind that The specific details and components of the APACHE IV may evolve over time as new versions or updates are developed.15\n\nThis study aimed to assess the combined SOFA and NLR scores as predictors of outcomes in patients with sepsis and to estimate the APACHE IV Score for the same patient population. This study aimed to compare the predictive capabilities of the combined NLR-SOFA score with the APACHE IV score in terms of mortality risk, length of stay in the intensive care unit (ICU), and need for mechanical ventilation among sepsis patients. This analysis aimed to provide valuable insights into the effectiveness of these scoring systems in guiding clinical decisions and improving patient care for individuals with sepsis.\n\nWritten consent will be taken from all the participants in the study.\n\nEthical committee: Datta Meghe Institute of Medical Sciences (Deemed to be University) IEC NO- DMIMS (DU)/IEC/2022/1091 aprooved on 27/06/2022.\n\nStudy status: Not yet started.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgement\n\nAll authors mentioned for the study have contributed equally to the study design, data curation, data availability, conceptuality, writing, and drafting.\n\n\nReferences\n\nEvans L, Rhodes A, Alhazzani W, et al.: Surviving sepsis campaign: international guidelines for management of sepsis and septic shock 2021. Intensive Care Med. 2021; 47(11): 1181–1247. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nde Jager CP , Wever PC, Gemen EF, et al.: The neutrophil-lymphocyte count ratio in patients with community-acquired pneumonia. PLoS One. 2012; 7(10): e46561. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBerhane M, Melku M, Amsalu A, et al.: The Role of Neutrophil to Lymphocyte Count Ratio in the Differential Diagnosis of Pulmonary Tuberculosis and Bacterial Community-Acquired Pneumonia: a Cross-Sectional Study at Ayder and Mekelle Hospitals, Ethiopia. Clin. Lab. 2019; 65(4). PubMed Abstract \| Publisher Full Text\n\nAzab B, Chainani V, Shah N, et al.: Neutrophil–Lymphocyte Ratio as a Predictor of Major Adverse Cardiac Events Among Diabetic Population: A 4-Year Follow-Up Study. Angiology. 2013; 64(6): 456–465. PubMed Abstract \| Publisher Full Text\n\nTomita M, Shimizu T, Ayabe T, et al.: Preoperative neutrophil to lymphocyte ratio as a prognostic predictor after curative resection for non-small cell lung cancer. Anticancer Res. 2011; 31(9): 2995–2998. PubMed Abstract\n\nVincent JL, Moreno R, Takala J, et al.: The SOFA (Sepsis-related Organ Failure Assessment) score to describe organ dysfunction/failure. On behalf of the Working Group on Sepsis-Related Problems of the European Society of Intensive Care Medicine. Intensive Care Med. 1996; 22(7): 707–710. PubMed Abstract \| Publisher Full Text\n\nWilliams L, Gannon J: Use of the SOFA Score in Pandemic Influenza — A Prospective Study. J. Intensive Care Soc. 2009; 10(3): 179–182. Publisher Full Text\n\nWesterdijk K, Simons KS, Zegers M, et al.: The value of the neutrophil-lymphocyte count ratio in the diagnosis of sepsis in patients admitted to the Intensive Care Unit: A retrospective cohort study. PLoS One. 2019; 14(2): e0212861. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnnane D, Bellissant E, Cavaillon JM: Septic shock. Lancet. 2005; 365(9453): 63–78. Epub 2005/01/11. Publisher Full Text\n\nZahorec R: Ratio of neutrophil to lymphocyte counts--rapid and simple parameter of systemic inflammation and stress in critically ill. Bratisl. Lek. Listy. 2001; 102(1): 5–14. English, Slovak. PubMed Abstract\n\nSalciccioli JD, Marshall DC, Pimentel MA, et al.: The association between the neutrophil-to-lymphocyte ratio and mortality in critical illness: an observational cohort study. Crit. Care. 2015; 19: 13. Epub 2015/01/20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHeffernan DS, Monaghan SF, Thakkar RK, et al.: Failure to normalize lymphopenia following trauma is associated with increased mortality, independent of the leukocytosis pattern. Crit. Care. 2012 Jan; 16(1): R12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAltas OF, Kizilkaya M: The effects of neutrophil-lymphocyte ratio, platelet-lymphocyte ratio and prognostic markers in determining the mortality in patients diagnosed with pneumonia in intensive care. Medeni. Med. J. 2021; 36(2): 130–137. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShimoyama Y, Umegaki O, Agui T, et al.: Neutrophil to lymphocyte ratio and platelet to lymphocyte ratio are superior to other inflammation-based prognostic scores in predicting the mortality of patients with gastrointestinal perforation. JA Clin. Rep. 2017; 3(1): 49. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZimmerman JE, Kramer AA, McNair DS, et al.: Acute Physiology and Chronic Health Evaluation (APACHE) IV: Hospital mortality assessment for today’s critically ill patients. Crit. Care Med. 2006; 34(5): 1297–1310. PubMed Abstract \| Publisher Full Text" }	[ { "id": "301706", "date": "22 Jul 2024", "name": "Narani Sivayoham", "expertise": [ "Reviewer Expertise Scoring systems in sepsis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for inviting me to review the manuscript, ‘Comparison of neutrophil lymphocyte ratio combined SOFA versus APACHE IV in assessing the prognosis of sepsis patients admitted to Medical Intensive Care Unit’. In this prospective cross-sectional study, the authors plan to compare the prognostic performance of the SOFA score combined with the neutrophil lymphocyte ratio with that of the APACHE IV score. The purpose of this study as I understand it is to improve the SOFA score by adding the neutrophil lymphocyte ratio and study its prognostic performance to a much more complex scoring system, the APACHE IV score. This is all the more important as it uses routinely available parameters. Whilst the purpose of the study is commendable, there are some areas in this study protocol that need clarification. My comments are as follows:\nThe title of the protocol implies that the population studied are those patients admitted to a medical intensive care unit. However, under methods, the authors state that the setting is, ‘all patients visiting the department of general medicine’. Please clarify the study population. The authors have described how blood will be drawn in this prospective cross-sectional study. Will the patients provide informed consent? The authors state that patients will be included if they meet the sepsis criteria. Which criteria are these? If it is the Sepsis-3 criteria, will they be collecting baseline blood results? What is meant by immune system disorders’ and ‘haematological disorders’? Outcomes—The authors have not specified the time period in which they will measure the primary outcome. This needs to be specified. The authors state that the blood sample analysis will take place within 15 minutes of collection. How will this be monitored? What will happen to samples that are not processed within 15 minutes? There are long lists of predictors, potential confounders and effect modifiers. How will they collect data on this? Will they be controlling for these? It is not clear why the definition of elevated blood pressure is included in the protocol. Please explain. The protocol lists several biases. However, it does not mention any systems in place to mitigate these biases. Thank you for providing a sample size calculation. Is the P=50% proportion the expected mortality rate? If so, how was this arrived at? Statistical tests- Please provide the statistical tests that will be used to compare the NLR combined SOFA score with the APACHE IV score What test will determine if the NLR combined SOFA score has higher predictive accuracy than the APACHE IV score? The manuscript could be streamlined. The descriptions of the different scoring systems are replicated throughout. The tense in which the protocol is written is not consistent. For example on page 5, under ‘confidentiality’, the following is stated: ‘The collected data will be kept confidential. The data were coded…..’\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-403
https://f1000research.com/articles/13-401/v1	26 Apr 24	{ "type": "Research Article", "title": "Approaches for sustainable professional skill development for vocational education students in Thailand", "authors": [ "Naksit Sakdapat" ], "abstract": "Background This article presents a research study that aims to explore sustainable approaches for developing professional skills in vocational education students in Thailand. This is the second phase of the research, which utilizes a qualitative research methodology.\n\nMethodology The key informants in this study are administrators of vocational education institutions, teachers, and students currently enrolled in vocational education institutions in Thailand, totaling 36 participants. The research uses a purposive sampling method and snowball sampling method. Data collection methods include document analysis, in-depth structured interviews, and observation. The results of the interviews are analyzed, and the content analysis is summarized. The research process consists of 4 steps: 1) literature review, 2) data collection, 3) data analysis, and 4) verification and confirmation.\n\nResults The research findings highlight several key considerations, including: 1) factors influencing the development of professional skills among vocational education students, such as curriculum design, support and counseling, practical training in workplaces, interactive learning, problem-solving and analytical thinking skills development, practical learning, and supportive learning environments, 2) approaches for sustainable professional skill development involve employing the appropriate approaches for self-development. The steps include setting clear goals and plans, active learning and training, technology skill development, experiential learning, problem-solving skill development, participation in professional activities, self-reflection, and continuous self-improvement.\n\nConclusion These approaches aim to enhance the competencies of vocational education students, ensuring quality and efficiency as part of lifelong learning and sustainable development.", "keywords": [ "Self-development", "professional skills", "sustainable development", "skill development", "self-improvement", "problem solving skills", "experiential learning." ], "content": "Introduction\n\nEducation is crucial for the creation of a high-quality workforce with capabilities that support national development, particularly in vocational education. The goal is to produce a skilled workforce that meets the demands of the labor market, contributes to the economic advancement of the country, and enhances the competitiveness of the nation. However, the current development of vocational education reveals that it does not align with the needs of businesses. Moreover, there is a decline in the number of students pursuing vocational education, leading to a shortage of both quantity and quality in the workforce in production and labor markets (Office of the Vocational Education Commission, 2010). In essence, the quality-oriented goal aims to develop individuals with problem-solving abilities and professional skills. Meanwhile, the quantity-oriented goal aims to increase the workforce at the middle level to at least 60% of the total workforce (Office of the National Economic and Social Development Council, 2022). Additionally, basic competency and professional skills necessary for work in educational institutions that offer vocational education are not acknowledged by employers. This includes a lack of skills in practical work, expertise in foreign languages and/or computer skills, and problems related to studying not aligning with the job market’s needs or choosing majors based on popular trends without considering the workforce needs of businesses (Euapipattanakul, 2022). From the aforementioned problem, the National Economic and Social Development Plan (2023) reported on the situation of education and national development in Thailand, providing recommendations to address the issues. Two key points were emphasized: the need to expedite the development of the quality of Thai education, focusing on developing the technological and innovative skills of vocational education graduates. Furthermore, there should be attention to parental values regarding vocational education, where there is a preference for general education over vocational education (Jedynak et al., 2021). This contradicts the direction of national development, impacting resource allocation for education significantly (Rojananan, 2016). The report on the production status and trends in vocational education in Thailand found that the proportion of students at the professional certificate level compared to the general stream is 60:40. Notably, there has been an increase in the use of professional-level labor from 9.5% in 2007 to 11.9% in 2017, respectively. However, the Thai industrial system still heavily employs less skilled professional labor. This reveals an increase in the proportion of professional-level labor, but it does not fully align with the government’s expectations for vocational education to play a key role in developing the country, especially with the trend of promoting Industry 4.0 under the Eastern Economic Corridor (EEC) framework (Office of the Education Council, Ministry of Education, 2021). It is necessary to use vocational education labor up to 173,705 people, but it still falls short of producing enough skilled labor (excess demand) by 55,462 people or 32%. This demonstrates that Thailand still faces challenges in producing labor that does not meet the requirements in deficient fields, as the number of unemployed exceeds the shortage in every education level. The professional certificate level has a job vacancy rate 2.1 times higher than the shortage.\n\nTherefore, it is essential to develop students at the professional level to align with and sufficiently meet the workforce needs in both quantity and quality (Mesintree, 2016) . This is to respond to the country’s development policies and align with the sustainable development goals set by the global community (World Bank, 2021). Increasing access to education for the population is a key goal for the development of every country (Office of the Education Council, 2021). This aligns with Sandra M. Kaiser (2000), who emphasized that the success of vocational learning is influenced by various factors, including teachers, leadership, organizational systems, organizational structures, organizational culture, organizational atmosphere, organizational unity, organizational management, mission, strategy, government support, etc. (Chanchaona & Santichaianan, 2012).\n\nThis agrees with the National Economic and Social Development Plan No. 13 (2023-2027). Office of the National Economic and Social Development Council (2022) outlines the development of human resources towards Thailand 4.0. The emphasis is on developing analytical thinking skills and professional skills to prepare for entry into the labor market. Planning and developing human resources that support industry, technology, and innovation are crucial. This is vital for developing human resources with necessary skills for future life and work in the 21st century, including using professional skills in the 21st century. Developing human resources is the most critical factor for the success of every country in transforming its economic structure. Supporting factors for professional skills development include education standards (Muldoo, 2009), skill assessment (Treleaven & Voola, 2008), curriculum and teaching methods (Ogbuanya & Chukwuedo, 2017).\n\nUnder the supervision of the Office of the Vocational Education Commission in Thailand, vocational education institutions consist of 433 colleges with more than ten thousand students. These institutions are a significant force in Thailand’s development. The aforementioned principles and reasons have led the researchers to be interested in the factors that affect the professional skills of students in vocational education institutions.\n\nThis study aims to explore the factors influencing the professional skills of students in vocational education institutions in Thailand. The research findings can serve as a guideline for developing sustainable professional skills of students in vocational education institutions in Thailand. This will contribute to creating a conducive learning environment for sustainable professional development, leading to suitable employment opportunities. Additionally, it can serve as a model for other countries and contribute to establishing a global network for the professional development of vocational education students in the future.\n\n\nLiterature review\n\nKaiser, Sandra M. (2000) studied factors that influence becoming a learner of professional skills, which are related to 8 factors: Leadership, Organizational Culture, Mission and Strategy, Management Practice, Organizational Structure, Organizational System, Working Climate, and Motivation.\n\nThe concept of Self-Efficacy Theory suggests that individuals seek things that align with their needs and choose challenging activities that come from internal motivation (Eccies, 2002). Internal motivation persists when individuals feel they have the ability and autonomy to determine for themselves, aligning with the perception of one’s abilities (Bandura, 1986). It is an individual’s assessment of their ability to generate and manage the actions required to achieve predetermined results. The perception of one’s abilities is the most influential variable leading to behavioral change and actions, significantly influenced by the belief in their ability to predict those behaviors (Bandura, Adams, Hardy & Howells, 1980).\n\nIn the Federal Republic of Germany, vocational education management emphasizes collaboration between educational institutions and businesses in a bilateral system. This collaboration includes jointly developing curricula, implementing learning processes that focus on knowledge, skills, and practical training. The goal is to equip learners with competencies that align with the labor market’s needs and provide career pathways within the business sector. Additionally, there is a focus on assessment and evaluation processes that support the success factors of vocational education management in Germany. These factors encompass (1) creating awareness of the value of entering the vocational education system, (2) emphasizing the importance of investing in education for future workforce development, and (3) prioritizing work-based learning (WBL) (Solga, Protsch, Ebner & Brzinsky-Fay, 2014).\n\nIn Australia, due to the diverse backgrounds of the country, including differences in ethnicity, religion, and culture, the country is characterized as a multicultural nation. The educational management objective is to provide alternative opportunities for learners with diverse readiness and preparedness within and outside the formal education system. The Technical and Further Education Institutions (TAFE) is established by the state to manage vocational education in the country. The 7 success factors for managing vocational education in schools include (1) readiness and diversity of curricula, (2) close collaboration between educational institutions, businesses, government, and the private sector, (3) readiness and quality of educational institutions, (4) motivating institutions to provide training in preparing learners’ skills, (5) maintaining high-quality training standards, (6) ensuring learners’ quality in terms of knowledge, abilities, skills, and (7) clear directions and objectives for professional learning and career pathways for learners (Agbola & Lambert, 2010).\n\nIn Taiwan, the country employs a comprehensive high school system that focuses on providing students with the option to explore and discover whether they want to pursue general or vocational education. The three objectives of this system are (1) to create alternatives for students who are not ready to enter the workforce or pursue traditional education systems, (2) to integrate academic and vocational education at the high school level to create a better learning environment and more educational opportunities, and (3) to reduce the differences in the learning systems for students (Huang & Lee, 2012).\n\nThailand follows the policy of vocational education development under the National Education Development Plan for Vocational Education 2017-2036. This policy, established by the Ministry of Education, aims to align learner production with the country’s development needs following the Thailand 4.0 policy. The focus is on developing learners’ professional competencies, including (1) the ability to apply knowledge, (2) the ability to apply skills in their respective professions, (3) the ability to adapt to professions, and (4) the ability to work collaboratively and develop professional skills (Moenjak & Worswick, 2003).\n\nUpon reviewing the literature used in this research, it is evident that education policies supporting vocational education in nearly every country are typically within the Ministry of Education. This may be a unit within the ministry, serving as a policy development framework. When combined with self-development guidelines and factors that promote professional learning, this can create a comprehensive approach to developing vocational skills, covering various dimensions.\n\n\nMethods\n\nThis research is the second phase employing a qualitative research method (Hennink, Hutter & Bailey, 2020) to study sustainable professional skill development approaches for vocational students in Thailand. The research has received ethical clearance from The University of Thai Chamber of Commerce under the code Expedited UTCCEC/014/2565. The study involves key informants, including educational institution administrators, teachers, and vocational students totaling 36 individuals. A written consent for participation in the study has been obtained from all key informants, including educational institution administrators, teachers, and vocational students, prior to the collection of data. The key informants were selected using purposive sampling based on predefined criteria (Ames, Glenton & Lewin, 2019) and snowball sampling (Naderifar, Goli & Ghaljaie, 2017). The criteria include (1) administrators or directors of public vocational institutions with a minimum of 3 years of experience, (2) teachers with at least 3 years of teaching experience in vocational institutions, and (3) vocational students. Research tools include structured open-ended interviews and observations.\n\nThe research process comprises 4 stages (Figure 1): (1) Literature review and document study – The first stage involved conducting a thorough review of the existing literature and relevant documents related to sustainable professionEthical skill development approaches for vocational students in Thailand. This literature review helped to identify the key concepts and theories that are relevant to the research question. (2) Data collection and identification of relevant components – The second stage involved data collection through structured open-ended interviews and observations. The key informants, including educational institution administrators, teachers, and vocational students totaling 36 individuals, were selected using purposive sampling based on predefined criteria. The data collected from the interviews and observations were then analyzed to identify the relevant components related to sustainable professional skill development approaches. (3) Analysis and synthesis of administrators’ roles – The third stage involved the analysis and synthesis of administrators’ roles in sustainable professional skill development approaches. The data collected were analyzed using content analysis, categorizing data into four groups and indexing. The meaning of the discovered data was explained and analyzed in terms of structural features. This helped to identify the key roles of administrators in sustainable professional skill development approaches. (4) Data analysis using content analysis - The final stage involved data analysis using content analysis, categorizing data into four groups and indexing. The interpretation of the meaning of the data led to new data compilation to connect concepts and theories used as a framework according to the objective. After that, the verification and confirmation were performed. This helped to verify the findings of the study and confirm the effectiveness of the sustainable professional skill development approaches identified in the study (Sakdapat, 2024).\n\nThe development of vocational students’ professional skills in vocational institutions is influenced by several significant factors, affecting preparedness for various vocational professions. These factors include:\n\n1. Curriculum Design: Institutions should focus on creating learning experiences that equip students with skills and practical knowledge relevant to real-world work. However, interviews with students indicate that, following the COVID-19 situation, curricula have not been adjusted to align with the practical aspects of learning, leading to a gap in skills. Students express the need for more diverse courses, such as entrepreneurship or new technologies, to better meet their learning needs.\n\n“I want the college to offer more than this or ask students about their interests, such as becoming an entrepreneur, new technologies, because many of my friends have to study online or find books to read, incurring additional expenses.” – Interviewee A\n\nCurrently, students’ needs are diverse and universities should develop curricula that align with these needs. Even though vocational education curricula are adjusted every five years, the content of the subjects remains largely unchanged or undergoes minimal modifications, making the education system outdated and unresponsive to the country’s needs. Vocational education programs should not overly emphasize general foundational competencies. Instead, they should focus on practical subjects to facilitate experiential learning, aligning with the requirements of the industrial sector.\n\n2. Support and Counseling: Students believe that appropriate guidance and support from experienced teachers and senior peers help them develop skills and knowledge. Interviews with students reveal that advice from alumni who have completed their studies, guidance on work, and self-development contribute to a better understanding of how to develop oneself.\n\n“Initially, I did not know what to do after graduation and joined the program following my friends. However, when I heard advice from senior students about working and self-development, it helped me understand what I should do. Now, I am learning English to get a higher salary.” – Interviewee B\n\nThis shows that advice from experienced individuals in the field plays a crucial role in helping students plan for their future.\n\n3. Internship in Business Organizations: Students believe that having the opportunity to intern in various organizations helps them gain experience and understanding of the specific professional field they are interested in. While there are mandatory courses related to internships, students express a desire for additional elective courses tailored to their interests. This aligns with the institution’s management to coordinate with the private sector to increase opportunities for internships or real-world work.\n\n“I would like the university to have internship programs abroad because Thai vocational students are capable, and it would also help expand job opportunities. For example, in countries like Korea and Japan where salaries are high. I personally would like to work legally in those countries, so I hope the university can initiate such programs.” - Interviewee C\n\n4. Problem-Solving and Analytical Thinking Skills Development: Input from teachers and administrators reveals that systematic thinking is considered a crucial factor in education. However, this process takes time to yield results, and sometimes, students may become discouraged, requiring the institution to find additional courses or activities to foster students’ development.\n\n“The traditional vocational education format focused on skill mastery, leading to the retention of traditional approaches in curriculum or teaching methods. However, the university has now collaborated with private factories, organized competitions, allowing students to practice critical thinking in real-world work environments.” - Interviewee D\n\nDeveloping systematic thinking and presenting reasoned ideas enables efficient problem-solving in real-world situations.\n\n5. Practical Learning: Opportunities for hands-on experimentation, trial and error, are emphasized contributing to learning from experience and adapting to failures in practice (Sakdapat, 2023). The interviewees provide additional insights, stating that through internships or practical courses. They discovered persistent errors that needed correction. In the classroom, this experience is viewed positively as there are teachers and peers to provide assistance. However, once in the workforce, such support may not be readily available.\n\n6. Supportive Learning Environment: The learning environment and facilities that foster learning, such as convenient learning spaces, technology used to support learning, and opportunities to access necessary information, significantly impact learning. According to the information provided, the classroom atmosphere, including learning equipment, greatly influences the learning experience. Having sufficient computers, up-to-date and modern facilities in universities, and updating technology in industrial workshops or introducing new tools contribute to awakening students’ awareness and increasing interest. Administrators and teachers share the opinion that there is an intention to develop modern tools, but there is a budget constraint. Therefore, students must collaborate to maintain and care for various equipment for future generations to use.\n\nAs for sustainable professional skill development for vocational education students in Thailand, surveys and document analysis reveal the needs, problems, and obstacles affecting the development of students’ professional skills. The following are identified approaches for sustainable development of students’ professional skills:\n\nDeveloping flexible and adaptive skills: Schools should promote collaboration with external organizations to provide diverse work-related skills. Integration of knowledge from various disciplines, such as technology and essential languages, is essential. Preparing for unforeseen changes and simulating various situations allows learners to apply knowledge to real situations, promoting readiness for unexpected changes. This is a crucial foundation for self-development towards sustainability.\n\nSelf-initiation and self-care skills: Educational institutions must provide facilities and allocate spaces to promote learning and creative thinking. Creating an environment and learning tools is vital for stimulating student learning. Punctuality, innovation, community learning, thinking about others, and contributing to society should be promoted. In the context of work, vocational students may become entrepreneurs, employees, or government officials, all of whom have roles and importance in society. Considering others and applying ethical principles is another approach that should be promoted to students for long-term responsibility toward society.\n\nSocial and Intercultural Skills under Global Societal Changes: Educational institutions need to collaborate with organizations from different countries to develop curricula that promote communication and social skills across cultures. Teachers should provide opportunities for students to develop communication and social skills, such as student exchange programs. Students should understand the role of cultural differences as a fundamental aspect of coexistence. Emphasizing the global citizenship role, which highlights the importance of everyone contributing to the development of society, making decisions, and responding to challenges at both local and global levels, is crucial.\n\nWork Performance and Responsibility Skills are assessable. Schools and teachers must be role models for work performance and responsibility in practice. Students should actively participate in planning, execution, and problem-solving, fostering a sense of responsibility in their work. Students should be trained to think in management perspectives, considering ethical principles while working, and participating in business practices that prioritize long-term sustainability. This includes active involvement in societal development and environmental conservation, aligning with the principles of social responsibility.\n\nLeadership and Responsibility Skills: Educational institutions should collaborate with other educational organizations, businesses, and alumni to promote students’ leadership qualities and create a network for collaborative work. Students must be self-aware and proactive in planning and problem-solving. They should be open to listening to others’ opinions and train themselves to think critically and access various perspectives when addressing different issues (Sakdapat, 2022). Learning from real-world data and utilizing one’ professional learning abilities to analyze systematically will enable individuals to perceive the multidimensional aspects of problems. This approach goes beyond viewing problems from a single dimension, allowing students to develop themselves into leaders who are self-reliant and supportive of others. This capability aligns with the desired outcome of fostering sustainable personal development in the 21st century.\n\n\nDiscussion and Conclusions\n\nThe sustainable development of vocational skills for vocational students is a developmental approach that requires collaboration from all sectors. This includes students themselves, who must begin developing themselves to align with the lifelong learning model. The ability to rely on oneself and build sufficient resilience to cope with changes in various aspects, such as social, economic, or experiential learning in workplaces, is crucial. Learning and self-development through collaboration with others for knowledge exchange, cultivating a learning attitude through the development of tools or learning methods beneficial to oneself, and reflecting on learning outcomes and self-assessment all contribute to recognizing progress, areas for improvement, and setting goals for short and long-term professional skill development.\n\nIn terms of curriculum design, the educational structure, and policies, there should be a continuous review of the curriculum, making adjustments to suit the changing context and addressing the needs of the labor market and global changes. Emphasis should be placed on environmental awareness, ethical practices, transparency in work, the use of technology and innovation to facilitate easier access to knowledge, and the creation of professional networks spanning across public, private, and governmental sectors. Furthermore, the sustainable development of vocational skills requires determination and unwavering commitment. Consistent effort and adequate time for practice and skill improvement are essential factors in developing vocational skills at the vocational education level. The impact of skill development extends beyond individual sections of society; it elevates the education system, sets standards for society, and fosters positive attitudes toward vocational education. This leads to the development of human resources on a broader scale. Vocational education institutions play a crucial role in vocational training. Administrators and teachers are pivotal in the direction of reforming academic work, quality development, behavioral changes, and providing opportunities for collaborative thinking and work with students. Creating a learning society, offering suitable and effective learning resources, and facilitating a conducive environment for collaborative learning contribute to the overall development of vocational skills.\n\nIn the context of Thailand, the Office of the Vocational Education Commission has set guidelines for the development of quality in vocational education for students, emphasizing the importance of driving curriculum development, including measurement and evaluation, towards enhancing the quality of learners (Office of Vocational Commission, 2018). The government recognizes the significance of driving the economy by emphasizing vocational education. During the years 2017-2023, various events led to uncertainties both in Thailand and globally. This included economic uncertainties on a global scale and the impact of pandemic situations that affected the lifestyles of people worldwide. It is an era where the world has to face unpredictable events, known as the VUCA or VUCA World, the world characterized by Disruptive Technology. The dimension of preparing the population to cope with change is greatly challenged (LeBlanc, 2018). When considering the patterns of vocational education management in Thai and Taiwanese schools, similarities in policies can be observed. Both countries follow a comprehensive high school model, emphasizing that students explore and discover whether they want to pursue general or vocational education. In Taiwan, there is a blending of both curriculum types to stimulate overall educational development. The 3 main goals are (1) to provide options for students not ready for vocational or traditional academic paths, (2) to integrate academic and vocational education to create a better learning environment and increase educational opportunities, and (3) to reduce disparities in the learning systems of students. Thailand can adopt these approaches to adapt and develop teaching and learning methods that align with the needs of learners.\n\nTo align with the sustainable development context, the development model that meets people’s needs should have a strategic national relationship. This involves creating competitiveness in development, enhancing and cultivating human resources, and promoting social opportunities and equality. The development of the country’s economy necessitates a focus on the development of science, technology, and research to accelerate the creation of knowledge in science, technology, and innovation. This should go hand in hand with developing individuals through tertiary education institutions, which need to collaborate with research and development institutions to become Future Changers, the driving force in preparing Thais for the 21st century. It is crucial to drive economic structural reforms that focus on values and play a crucial role in transitioning towards an innovative-based economy. Therefore, it is necessary to adapt and change roles and missions simultaneously with enhancing the potential of both higher education and vocational education institutions. Developing personnel or students at the vocational education level is about developing the country’s human capital to have the capacity and readiness to lead life in the 21st century, contributing significantly to the country’s development, stability, and sustainability. This aligns with the government’s goal of developing human capacity to respond to the country’s development and create competitiveness on the global stage, stimulating grassroots economic growth towards Thailand 4.0. It builds confidence and creates the capability to compete globally, both in the short and long term. The government, therefore, has policies to integrate science, research, and innovation to drive the country’s development in the economic, community, and social sectors. It emphasizes the commercial application of science, research, and innovation in agriculture, industry, and services for maximum efficiency. It also emphasizes the importance of social innovation and innovation in the local context to solve problems and create opportunities. This is concurrent with developing human capital in both academic and high-level vocational aspects, preparing them for the digital age and driving Industry 4.0. This aligns with sustainable development goals 4, 8, and 9 in the 2030 Sustainable Development Agenda (FUND, 2015).\n\nThe results of the sustainable development of vocational skills among vocational education students in Thailand can lead to the following recommendations based on the research:\n\n1. Education Standards Impact on Learning Skills and Innovation: Education standards have an impact on students’ learning skills and innovation in vocational education. Schools should have policies to contribute to the development of creativity and innovation in students. Additionally, there should be standards for evaluating educational outcomes, using assessments based on students’ work and diverse evaluation methods.\n\n2. Curriculum and Teaching Methods Impact on Learning Skills and Innovation: The curriculum and teaching methods have an impact on students’ learning skills and innovation. Educational institutions should design curricula that bridge the gap between students and the needs of employers. This should involve adopting new teaching formats that align with the present and future eras, considering the integration of students’ knowledge to solve real-world problems through teaching methods. This will facilitate experiential learning for students.\n\nThe research has received ethical clearance from The University of Thai Chamber of Commerce under the code Expedited UTCCEC/014/2565, and the research was approved on November 27, 2023. The study involves key informants, including educational institution administrators, teachers, and vocational students, totaling 36 individuals. Written consent for participation in the study has been obtained from all key informants, including educational institution administrators, teachers, and vocational students, prior to the collection of data. They were informed of the scope of the research, and they were also given the choice to withdraw from the study at any time. All the participants completed the study, and the researchers’ assured participants that the details will be kept confidential. The study adheres to the principles of the Declaration of Helsinki.", "appendix": "Data availability statement\n\nFigshare: Approaches for Sustainable Professional Skill Development for Vocational Education Students in Thailand. https://doi.org/10.6084/m9.figshare.24924297.v2\n\nThe project contains the following underlying data:\n\nThe data consists of testimonials from the participants, sharing their experiences and perspectives on the benefits of attending the vocational school. Topics covered include fields of study, reasons for choosing the school, scholarships, and job opportunities post-graduation.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nReporting guidelines\n\nFigshare: SRQR Checklist for Approaches for sustainable professional skill development for vocational education students in Thailand, https://doi.org/10.6084/m9.figshare.24924297.v2\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nI would like to express my gratitude to QUVAE Research and Publications for their support in depositing the raw data to the Figshare repository and for their assistance with the submission.\n\n\nReferences\n\nAgbola FW, Lambert DK: Skilling Australia for the future? A study of quality assurance in Australia’s vocational education and training. J. Vocat. Educ. Train. 2010; 62(3): 327–349. Publisher Full Text\n\nAmes H, Glenton C, Lewin S: Purposive sampling in a qualitative evidence synthesis: A worked example from a synthesis on parental perceptions of vaccination communication. BMC Med. Res. Methodol. 2019; 19(1): 1–9. Publisher Full Text\n\nBandura A, Adams NE, Hardy AB, et al.: Tests of the generality of self-efficacy theory. Cogn. Ther. Res. 1980; 4(1): 39–66. Publisher Full Text\n\nBandura A: Social foundations of thought and action: a social cognitive theory. Englewood Cliffs, N.J.: Prentice-Hall; 1986.\n\nChanchaona S, Santichaianan K: Guidelines for promoting an increase in the proportion of high school students. 2009-2016, Office of the Secretariat of the Education Council. Ministry of Education; 2012.\n\nEuapipattanakul C: Comparative study of vocational education administration systems in Thailand and leading industrialized countries. Bangkok: Srinakharinwirot University; 2022. (Doctoral degree thesis).\n\nEccies JS: Annual Review of Psychology: Motivational Beliefs, Values and Goals.2002. Retrieved December 17, 2008.\n\nFUND, S: Sustainable development goals.2015. Reference Source\n\nHuang HI, Lee CF: Strategic management for competitive advantage: a case study of higher technical and vocational education in Taiwan. J. High. Educ. Policy Manag. 2012; 34(6): 611–628. Publisher Full Text\n\nHennink M, Hutter I, Bailey A: Qualitative research methods. Sage; 2020.\n\nJedynak M, Czakon W, Kuźniarska A, et al.: Digital transformation of organizations: what do we know and where to go next? J. Organ. Chang. Manag. 2021; 34(3): 629–652. Publisher Full Text\n\nKaiser SM: Mapping the Learning Organization: Exploring a Model of Organizational Learning. U.S.A.: Louisiana State University; 2000. Dissertation.\n\nLeBlanc PJ: Higher education in a VUCA world. Change: The Magazine of Higher Learning. 2018; 50(3-4): 23–26. Publisher Full Text\n\nMesintree S: Concepts about Thailand 4.0.2016. Reference Source\n\nMoenjak T, Worswick C: Vocational education in Thailand: a study of choice and returns. Econ. Educ. Rev. 2003; 22(1): 99–107. Publisher Full Text\n\nMuldoo R: Recognizing the enhancement of graduate attributes and employability through part-time work while at university. Act. Learn. High. Educ. 2009; 10(3): 237–252. Publisher Full Text\n\nNaderifar M, Goli H, Ghaljaie F: Snowball sampling: A purposeful method of sampling in qualitative research. Stride. Dev. Med. Educ. 2017; 14(3). Publisher Full Text\n\nNational Economic and Social Development Plan No. 13 (2023-2027): 2023. Retrieved March 25. Reference Source\n\nOffice of the Basic Education Commission: Basic education core curriculum B.E. 2551 (A. D. 2008). Bangkok: Ministry of Education; 2010.\n\nOffice of the Education Council, Ministry of Education: Thai Education Report 2019-2021. Bangkok: Prickwan Graphic; 2021.\n\nOffice of the National Economic and Social Development Council, Office of the Prime Minister: 2022.\n\nOffice of Vocational Commission: Vocational Standard 2018. Bangkok: Office of Vocational Commission; 2018.\n\nOgbuanya TC, Chukwuedo SO: Career-training mentorship intervention via the Dreyfus model: Implication for career behaviors and practical skills acquisition in vocational electronic technology. J. Vocat. Behav. 2017; 103: 88–105. Publisher Full Text\n\nRojananan J: Documents for seminar on Thailand 4.0 policy and vocational workforce production. Bangkok: Office of the National Economic and Social Development Board; 2016.\n\nSolga H, Protsch P, Ebner C, et al.: The German vocational education and training system: Its institutional configuration, strengths, and challenges (No. SP I 2014-502). WZB Discussion Paper.2014.\n\nSakdapat N: Analysis of the Path of influence of work skills in the new normal life of the undergraduate students in Thailand. Social Space. 2022; 22(3): 152–168.\n\nSakdapat N: Psychosocial Factors Correlated with Cooperation Skills in New Normal of Undergraduate Students. J. Behav. Sci. Dev. 2023; 15(1): 83–107.\n\nSakdapat N: Approaches for Sustainable Professional Skill Development for Vocational Education Students in Thailand. Dataset. figshare. 2024. Publisher Full Text\n\nTreleaven L, Voola R: Integrating the development of graduate attributes through constructive alignment. J. Mark. Educ. 2008; 30(2): 160–173. Publisher Full Text\n\nWorld Bank: World development report: Learning to realize education’s promise 2021. Washington DC: 2021." }	[ { "id": "274222", "date": "29 May 2024", "name": "Joseph Mesuwini", "expertise": [ "Reviewer Expertise TVET /WIL / WBE/WBL/ Technology education/ vocational education/" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe abstract is comprehensive. However, it is silent about the theory used in the study.\nThe introduction was done with the most recent sources cited.\nThe literature review was much weaker in terms of the recency of sources. Most recent source was 2014 and dated one was 1980. I asked the significance of dated sources. Most recent sources could spice your study and attract audience.\nMethods were clear. Data triangulation was not shown. The theory underlying the study was not stated in the abstract and in the manuscript.\nResults were explained and supported with comments.\nDiscussion of findings was done. I feel that the researcher could have shown the link between the findings and the literature. What does theory say, and how does it speak to your research? Generally, academic effort was shown in the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "297903", "date": "03 Jul 2024", "name": "Kittisak Jermsittiparsert", "expertise": [ "Reviewer Expertise Political Science", "Public & Private Management", "International Political Economy", "Social Research" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic of this research is interesting and useful, both academically and practically. However, there are limitations that make this article's proposal a question of whether and to what extent it is the correct answer.\nThe biggest question is selecting the 36 key informants. Will the answers received from them be answers that actually lead to sustainable professional skill development? What are the clear and appropriate criteria for selecting answers that are of sufficient value, not just the opinions of administrators, teachers, or students, that are not useful? The author should pay great attention to the quality and suitability of key informants, because if they are not the ones who can provide answers to the research questions, the data obtained and analyzed will lead to inaccurate conclusions.\nThe literature review also requires a synthesis of relevant research/case studies from other countries to outline the issues to be considered/framework of the study.\nResearch results should be expanded to be more detailed and concrete, at least until they are sufficient to be considered approaches for sustainable development. A brief summary followed by an interview with a single key informant may not be comprehensive enough.\nConclusion and discussion should expand to a broader picture beyond the case study itself. In this case, it must move away from Thailand to a broader approach to developing this skill that is discussed with case studies from other countries. Likewise, the suggestion must not be a suggestion for what Thailand needs to do, but a broad academic suggestion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "290628", "date": "04 Jul 2024", "name": "Suranto Suranto", "expertise": [ "Reviewer Expertise My expertise is in the field of (1) vocational education", "(2) entrepreneurship" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe results of the correction have been submitted in the article, can be found here, please pay attention and revise them according to the journal article guidelines \"Minor Revision\"\n1.Revision Major: for background, (write a citation, provide real condition data from national data, also provide a portrait of the problems that occur 2-3 problems, explain the reasons for the urgency of the research, and research output targets and describe plans for implementing research results).\n2. \"This includes a lack of skills in practical work, expertise in foreign languages and/or computer skills, and problems related to studying not aligning with the job market's needs or choosing majors based on popular trends without considering the workforce needs of businesses (Euapipattanakul, 2022).\"\n\nShow data and sources, in the form of problem numbers (country or regional scope). Explain in detail the problem: 1, 2, 3 etc\n3.\"This contradicts the direction of national development, impacting resource allocation for education significantly (Rojananan, 2016).... \"\nAnd Explain and describe what it means, contrary to national development in Thailand\n4. \"This demonstrates that Thailand still faces challenges in producing labor that does not meet the requirements in deficient fields, as the number of unemployed exceeds the shortage in every education level. The professional certificate level has a job vacancy rate 2.1 times higher than the shortage.\"\nThe research sample is focused on vocational school or diploma graduates?\n5. \"This aligns with Sandra M. Kaiser (2000), who emphasized that the success of vocational learning is influenced by various factors, including teachers, leadership, organizational systems, organizational structures, organizational culture, organizational atmosphere, organizational unity, organizational management, mission, strategy, government support, etc. (Chanchaona & Santichaianan, 2012). \"\n\nDescribe the solution to meet quality and quantity guarantees, at what level of education?\n6.\"Supporting factors for professional skills development include education standards (Muldoo, 2009), skill assessment (Treleaven & Voola, 2008), curriculum and teaching methods (Ogbuanya & Chukwuedo, 2017). \"\n\nDescribe the solution for scope level education\n7.\"The aforementioned principles and reasons have led the researchers to be interested in the factors that affect the professional skills of students in vocational education institutions. \"\nEmphasized, is the scope of the research at the student level or at vocational school students? and what professional skills are, in detail\n8. \"Additionally, it can serve as a model for other countries and contribute to establishing a global network for the professional development of vocational education students in the future.\"\nDescribe the problem portrait, research urgency, research scope, final target\n9.Revision for literature review: \"When combined with self-development guidelines and factors that promote professional learning, this can create a comprehensive approach to developing vocational skills, covering various dimensions.\"\n\nGood idea, but provide article citations that are relevant and appropriate to the study, at vocational schools or universities, as well as the expected criteria for professional skills in the 4.0 era\n10.Revision for Methods: \"This research is the second phase employing a qualitative research method (Hennink, Hutter & Bailey, 2020) to study sustainable professional skill development approaches for vocational students in Thailand.\"\nIf you are discussing vocational school students, you don't need to discuss university students. Please detail the sample or population in your research and what research approach you use?\n11.\"Research tools include structured open-ended interviews and observations.\"\n\nUsing 36 as a sample, is that enough? then the sampling method and explain the criteria for skilled and professional\n12.\"For Supportive Learning Environment: \"\n\nHave the 6 stages been tested as model steps or not? explain\n13.\"This approach goes beyond viewing problems from a single dimension, allowing students to develop themselves into leaders who are self-reliant and supportive of others. This capability aligns with the desired outcome of fostering sustainable personal development in the 21st century.\"\n\nExplain the skilled, professional criteria desired for graduates by companies or users, of course based on user preferences or other data\n15.For References: (a) cite more articles from Scopus journals, (2) for each article cited, a DOI address is given, (3) writing articles follows the guidelines of journals\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-401
https://f1000research.com/articles/13-400/v1	26 Apr 24	{ "type": "Study Protocol", "title": "Randomised controlled trial of preoperative antibiotic prophylaxis in the prevention of surgical site infections in tertiary care hospital of central India", "authors": [ "Dr. Simran Dhole", "Dr Chandrashekhar Mahakalkar", "Dr Chandrashekhar Mahakalkar" ], "abstract": "Background Surgical site infections (SSI) remain a significant concern in the realm of surgical interventions, posing a threat to both patient well-being and healthcare systems. This study protocol outlines a rigorous investigation aimed at assessing the effectiveness of pre-operative antibiotic prophylaxis in the prevention of SSIs in clean and clean-contaminated surgical cases within the tertiary care setting of central India. The primary aim is to determine the best suitable antibiotic regimen, optimal timing for administration, and the associated economic burden of SSIs.\n\nMethod The study utilizes a Randomized Controlled Trial (RCT) design with four intervention groups, each receiving distinct antibiotic prophylaxis protocols. Comprehensive post-operative monitoring, adhering to the Centers for Disease Control and Prevention (CDC) guidelines, will be employed to identify SSI occurrences. Key data collection points include clinical evaluations, temperature monitoring, wound inspection, pain assessments, and culture and sensitivity testing.\n\nExpected outcome The study also emphasizes post-operative follow-up assessments, incorporating outpatient visits at 15-, 30-, and 90-days post-surgery. These evaluations will be instrumental in assessing the time duration for effective prophylactic antibiotic administration and determining the economic burden associated with SSI. The findings of this research endeavor hold the potential to enhance patient outcomes, minimize SSI incidences, and reduce the economic impact of SSIs on healthcare systems. By optimizing pre-operative antibiotic prophylaxis practices, this study aims to advance evidence-based guidelines for SSI prevention in clean and clean-contaminated surgical cases.\n\nCTRI REF/2023/07/070549", "keywords": [ "Surgical Site Infections", "Pre-operative Antibiotic Prophylaxis", "Randomized Controlled Trial", "Post-operative Monitoring", "Tertiary Care Hospital", "Economic Burden" ], "content": "Introduction\n\nSurgical site infections (SSIs) continue to be a significant concern within the realm of surgical procedures, posing a substantial threat to patient well-being and a substantial economic burden on healthcare systems. SSIs are among the most prevalent healthcare-associated infections worldwide, accounting for a considerable proportion of postoperative complications and prolonged hospital stays.1 Consequently, SSIs contribute to increased healthcare costs, decreased patient quality of life, and an elevated mortality risk.2\n\nPreventive measures, such as pre-operative antibiotic prophylaxis, have been a cornerstone in the battle against SSIs. While prophylactic antibiotics are considered standard practice in many surgical settings, questions linger regarding the most effective antibiotic regimens and the optimal timing of administration.3 This study seeks to address these issues by conducting a randomized controlled trial (RCT) to assess the efficacy of pre-operative antibiotic prophylaxis in preventing SSIs, specifically in clean and clean-contaminated surgical cases.\n\nThe World Health Organization (WHO) recognizes the importance of evidence-based strategies for SSI prevention, emphasizing the need for tailored approaches to specific surgical contexts.4 In alignment with this global perspective, our study is set in a tertiary care hospital in central India. By focusing on this setting, we aim to provide insights and recommendations relevant to the local healthcare landscape and can be extrapolated to comparable healthcare environments.\n\nThis RCT design randomly allocates patients to different antibiotic prophylaxis groups, offering a platform to rigorously assess the efficacy of distinct antibiotic regimens and their associated impact on SSI incidence. Additionally, this study emphasizes meticulous post-operative monitoring per the Centers for Disease Control and Prevention (CDC) guidelines.5 This approach is essential for early detection and management of SSIs, ultimately contributing to the generation of robust data.\n\nThe economic repercussions of SSIs are profound, encompassing not only direct medical costs but also indirect expenses, such as extended hospital stays and potential legal consequences.6 Understanding the economic burden of SSIs is integral to the broader objective of enhancing patient outcomes and healthcare system efficiency.\n\nThe outcomes of this investigation hold the promise of advancing evidence-based guidelines for SSI prevention in clean and clean-contaminated surgical cases. By optimizing pre-operative antibiotic prophylaxis practices, we aim to mitigate the occurrence of SSIs and curtail their associated economic costs, ultimately enhancing patient care and healthcare sustainability.\n\nThe study aims to investigate the efficacy of pre-operative antibiotic prophylaxis in preventing surgical site infections (SSI) in clean and clean-contaminated surgical cases in a tertiary care hospital in central India.\n\n\n\n1. Determination of SSI incidence: The primary objective is to determine the incidence of surgical site infections in patients undergoing elective surgery in the clean and clean-contaminated categories.\n\n2. Identification of best preoperative antibiotic prophylaxis: To assess the best preoperative antibiotic prophylaxis in preventing surgical site infections.\n\n3. Time interval for antibiotic prophylaxis: To determine the optimal time interval for administering preoperative antibiotic prophylaxis.\n\n4. Economic burden estimation: To estimate the economic burden of patients who develop surgical site infections.\n\n\nMethods\n\nThe study will be conducted in the Department of Surgery at Jawaharlal Nehru Medical College (JNMC) and Acharya Vinoba Bhave Rural Hospital (AVBRH) in Wardha, Maharashtra, India. These facilities serve as the study locations set up for the 2023-2024 period.\n\n\n\n• Patients undergoing elective surgery in the clean and clean-contaminated categories.\n\n• Age between 5 and 60 years.\n\n• Presence of specific comorbidities.\n\n• Both genders are included in the study.\n\n\n\n• Patients undergoing contaminated surgical cases.\n\n• Patients with uncontrolled diabetes.\n\n• Obese patients.\n\nPatients will be divided into four groups based on the timing and type of preoperative antibiotic prophylaxis they receive:\n\n1. Group A: Patients receive a preoperative single dose of ceftriaxone (Ceftrisol Plus) CAS [104376-79-6] 4gm, administered 31-60 minutes before surgery.\n\n2. Group B: Patients receive a preoperative single dose of Augmentin 1.2gm (amoxicillin-clavulanate) CAS No: 74469-00-4, administered 31-60 minutes before surgery.\n\n3. Group C: Patients receive a preoperative single dose of ceftriaxone, administered 0-30 minutes before surgery.\n\n4. Group D: Patients receive a preoperative single dose of Augmentin, administered 0-30 minutes before surgery.\n\n\n\n1. Primary outcome: Determination of the best suitable antibiotic for preventing surgical site infections in clean and clean-contaminated cases.\n\n2. Secondary outcomes:\n\n• Effective time duration for the administration of prophylactic antibiotics.\n\n• Estimation of the economic burden associated with surgical site infections.\n\n\n\n1. Pre-intervention evaluation: This involves collecting clinical history, conducting clinical examinations, and routine tests (complete blood count, kidney function tests, liver function tests, random blood sugar, electrocardiogram).\n\n2. Surgery and antibiotic administration: Participants receive the allocated preoperative antibiotic prophylaxis.\n\n3. Post-operative monitoring: Post-operative monitoring, as per the guidelines provided by the Centers for Disease Control and Prevention (CDC).7\n\nTiming and duration of post-operative monitoring: The CDC recommends the vigilant monitoring of patients for at least 30 days following their surgical procedure, with a more extended duration, up to 90 days, for cases involving implant placement. This extended monitoring period ensures the detection of delayed infections that may occur post-surgery.\n\nClinical evaluation: Post-surgery, patients will undergo routine clinical evaluations. This includes a comprehensive assessment for any signs or symptoms of SSI. Clinical indicators include redness, swelling, tenderness, delayed wound healing, warmth around the surgical site, and purulent discharge. Any such manifestations should be recorded and evaluated promptly.\n\nTemperature monitoring: Body temperature monitoring is a vital part of post-operative assessment. Measurement of the patient’s temperature should be conducted at regular intervals. A fever, a body temperature exceeding 38.0 degrees Celsius, can be an early indicator of infection and should be closely monitored.\n\nWound inspection and assessment: Routine wound inspection is necessary. During these assessments, examining the surgical incision site for any abnormal changes is crucial. This includes looking for signs of infection, such as purulent discharge or localized redness. Any deviations from the expected healing process should be noted.\n\nAssessment of pain: Pain assessment is integral to post-operative monitoring. Significant localized pain at the surgical site can strongly indicate infection. Monitoring pain levels and changes in pain perception is essential to early detection.\n\nSwelling and tenderness: Continual monitoring for localized swelling and tenderness around the surgical incision site is paramount. These are common indicators of SSI, and any observed symptoms should be documented and addressed promptly.\n\nCulture and sensitivity testing: In cases where infection is suspected, the collection of swabs or samples from the surgical site is necessary. These samples should be forwarded for culture and sensitivity testing to identify the microorganisms responsible for the infection and their antibiotic sensitivity profiles. These results are crucial for effective treatment planning.\n\nWound dressing changes: If dressings are in place, they should be regularly inspected for signs of soakage or infection. Soiled or infected dressings should be changed, and the wound should be re-evaluated to assess the progression of healing and any signs of SSI.\n\nSuture removal and follow-up appointments: Sutures or staples should be removed according to the established timeline, typically around the 7th day post-surgery. Additionally, it is essential to schedule follow-up appointments for patients at specific intervals, such as 15, 30, and 90 days after their surgical procedures. During these follow-up visits, a thorough assessment should be conducted to evaluate temperature, pain, tenderness, and any indications of localized infection.\n\nDetailed documentation: Comprehensive records should be maintained for all post-operative monitoring activities. This includes detailed documentation of temperature measurements, wound assessments, culture reports, and any interventions or treatments administered in response to suspected infections. Accurate record-keeping is crucial for analyzing and evaluating the study’s primary and secondary outcomes.\n\nUnblinding procedure: In situations where unblinding is necessary due to patient safety or treatment requirements, a well-defined and documented procedure should be in place to ensure the study’s integrity is maintained throughout the process.\n\n4. Follow-up visits: Participants are followed up at specific intervals postoperatively: 15 days, 30 days, and a final visit at 90 days.\n\n5. Active surveillance: Active surveillance is conducted throughout the postoperative period to monitor patient outcomes.\n\nRecruitment: Patients who meet the inclusion criteria and do not fall under the exclusion criteria are eligible for recruitment. Informed consent will be obtained from all patients before enrollment. Recruitment occurs at the study locations (JNMC and AVBRH) as part of the patient evaluation process for elective surgery in the clean and clean-contaminated categories. The study will ensure that patients are informed about the study’s objectives, procedures, and potential risks and benefits before obtaining their consent for participation.\n\nThe sample size for the study has been calculated to be 200 patients based on the formula:\n\nWhere:\n\n• α (alpha) = 0.05 (significance level, typically set at 0.05 for a 95% confidence level)\n\n• p (proportion) = 0.033 (the estimated proportion of surgical site infection in patients postoperatively as per the reference article)\n\n• d (estimated error) = 0.05 (5% margin of error)\n\nBy plugging in these values, get:\n\n\n\n1. Randomization: The allocation of patients to different intervention groups will be performed through computer-generated randomization. This process ensures that each patient has an equal chance of being assigned to any of the four study groups (Group A, B, C, or D). Randomization will be conducted by an independent statistician not directly involved in patient recruitment or care to reduce bias. The randomization sequence will be concealed until the point of assignment.\n\n2. Concealment of allocation: The randomization sequence will be kept in sealed, opaque envelopes, and the allocation will occur just before the administration of preoperative antibiotics. This process ensures that the clinical team and patients know their group assignment once the intervention is administered.\n\n3. Assignment of interventions: Based on the assigned group, patients will receive preoperative antibiotic prophylaxis per the study protocol. The assignment will be performed by a nurse or healthcare professional not part of the primary clinical team.\n\n\n\n1. Double-blind procedure: Both patients and the clinical team responsible for patient care will be blinded to the group assignment. The antibiotics used in the study will be prepared and labeled by a pharmacy team who are not directly involved in the patient’s care. This ensures that the identity of the antibiotics remains concealed from the clinical team and patients.\n\n2. Data collection: The personnel responsible for data collection and outcome assessment will be kept separate from the clinical team providing patient care. They will need access to information about the patients’ group assignments. This separation helps maintain blinding during data collection and outcome assessment.\n\n3. Unblinding procedure: An unblinding procedure will be in place in emergencies where knowledge of the group assignment is essential for patient safety. The unblinding process will be overseen by an unblinded third party to ensure the integrity of the study remains intact.\n\n\n\n1. Pre-operative evaluation: Detailed pre-operative evaluations will be conducted for each patient before surgery. This includes clinical history, proforma, physical examination, and routine laboratory tests, such as complete blood count, kidney function tests, liver function tests, and random blood sugar levels. Electrocardiograms will also be performed to assess cardiac health.\n\n2. Allocation and intervention data: Data related to the allocation of patients to specific intervention groups (Groups A, B, C, or D) and the timing of antibiotic administration will be recorded. This includes the type of antibiotic administered, the timing of administration about the surgery (in minutes), and any deviations from the protocol.\n\n3. Surgical procedures: Details of the surgical procedures, including the type of surgery, duration, and any complications encountered during the surgery, will be documented.\n\n4. Post-operative management: Patients will be monitored during their post-operative period following surgery. This includes assessing signs and symptoms of surgical site infections and any other complications that may arise. The presence of fever, pain, tenderness, redness, swelling, delayed healing, or any other relevant indicators will be recorded.\n\n5. Microbiological data: Swabs will be collected from the surgical site for culture and sensitivity testing in cases where infection is suspected. The results of these tests, including the types of organisms and their antibiotic sensitivity profiles, will be documented.\n\n6. Follow-up visits: Patients will undergo follow-up visits on days 15, 30, and 90 postoperatively. Data related to fever, purulent discharge, pain, tenderness, local swelling, culture results, and any changes in total leukocyte count (TLC) will be collected during these visits. These data points will help assess patient recovery and the occurrence of SSIs.\n\n\n\n1. Data entry and storage: All collected data will be entered into a secure electronic database with restricted access. The data will be organized and stored in a way that ensures patient confidentiality and data integrity.\n\n2. Quality control: Regular checks and quality control measures will be implemented to ensure the accuracy and completeness of the data.\n\n3. Data security: Measures will be taken to safeguard the data against unauthorized access or loss. Backup procedures and encryption will be used to protect the data.\n\n4. Data monitoring committee: An independent data monitoring committee may oversee the data collection process and ensure data quality and integrity.\n\nIn the statistical analysis, Firstly, descriptive statistics, encompassing measures like means, medians, standard deviations, and frequencies, will provide an overview of patient characteristics and baseline data. Secondly, inferential statistics will be the focus of the primary analysis, involving a comparison of surgical site infection incidence across the four intervention groups (Groups A, B, C, and D). Statistical tests like chi-squared and t-tests will be employed to evaluate outcome differences. Thirdly, survival analysis techniques, including Kaplan-Meier curves and Cox proportional hazards models, will be used to assess the time until the occurrence of surgical site infections (SSI). Additionally, economic analysis will be conducted, estimating the economic burden through cost-effectiveness analysis, involving the assessment of SSI-associated costs and healthcare utilization, with the computation of cost-effectiveness ratios. Multivariable regression analysis will be employed to account for potential confounding variables, utilizing logistic regression for binary outcomes and linear regression for continuous outcomes. The entire statistical analysis will be conducted using the R studio Version 4.3.1 software package, and results will be considered statistically significant if the p-value is below a predetermined alpha level of 0.05.\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol (Reference number: DMIHER (DU)/IEC/2022/57. Date:18-07-2022). Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has yet to start. After the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nThe primary objective of this study is to determine the most effective antibiotic prophylaxis regimen for preventing SSIs in clean and clean-contaminated surgical cases. Evidence from previous studies has highlighted the importance of selecting appropriate antibiotics with optimal coverage for the specific pathogens associated with the surgical procedure.8 Our RCT design, which randomly assigns patients to different antibiotic groups, provides a robust platform for assessing the comparative efficacy of antibiotic regimens.\n\nThe study is particularly relevant given the varying resistance patterns of pathogens in different regions and healthcare settings.9 By conducting this research in a tertiary care hospital in central India, we aim to provide insights tailored to the local epidemiological context. These findings will be invaluable for clinicians and healthcare systems in similar settings, enhancing their capacity to make informed decisions about pre-operative antibiotic prophylaxis.\n\nAnother critical aspect of the study is evaluating the optimal timing for antibiotic administration. Recent research has indicated that the timing of antibiotic prophylaxis relative to the incision significantly prevents SSIs.10 Our study includes groups receiving antibiotics 30 minutes or 60 minutes before surgery, allowing for a comparison of their efficacy. The outcomes will provide valuable guidance to surgeons regarding the ideal timing of antibiotic administration to maximize SSI prevention.\n\nThe economic burden of SSIs extends beyond direct medical costs and includes indirect expenses, such as prolonged hospital stays, legal consequences, and the impact on healthcare system efficiency.11 This study’s focus on estimating the economic burden of SSIs offers a comprehensive perspective on the true costs associated with these infections. Understanding the financial implications of SSIs is pivotal for healthcare providers and policymakers aiming to allocate resources efficiently and reduce the overall economic impact of SSIs.\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol (Reference number: DMIHER (DU)/IEC/2022/57. Date:18-07-2022). Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.\n\n\nAuthor contribution\n\n\n\n1. Dr. Simran Dhole: Methodology, Project Administration, Writing – Original Draft Preparation, Writing – Review & Editing\n\n2. Dr. Chandrashekhar Mahakalkar: Methodology, Project Administration, Writing – Original Draft Preparation, Writing – Review & Editing", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Proforma for the data collections ‘Randomised controlled trial of preoperative antibiotic prophylaxis in the prevention of surgical site infections in tertiary care hospital of central India’, https://doi.org/10.5281/zenodo.10983223.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo SPIRIT checklist for ‘Randomised controlled trial of preoperative antibiotic prophylaxis in the prevention of surgical site infections in tertiary care hospital of central India’, https://doi.org/10.5281/zenodo.10983159.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAllegranzi B, Pittet D: Role of hand hygiene in healthcare-associated infection prevention. J. Hosp. Infect. 2009; 73: 305–315. Publisher Full Text\n\nCostabella F, Patel KB, Adepoju AV, et al.: Healthcare Cost and Outcomes Associated With Surgical Site Infection and Patient Outcomes in Low- and Middle-Income Countries. Cureus. 15: e42493. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCrader MF, Varacallo M: Preoperative Antibiotic Prophylaxis. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023.\n\nSurgical site infection: Accessed: October 17, 2023. Reference Source\n\nHealthcare Equipment\|Disinfection & Sterilization Guidelines\|Guidelines Library\|Infection Control\|CDC.2019. Accessed: February 20, 2024. Reference Source\n\nAnderson DJ, Podgorny K, Berríos-Torres SI, et al.: Strategies to Prevent Surgical Site Infections in Acute Care Hospitals: 2014 Update. Infect. Control Hosp. Epidemiol. 2014; 35: 605–627. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSurgical Site Infection\|Guidelines\|Infection Control\|CDC: 2019. Accessed: October 17, 2023. Reference Source\n\nBratzler DW, Houck PM: Surgical Infection Prevention Guideline Writers Workgroup: Antimicrobial prophylaxis for surgery: an advisory statement from the National Surgical Infection Prevention Project. Am. J. Surg. 2005; 189: 395–404. PubMed Abstract \| Publisher Full Text\n\nAllegranzi B, Pittet D: Healthcare-associated infection in developing countries: simple solutions to meet complex challenges. Infect. Control Hosp. Epidemiol. 2007; 28: 1323–1327. PubMed Abstract \| Publisher Full Text\n\nWeber WP, Marti WR, Zwahlen M, et al.: The timing of surgical antimicrobial prophylaxis. Ann. Surg. 2008; 247: 918–926. Publisher Full Text\n\nde Lissovoy G , Fraeman K, Hutchins V, et al.: Surgical site infection: incidence and impact on hospital utilization and treatment costs. Am. J. Infect. Control. 2009; 37: 387–397. Publisher Full Text" }	[ { "id": "280716", "date": "27 May 2024", "name": "Stefan Acosta", "expertise": [ "Reviewer Expertise Vascular surgery", "surgical site infections" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall evaluation: This study protocol is well written. The study intends to avoid common biases such as performance or assessor bias. There will be computer-generated randomization. Also state (in Methods) whether this study will receive industry company funding or if the investigators have any connection with industry providing the antibiotics. 90-day follow up is optimal and is a major strength of this study. I think the authors should add cases – approximately 20% to the sample size estimation for loss to follow-up, especially for the 90-day follow up mark. These methodological strengths are merited to be outlined in the discussion, especially the double-blind design, since outcome assessor bias often is a problem in these kinds of studies where the investigators in charge also evaluate the wounds.\nThis kind of study requires funding to be run comfortably. How will this be achieved? Research nurse? Some information on funding should be stated in the manuscript (In Methods).\nIntroduction: Some words on the antimicrobial profiles of the two given antibiotics would be appropriate, and why you choose these antibiotics. Some words on the expected type of surgery. Expected percentage of laparotomy?\nSpecific com:\n1. CTRI should be spelled out. I believe this is a formal registration of the study protocol in a clinical register 2. Secondary outcomes. “Effective time duration” – you mean “effective time period of preoperative administration of prophylactic antibiotics” 3. Sample size calculation – state the reference article (stating that the SSI rate is 3.3%) here as well.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "305239", "date": "02 Aug 2024", "name": "John Alverdy", "expertise": [ "Reviewer Expertise molecular pathogenesis of postoperative infection" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe statement “Additionally, this study emphasizes meticulous post-operative monitoring per the Centers for Disease Control and Prevention (CDC) guidelines.5 This approach is essential for early detection and management of SSIs, ultimately contributing to the generation of robust data” is in need of revision. It is not clear to this reviewer how the study will be able to assess those patients that actually suffer from an SSI. The CDC criteria state that if a clinician observes a postoperative wound and deems it to be “infected” then it is logged as an SSI. Most SSIs today are superficial wound infections, most are not opened and most are treated non-operatively with antibiotics only. Using this CDC guideline approved method, the CDC criteria cannot distinguish between those superficial SSIs (which represent the majority >75%) that are actually SSI versus those that are are simply postoperative inflammation. The assertion that the PI will “swab all wounds” in which an SSI is suspected cannot account for this, swabbing a closed wound will only yield skin flora which cannot be deterministically linked to the SSI itself. The only way to do this would be to open all wounds, inspect them and determine which is actually infected—which itself is complicated. So investigators call this a “pragmatic trial” meaning, this is all we can do to get the answer, which belies the methods needed. However, in India, where multi-drug resistant strains are emerging as highly threatening to surgical patients and based on emerging knowledge in the field that today many (but not all) infections arise from pathogens endogenous to the patient not exogenously, (see Long DR, et.al.2024 (Ref 1) while a single IV dose of an antibiotic is probably safe, broadening coverage in complete ignorance to its long term effects needs to be carefully considered (although this is a universal trend in surgery—meaning if some is good, more is better). A better (and of course more expensive way) to do this is to swab wounds just prior to closure and also swab the mouth, rectum, skin and urine, bank samples for later analysis, and when an SSI develops retrieve the sample from the SSI and use NGS (next generation sequencing) to determine the resistance genes present and where the pathogen actually came from. This requires strain-level genetic analysis and of course retrieval of the pathogen actually in the SSI site. No one will do this, cuz its too costly and labor intensive. But is has been done (see- ref 1) and is the only way to drive SSI rates from where they are now down toward zero. Empirically adding more and showing a P value of a difference does not reconcile “within-group” differences. For example, if group A (standard antibiotics) has a SSI rate of 20% and broader antibiotic coverage (group B) results in a lower SSI rate of 10% and the P value is <0.05, why did 80% of group A patients NOT develop an SSI and why did 10% of group B patients still develop an SSI? Without this information, independent of the noisy swab data intended to be obtained in this study, not much will be learned except that if some is good then more is better (perhaps then the answer to driving the 10% further down is to add a second antibiotic, then if it ends up at 3-5% then add a third antibiotic and so on).\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-400
https://f1000research.com/articles/13-398/v1	26 Apr 24	{ "type": "Study Protocol", "title": "Randomised control trial on management of early avascular necrosis of femoral head by core decompression with bisphosphonate therapy versus core decompression in tertiary care hospital in central India", "authors": [ "Ashutosh Lohiya", "Naresh Dhaniwala", "Naresh Dhaniwala" ], "abstract": "Background This study outlines a randomised control trial to assess the efficacy of Core Decompression with and without Bisphosphonate Therapy in managing early Avascular Necrosis of the femoral head. Avascular Necrosis, a debilitating condition, necessitates exploration of interventions to mitigate progression. The trial is conducted at Jawaharlal Nehru Medical College and Acharya Vinoba Bhave Rural Hospital, Sawangi, Wardha, focusing on clinical, radiographic, and patient-reported outcomes.\n\nMethods Skeletally mature participants diagnosed with stage 1 or 2 Avascular Necrosis of the femoral head will be randomly assigned to either Core Decompression with Bisphosphonate Therapy or Core Decompression Alone. Data collection from July 2022 to September 2024 will involve preoperative assessments, intraoperative details, postoperative care records, and followup evaluations at six weeks, three months, six months, and nine months. Statistical analyses will encompass primary outcomes assessed by Harris Hip Score, secondary outcomes including pain reduction and radiographic changes, and subgroup analyses.\n\nExpected Outcome Anticipated outcomes involve insights into the comparative effectiveness of the two interventions. Primary analyses will reveal variations in Harris Hip Score changes over time, while secondary analyses will shed light on pain reduction, radiographic changes, and potential complications. Subgroup analyses may discern nuances based on etiological factors. The results aim to inform clinical practice, guiding the optimal management of early Avascular Necrosis of the femoral head.", "keywords": [ "Avascular Necrosis", "Femoral Head", "Core Decompression", "Bisphosphonate Therapy", "Randomized Control Trial", "Harris Hip Score", "Radiographic Changes", "Clinical Outcomes", "Skeletal Maturity", "Orthopedics." ], "content": "Introduction\n\nAvascular Necrosis of the femoral head (AVNFH) is a debilitating condition characterised by the disruption of blood supply to the femoral head, leading to ischemic necrosis and subsequent structural damage. It commonly affects individuals in the prime of their lives, resulting in pain, functional impairment, and, if left untreated, progression to hip joint degeneration. The aetiology of AVNFH is diverse, encompassing traumatic injuries, corticosteroid use, and systemic diseases such as sickle cell anaemia and systemic lupus erythematosus.1\n\nCore decompression has emerged as a promising surgical intervention for early-stage AVNFH, aiming to alleviate pain and halt disease progression by reducing intraosseous pressure and promoting revascularisation. Despite its potential benefits, the variable success rates reported in the literature underscore the need for further investigation into adjuvant therapies to optimise outcomes.\n\nBisphosphonates, known for their anti-resorptive properties and positive effects on bone metabolism, have shown promise as an adjunctive treatment in AVNFH.2 Alendronate, a bisphosphonate, has demonstrated its efficacy in improving bone density and reducing the risk of fractures in osteoporosis.3 However, the role of bisphosphonate therapy in conjunction with core decompression for AVNFH management remains an active research area.\n\nThis proposed randomised control trial seeks to contribute to the existing body of knowledge by rigorously evaluating the combined use of core decompression and bisphosphonate therapy to manage early AVNFH. Drawing on the foundational work of Steinberg and colleagues,4 who highlighted the importance of early intervention and the potential benefits of bisphosphonates, this study aims to provide valuable insights into the comparative effectiveness of these treatment modalities.\n\nBy elucidating the optimal approach to early AVNFH management, this research can enhance clinical decision-making and improve patient outcomes in a population susceptible to significant morbidity. The study’s foundation rests on the compelling need to address the challenges posed by AVNFH, emphasising the potential impact of a tailored, multidisciplinary treatment approach.\n\nTo evaluate the efficacy and safety of Core Decompression in managing early Avascular Necrosis of the femoral head, comparing outcomes with or without adjuvant bisphosphonate therapy.\n\nTo determine the impact of Core Decompression with bisphosphonate therapy compared to Core Decompression alone on the overall functional outcomes in patients with early-stage Avascular Necrosis of the femoral head, as measured by changes in the Harris Hip Score.\n\n\n\n1. To assess and compare the reduction in pain levels between the two treatment groups using the Visual Analogue Scale (VAS).\n\n2. To evaluate and compare the radiographic changes in the femoral head in patients undergoing Core Decompression with bisphosphonate therapy versus Core Decompression alone.\n\n3. To analyze and compare the incidence of complications and adverse events between the two treatment groups.\n\n\nMethods\n\nThe study will be conducted at Jawaharlal Nehru Medical College and Acharya Vinoba Bhave Rural Hospital, Sawangi, Wardha, in the Department of Orthopedics. The study will follow a prospective interventional design, with data collection from July 2022 to July 2024 and data analysis scheduled for August 2024 to September 2024.\n\n\n\n1. Skeletally Mature Patients: Adults who have reached skeletal maturity will be eligible for inclusion.\n\n2. Avascular Necrosis of Femoral Head (AVNFH): Patients diagnosed with Avascular Necrosis of the femoral head in stage 1 and stage 2, irrespective of the aetiology.\n\n3. Willingness to Undergo Surgery: Patients willing to undergo surgical intervention for inclusion in one or both hips.\n\n\n\n1. Previously Operated Hips: Patients with previous hip surgeries will be excluded.\n\n2. Arthritic Changes in Involved Hip: Cases presenting with arthritic changes in the involved hip joint will be excluded.\n\n3. Unwillingness for Surgery: Patients unwilling to undergo the prescribed surgical intervention.\n\nPatients meeting the inclusion criteria will be randomised into two groups:\n\nGroup 1: Core Decompression with Bisphosphonate Therapy Patients in this group will undergo core decompression surgery combined with bisphosphonate therapy.\n\n\n\n1. Preoperative Antibiotic Prophylaxis: Ceftriaxone antibiotic for 24 hours (3 doses) post-surgery to prevent infection.\n\n2. Analgesic Regimen: Analgesics will be prescribed for five days postoperatively to manage pain.\n\n3. Calcium and Vitamin Supplementation: Calcium and vitamin supplements will be provided for one-month post-surgery to support bone healing.\n\n4. Bisphosphonate Therapy: Alendronate (70 mg) will be administered once weekly for nine months for odd-numbered participants in this group.\n\nGroup 2: Core Decompression Alone Patients in this group will undergo core decompression surgery without bisphosphonate therapy.\n\n\n\n1. Preoperative Antibiotic Prophylaxis: Similar to Group 1, ceftriaxone antibiotic for 24 hours (3 doses) post-surgery.\n\n2. Analgesic Regimen: Similar to Group 1, analgesics will be prescribed five days postoperatively.\n\n3. Calcium and Vitamin Supplementation: Similar to Group 1, calcium and vitamin supplements will be provided for one-month post-surgery.\n\nPrimary outcome\n\nThe study’s primary outcome is the comparison of overall functional outcomes between the two intervention groups, as measured by changes in the Harris Hip Score5 at the defined followup time points (6 weeks, three months, six months, and nine months). The Harris Hip Score assesses pain, function, absence of deformity, and range of motion, providing a comprehensive evaluation of hip joint health.\n\nSecondary outcomes\n\n1. Pain Reduction (Visual Analogue Scale - VAS)6: Comparison of pain levels between the two groups using the Visual Analogue Scale at each followup visit. This assessment will provide insights into the immediate and sustained pain relief the interventions achieve.\n\n2. Radiographic Changes in Femoral Head: Evaluation of radiographic changes in the femoral head using X-ray and MRI at each followup visit. This will include assessing structural changes, necrotic areas, and the progression or resolution of Avascular Necrosis.\n\n3. Complications and Adverse Events: Monitoring and comparison of the incidence of complications and adverse events in both intervention groups. This will include surgical complications, bisphosphonate-related side effects, and any unexpected events affecting patient outcomes.\n\nThis means 29 or more measurements/surveys are needed to have a confidence level of 95% that the real value is within ±5% of the measured/surveyed value. Prevalence of AVN taken.7\n\n\n\n1. Identification of Potential Participants: Patients presenting with hip pain at the Department of Orthopedics, Jawaharlal Nehru Medical College, and Acharya Vinoba Bhave Rural Hospital, Sawangi, Wardha, will be screened for potential inclusion.\n\n2. Clinical Evaluation: Patients with suspected Avascular Necrosis of the femoral head will undergo a thorough clinical evaluation, including history, physical examination, and relevant investigations.\n\n3. Radiological Assessment: Radiological assessments, including X-ray and MRI, will be performed to confirm the diagnosis and stage of the Avascular Necrosis. Only patients in stage 1 and stage 2 will be considered for inclusion.\n\n4. Informed Consent: Eligible patients will be provided detailed information about the study, its objectives, interventions, and potential risks and benefits. Informed consent will be obtained from those willing to participate.\n\n5. Randomization: Randomization will be conducted using a simple randomisation method to allocate participants into either the Core Decompression with Bisphosphonate Therapy or the Core Decompression Alone group.\n\n6. Baseline Assessments: Baseline assessments, including demographic details, medical history, and baseline clinical and radiological data, will be collected from enrolled participants.\n\n7. Surgical Intervention: Participants will undergo the assigned surgical intervention according to the randomisation. Core decompression with or without bisphosphonate therapy will be performed based on the allocated group.\n\n8. Postoperative Care: Participants will receive postoperative care according to the defined protocol, including antibiotic prophylaxis, analgesics, and supplementary medications.\n\n9. Follow-up Visits: Participants will be scheduled for followup visits at six weeks, three months, six months, and nine months postoperatively for clinical and radiological assessments.\n\n10. Data Collection: Clinical, radiological, and laboratory data will be collected at each followup visit to assess the predefined outcomes.\n\nThe allocation of participants into the two intervention groups, Core Decompression with Bisphosphonate Therapy and Core Decompression Alone, will be performed using a simple randomisation method. Randomisation aims to minimise selection bias and ensure that each participant has an equal chance of being assigned to either group, thus promoting the validity of the study results.\n\nGiven the nature of the interventions, it may be challenging to blind the participants and the surgical team to the assigned treatment. However, efforts will be made to minimise bias in the assessment of outcomes through the following strategies:\n\n1. Blinding of Outcome Assessors: Individuals responsible for collecting and assessing primary and secondary outcome measures, such as Harris Hip Score, Visual Analogue Scale, and radiographic evaluations, will be blinded to the treatment allocation. This blinding will help minimise potential bias in outcome assessments.\n\n2. Data Analysis Blinding: Data analysis will be conducted by individuals who must be aware of the treatment allocation. Coding or labelling of treatment groups will be used to blind the statisticians involved in data analysis.\n\n3. Blinding of Participants: While blinding participants may be challenging due to the nature of the surgical interventions, efforts will be made to minimise participant bias by emphasising the importance of objective reporting during followup assessments.\n\nThe data collection process for the randomised control trial on managing early avascular necrosis of the femoral head will involve a systematic approach to gathering relevant information at various stages of the study. The data collection process includes the following steps:\n\n1. Preoperative Data Collection:\n\n• Clinical Assessment: Demographic details, medical history, and baseline clinical information will be recorded, including age, sex, risk factors, and duration of the illness.\n\n• Radiological Assessment: X-ray (AP pelvis with Both hip and Lateral view of the affected hip) and MRI (pelvis with both hips) will be performed for staging AVNFH using the FICAT-ARLET classification.\n\n2. Randomization and Intervention:\n\n• Randomization will be conducted, and participants will be allocated to either the Core Decompression with Bisphosphonate Therapy group or the Core Decompression Alone group.\n\n• Surgical interventions will be performed according to the assigned group, and data related to the surgical procedure will be documented.\n\n3. Intraoperative Data Collection:\n\n• Data related to the intraoperative period, such as the duration of surgery, specific steps taken during core decompression, and any intraoperative complications, will be recorded.\n\n4. Postoperative Care:\n\n• Details of postoperative care, including antibiotic administration, analgesic usage, and supplementary medications, will be documented.\n\n5. Laboratory Data:\n\n• Blood investigations will be performed preoperatively, including inflammatory parameters (ESR, CRP), coagulation profile (APTT, PT-INR, BT, CT), CBC, homocysteine level, prothrombin time, platelet count, liver function tests (LFT), kidney function tests (KFT), and sickling tests (early and late).\n\n6. Follow-up Visits:\n\n• Participants will be scheduled for followup visits at six weeks, three months, six months, and nine months postoperatively.\n\n• Clinical data will be collected at each followup, including pain assessment using the Visual Analogue Scale (VAS),8 range of motion, tenderness, ability to walk, and any signs of instability.\n\n• Radiological assessments will be performed at each followup, with an X-ray and MRI if needed.\n\n7. Bisphosphonate Administration (for Odd-numbered Groups):\n\n• For participants in the odd-numbered groups receiving bisphosphonate therapy, adherence to alendronate (70 mg) once weekly for nine months will be monitored.\n\n8. Data Validation and Quality Control:\n\n• Regular checks for data completeness, accuracy, and consistency will be conducted to ensure the reliability of collected information.\n\n• Any missing or inconsistent data will be addressed promptly, and corrective actions will be taken.\n\n9. Data Analysis:\n\n• Data analysis will be conducted during the predetermined period (August 2024 to September 2024) using appropriate statistical methods.\n\nEffective data management is crucial to ensure the accuracy, security, and integrity of study data throughout the randomised control trial on managing early Avascular Necrosis of the femoral head.\n\n1. Data Collection Tools: Standardized and pre-printed data collection forms will record information consistently. Electronic data capture systems may also be employed for efficient data management.\n\n2. Data Entry: Double data entry will be performed to minimise errors. Data entered electronically or manually will be validated to identify discrepancies and ensure consistency.\n\n3. Data Storage: All collected data will be securely stored in a designated database or file system. Access to the database will be restricted to authorised personnel to maintain confidentiality.\n\n4. Data Security: Strict measures will be implemented to safeguard the confidentiality and integrity of participant data. Password protection, encryption, and regular backup procedures will be employed.\n\n5. Data Monitoring: Periodic data monitoring will be conducted to identify and rectify any inconsistencies, missing data, or outliers. Any changes or corrections to the data will be documented with appropriate justifications.\n\n6. Quality Control: Quality control procedures will be established to ensure the accuracy and reliability of the collected data. This includes routine checks for completeness, accuracy, and adherence to the study protocol.\n\n7. Data Confidentiality: Participant confidentiality will be maintained by assigning unique identifiers rather than using participant names in the dataset. Access to identifiable information will be restricted to authorised personnel.\n\n8. Data Sharing Policy: Data sharing will be governed by institutional policies and ethical considerations. Access to the dataset may be granted to specific individuals or entities based on predefined criteria.\n\n9. Data Analysis: Data analysis will be conducted using statistical software, and the results will be reported in a manner that preserves the anonymity of participants.\n\n10. Data Archiving: Upon completion of the study, all relevant study documents and datasets will be archived according to institutional and regulatory requirements.\n\nThe statistical analysis for the randomised control trial on managing early Avascular Necrosis of the femoral head will employ a comprehensive approach to evaluate the effectiveness of Core Decompression with Bisphosphonate Therapy compared to Core Decompression Alone. Descriptive statistics will summarise demographic characteristics and compare baseline characteristics between groups to assess randomisation success. The primary outcome, changes in the Harris Hip Score over time, will undergo repeated measures analysis of variance or a mixed-effects model. Secondary outcomes, including pain reduction, radiographic changes, complications, and patient satisfaction, will be analysed using appropriate statistical tests. Subgroup analyses may explore variations in treatment effects based on etiological factors. Survival analysis methods may be applied for time-to-event outcomes. Missing data will be handled using imputation methods, and a significance level of 0.05 will be used for hypothesis testing using SPSS version 23. Data visualisation techniques will aid in interpreting trends, and, if applicable, the Data Safety Monitoring Board will review safety and efficacy data at predetermined intervals. The analysis plan, outlined in the study protocol, will guide the statistical methods to ensure a rigorous and meaningful evaluation of the interventions’ impact on Avascular Necrosis of the femoral head management.\n\nEthical considerations\n\nApproval and Informed Consent: The Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has approved the study protocol (Reference number: DMIHER (DU)/IEC/2022/45, Date: 18-07-2022). Additionally, the trial is registered with the Clinical Trials Registry – India (CTRI/2023/09/057253). Before study initiation, written informed consent will be obtained from all participants or their legal guardians, ensuring they are fully informed about the study’s objectives, procedures, potential risks, and benefits.\n\nUpon the conclusion of the randomised control trial on the management of early Avascular Necrosis of the femoral head, a thorough plan for ancillary and post-trial care will be executed to safeguard the participants’ well-being and ensure the ethical closure of the study. Participants will be informed about the trial’s completion, and details regarding continued medical care and followup appointments will be provided. A post-trial monitoring period will be instituted to assess long-term outcomes and potential complications, with participants monitored for an extended duration to detect any delayed effects or adverse events. Referral pathways and contact information for relevant healthcare providers will be given to facilitate ongoing care for participants requiring further attention. Participants will retain access to trial-related information, including their data, upon request, promoting transparency and addressing any queries or concerns. A summary of the trial results will be shared with participants, fostering transparency and respect in the researcher-participant relationship. Counselling services will be available to address emotional or psychological aspects of participation. Contact information for study coordinators or principal investigators will be provided for an extended period to allow participants to seek clarification or ask questions even after the trial’s completion. Data collected during the trial will be securely stored for an appropriate period, with procedures for data access outlined to protect participant confidentiality. Ethical oversight will persist beyond the trial’s completion, ensuring ongoing consideration of ethical considerations and participant welfare. This comprehensive plan underscores the commitment to ethical research conduct and prioritises the well-being of study participants.\n\nDissemination\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has yet to start. After the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nThe proposed randomised control trial investigating the management of early Avascular Necrosis of the femoral head (AVNFH) through core decompression with and without bisphosphonate therapy addresses a critical gap in our understanding of optimal treatment strategies for this debilitating condition. Avascular Necrosis, often associated with significant morbidity and impaired quality of life, necessitates effective interventions to mitigate its progression and impact on hip joint function.\n\nThe rationale for combining core decompression with bisphosphonate therapy stems from the multifaceted nature of AVNFH, involving both mechanical and metabolic factors. By reducing intraosseous pressure and promoting revascularisation, core decompression has shown promise in alleviating symptoms and preserving joint function.9 Bisphosphonates, recognised for their anti-resorptive properties, have the potential to modulate bone metabolism and enhance the reparative processes within the femoral head.2\n\nThis proposal is grounded in the broader context of AVNFH management, drawing insights from existing literature and pioneering studies. The work of Agarwala et al.,2 which demonstrated the efficacy of alendronate in AVNFH treatment, is a foundational reference supporting the potential benefits of bisphosphonate therapy. Additionally, the quantitative staging system proposed by Steinberg et al.4 contributes to understanding AVNFH severity, aiding in patient stratification and treatment decision-making.\n\nThe proposed study aims to build upon these foundations by systematically evaluating the combined approach of core decompression and bisphosphonate therapy. By incorporating patient-reported outcomes, radiographic assessments, and well-established measures such as the Harris Hip Score, the study aims to comprehensively understand treatment effectiveness and its impact on patients’ functional outcomes. However, the proposed trial also raises several considerations and potential challenges. If previous studies suggest its efficacy, ethical concerns surrounding including a control group without bisphosphonate therapy will be carefully addressed to ensure participant well-being. Additionally, the study’s generalizability may be influenced by the specific characteristics of the study population and variations in etiological factors contributing to AVNFH.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo Repository: Proforma for the data collections ‘Randomized control trial on managing early avascular necrosis of femoral head by core decompression with bisphosphonate therapy versus core decompression in tertiary care hospital in central India.” https://doi.org/10.5281/zenodo.10147069. 10\n\nZenodo Repository: SPIRIT checklist for ‘Randomized control trial on managing early avascular necrosis of femoral head by core decompression with bisphosphonate therapy versus core decompression in tertiary care hospital in central India’, https://doi.org/10.5281/zenodo.10146733.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nLiu N, Zheng C, Wang Q, et al.: Treatment of non-traumatic avascular necrosis of the femoral head (Review). Exp. Ther. Med. 2022; 23: 321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAgarwala S, Shah S, Joshi VR: The use of alendronate in the treatment of avascular necrosis of the femoral head: follow-up to eight years. J. Bone Joint Surg. Br. 2009; 91: 1013–1018. PubMed Abstract \| Publisher Full Text\n\nBlack DM, Cummings SR, Karpf DB, et al.: Randomised trial of effect of alendronate on risk of fracture in women with existing vertebral fractures. Fracture Intervention Trial Research Group. Lancet. 1996; 348: 1535–1541. PubMed Abstract \| Publisher Full Text\n\nSteinberg ME, Hayken GD, Steinberg DR: A quantitative system for staging avascular necrosis. J. Bone Joint Surg. Br. 1995; 77-B: 34–41. Publisher Full Text\n\nHarris Hip Score: Physiopedia. Accessed: December 29, 2023. Reference Source\n\nVisual Analogue Scale: Physiopedia. Accessed: December 29, 2023. Reference Source\n\nHsu H, Nallamothu SV: Hip Osteonecrosis. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023.\n\nAicher B, Peil H, Peil B, et al.: Pain measurement: Visual Analogue Scale (VAS) and Verbal Rating Scale (VRS) in clinical trials with OTC analgesics in headache. Cephalalgia. 2012; 32: 185–197. PubMed Abstract \| Publisher Full Text\n\nMont MA, Hungerford DS: Non-traumatic avascular necrosis of the femoral head. J. Bone Joint Surg. Am. 1995; 77: 459–474. Publisher Full Text\n\nSindhuja BG: Proforma for the data collections ‘Prospective comparative randomized clinical study for the comparison of two different doses of dexmedetomidine with bupivacaine in pediatric caudal anesthesia for infraumbilical surgeries in a tertiary hospital in central India’. Zenodo. 2023. Publisher Full Text" }	[ { "id": "285859", "date": "12 Jun 2024", "name": "Yasmin D Hailer", "expertise": [ "Reviewer Expertise Orthopedic Surgery", "Epidemiology", "AVN", "LCPD" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for allowing me to review the study.\nThe researchers aim to study the effect of Core Decompression with and without Bisphosphonate Therapy in managing early Avascular Necrosis of the femoral head of skeletally mature patients. The study design chosen is a randomized control trial. The study is designed as a single-center study. The primary outcome set as a change in Harris Hip Score at 6 weeks three months, six months, and nine months. As secondary outcomes, the study seeks to analyze pain reduction, radiographic changes, and potential complications.\nBackground The background is well-written and incorporates the most important literature. The study is well-designed to answer the research question. The choice of a randomized control trial is appropriate for the research question.\nMethods: Inclusion criteria:\nI would recommend inserting not only the stage of the AVNFH but also the classification system used. Do the authors include any ages with AVNFH? Especially female patients can reach skeletal maturity at the age of 12 to 14 years. Are the authors willing to include this age group as well? If so, a special focus on patients’ consent and parents’ consent should be undertaken and stated in the protocol. This should be also added to the section ‘informed consent’.\n\nExclusion criteria: It should be stated that patients who are not able to answer the questionnaire because of different reasons should be excluded. As well as patients with a history of necrosis of the jaw or intolerance to the drug or its components.\nSample size calculation The sample size calculation should be explained in more detail. For the primary outcome - change in HHS - what the minimal clinically important difference was taken into consideration?\nBlinding “Given the nature of the interventions, it may be challenging to blind the participants and the surgical team to the assigned Treatment”; .. While blinding participants may be challenging due to the nature of the surgical interventions …\nIt is unclear why blinding is a problem. All patients undergo surgery and the drug administration can be blinded by giving NaCl. The author should consider this to minimize the placebo effect, having in mind that the primary outcome is a PROM.\nFollow-up visits The authors should state why the patients will only be followed for nine months postoperatively.\nWithdrawals/dropouts/Cross-over The authors do not address the potential for withdrawals or dropouts in the study. Nevertheless, they should be prepared to replace such patients, particularly since the power calculation is uncertain even with full recruitment.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-398
https://f1000research.com/articles/13-397/v1	26 Apr 24	{ "type": "Study Protocol", "title": "Assessment of personality factors amongst alcoholics and non-alcoholics in rural part of Central India: A cross-sectional study", "authors": [ "Apurva Bezalwar", "Pradip Patil", "Pradip Patil" ], "abstract": "Background Consuming alcohol has a significant negative impact on an individual’s mental, physical, and overall health in India. Recent data from the World Health Organization reveals that alcohol consumption is a leading cause of numerous fatalities. Some individuals may turn to alcohol as a way to cope with grief and anxiety; however, it diminishes the brain’s serotonin levels, potentially leading to suicidal thoughts and changes in personality. Consequently, there is an immediate need for health education and awareness campaigns addressing the consequences of alcohol use. This research aims to assess and compare the influence of personality factors on individuals who are alcohol-dependent and those who abstain from alcohol, exploring their role in the development of alcohol-related disorders in rural areas.\n\nMethods This in-hospital cross-sectional study is conducted among adults aged 18 to 65 in the rural region of central India. Employing a non-probability sampling method, specifically the Daniel Formula, a sample size of 180 was determined from the accessible population. The research has received approval from the ethics committee. In both the inpatient and outpatient departments of the Psychiatry unit at the hospital, individuals diagnosed with alcoholism and their non-alcoholic counterparts will be approached. Prior to providing socio-demographic information and completing questionnaires on the Alcohol Use Disorders Identification Test (AUDIT), CAGE Questionnaire, and Sixteen Personality Factor Questionnaire (16 PF), informed consent will be obtained from the participants.\n\nExpected outcome Upon obtaining responses to the aforementioned questionnaires, we will be able to analyze and determine the correlation of personality factors between individuals who are alcohol-dependent and those who abstain from alcohol.", "keywords": [ "Personality", "questionnaire", "alcoholics", "rural" ], "content": "Introduction\n\nIn India, alcohol consumption significantly impacts the mental, physical, and overall well-being of individuals. According to recent data from the World Health Organization, the per capita total consumption of alcohol for individuals above 15 years of age is reported to be 6.2 liters per year or 13.5 grams of alcohol daily. Alcohol consumption is linked to approximately 5.1% of diseases, resulting in 3.3 million fatalities annually.1 The liver rapidly absorbs alcohol, and 95% to 98% of consumed alcohol is eliminated by the kidneys.2 Gururaj et al. found that hospital admission rates due to alcohol consumption have increased by 20% to 30%.3\n\nWhile some people turn to alcohol to alleviate depression and anxiety temporarily, it has adverse effects on the brain by depleting the neurotransmitter serotonin, leading to suicidal tendencies and personality changes.4 The consequences of alcohol consumption extend to various aspects, including economic, familial, social, and physical impacts on an individual’s health and personality. Notably, alcohol-related cases constitute 17.6% of emergencies in Indian hospitals.5 Hence, there is an urgent need for sensitization programs and health education to manage and control the consequences of alcohol consumption.\n\nThe primary objective of the present study is to assess personality factors among alcoholics and non-alcoholics, aiming to determine the association of these factors in the rural part of central India.\n\nTo evaluate personality factors among both individuals with alcohol dependence and those without.\n\n\n\n1. To examine the correlation of personality factors between individuals with alcohol dependence and those without.\n\n2. To investigate the influence of personality factors on the outcomes of alcohol-related disorders.\n\nAlcohol abuse contributes to three million fatalities globally annually, posing a significant public health concern. While personality is recognized as a crucial element in the origin of alcohol consumption, there is a notable lack of research in the context of alcoholics compared to non-alcoholics. Exploring this field would provide valuable insights into understanding the association of personality factors in both alcoholics and non-alcoholics.\n\n\nProtocol\n\nStudy design: Cross sectional comparative hospital based study.\n\nStudy population: Individuals diagnosed with alcoholism and their counterparts, who do not have a diagnosis of alcoholism, participating in both the inpatient and outpatient departments of the Psychiatry unit at a hospital situated in the rural region of central India.\n\nSample size:\n\n180 (90 alcoholics and 90 non alcoholics)\n\nFormula used:\n\nWhere, 2α/2 is the level of significance at 5% i.e. 95%\n\nconfidence interval = 1.96\n\nP = prevalence of drinking problem = 12.8% = 0.128\n\nd = desired error of margin = 7% = 0.07\n\nTherefore,\n\n\nMethods\n\nThe patients’ informed consent as well as socio-demographic information will be gathered. The following questionnaire’s will subsequently be given to the patients:\n\n1. Socio-demographic Performa\n\n2. Alcohol Use Disorders Identification Test (AUDIT)\n\n3. CAGE Questionnaire\n\n4. Sixteen Personality Factor Questionnaire (16 PF)\n\nThe Institutional Ethics Committee granted approval for the study with the reference number DMIMS (DU)/IEC/2022/14 on July 15, 2022. In this study, patients selected for participation will be requested to provide their informed consent.\n\n\n\n1. Age between 18-65 years.\n\n2. The patients who are clinically diagnosed with Alcohol Use Disorder using the International Classification of Diseases 10th revision (ICD-10) and ICD -11th revision (ICD -11) Diagnostic criteria for research.\n\n3. Patients and non-alcoholic counterparts who visit PSY OPD as well as IPD hospitalized patients and their non-alcoholic counterparts.\n\nPatients and non-alcoholiccounterparts willing for written informed consent.\n\n\n\n1. Patients and non-alcoholiccounterparts not willing for written informed consent.\n\n2. The patients who are acutely ill.\n\n3. The patients with other co-morbid psychiatric disorders.\n\n4. The patients with other co-morbid medical and surgical disorders\n\n\n\n1. Socio-demographic and Clinical Data Sheet: This study utilizes a semi-structured template specifically tailored for its purposes. The template encompasses details related to socio-demographic variables, such as the individual’s age, gender, educational background, marital status, religion, employment status, and domicile background. Additionally, the clinical data sheet captures information regarding the age of onset, precipitating factors, the course of illness, and any previous history of treatment.\n\n2. Alcohol Use Disorders Identification Test (AUDIT): The AUDIT is a 10-item screening tool developed by the World Health Organization (WHO) to evaluate drinking behaviors, alcohol-related issues, and assess the level of alcohol consumption. A score of 8 or higher indicates a potentially hazardous or harmful pattern of alcohol consumption. This tool is validated for use with both male and female individuals and is applicable across a diverse range of ethnic groups. Moreover, it is suitable for implementation in primary care settings. The AUDIT also includes a chart at the end that delineates the number of standard drinks in different types of alcoholic beverages.\n\n3. CAGE Questionnaire: It is a four question tool\n\nCut down Annoyed Guilty Eye-opener\n\nScoring for the CAGE questionnaire involves assigning 0 for “no” responses and 1 for “yes” responses to its items. A higher cumulative score is suggestive of potential alcohol-related problems, and a total score equal to or greater than two is considered clinically significant.\n\n4. Sixteen Personality Factor Questionnaire (16 PF): This tool, developed by Raymond Cattell, is designed to analyze the fundamental structural elements of personality. Its primary purpose is to predict human characteristics such as altruism, leadership skills, authoritarianism, and creativity based on core personality traits. As an internationally originated instrument, it has been translated into numerous languages globally. It has undergone significant revisions, and the latest edition comprises 187 multiple-choice questions. Designed for individuals aged 16 and above, the questionnaire is untimed and features clear, straightforward instructions, making it suitable for minimal supervision at both group and individual levels. The administration time is approximately 35-50 minutes for a traditional pencil-and-paper format and 25-40 minutes for a computer-based format. The publisher provides scoring services and reports. Recent translations are adapted to local norms, ensuring reliability and validity. This questionnaire finds applications in various contexts, including counseling, basic research, and medical and educational settings. Its purpose is to offer a comprehensive and integrated understanding of an individual, aiding in the development of self-awareness, fostering rapport and empathy, and addressing adjustment issues.\n\nThe data analysis using SPSS Software version 27.0 using appropriate statistical tools. According to the scores obtained by the tools applied – CHI SQUARE TEST, Z TEST, Pearson’s Correlation Coefficient will be applied to see the association between Personality factors among alcoholics and non alcoholics. Descriptive analysis will be used for obtaining socio-demographic data of the patients. Continuous variables will be calculated by mean and standard deviation.Categorical variables will be calculated by frequency and percentage.\n\nThe Institutional Ethics Committee has given approval for the study DMIMS (DU)/IEC/2022/14 on 15th July 2022 and informed consent will be taken from the targeted patients and their counterparts who will be participating in this study. All participants will be assured confidentiality. They will be informed of their right to opt out of the study at any time by withdrawing their consent. The goal of the study will be completely made clear to participants.\n\n\n\n1. The study design is cross sectional.\n\n2. Age of participants is 18 to 65 years.\n\n3. Adults with medical and surgical co-morbidities and with diagnosed psychiatric illnesses are not included in this study.\n\nOpen ended questionnaire will be used for data collection to avoid measurement bias.\n\n\nDiscussion\n\nA study done by Sharma et al. (2016)6 proposes that issues faced by alcoholics wives and coping mechanisms utilized by them were in the physical, psychological, social, and most prominently in the emotional domains. Several therapies were used successfully to lessen their pain and suffering.1\n\nBekman et al. (2010) noted the role of cognitive factors regarding the consequences of not drinking and drinking under peer pressure, This links the danger of emotional and personality-based factors to young adults’ decision not to drink, and they discovered that their beliefs about not drinking and drinking under peer pressure play major roles between affective and personality types on adolescence alcohol use The varied affective profiles of risk for beginning alcohol use and its use during adolescence may be explained by these cognitive variations, and they may also offer techniques for its prevention.5\n\nLittlefield and Sher (2010) concluded that the models presented are neither comprehensive nor contradictory, and they do not represent the particular way that personality could relate to problematic alcohol use. Instead, they indicate the many ways that personality may influence AUDs over the course of a person’s lifetime. Therefore, personality may have an effect on the amount of alcohol ingested and how it is used inappropriately through a number of concurrent pathways.7\n\nBeaudoin et al. (1997) seen as having the personality elements of adult children of alcoholics (ACOAs), who are depressed or alcoholic. These results suggested that the characteristics that set ACOAs apart from non-ACOAs include low self-esteem, high neuroticism, and high psychoticism, and that two ways in which ACOAs can display these characteristics are through drunkenness and depression.8\n\nMiller (1889) When personality characteristics between alcoholic and non-alcoholic brothers were compared, the two groups only differed on two scales: the non-alcoholic group differed more in dominance, while the alcoholic group differed more in heterosexuality.9\n\nOnce we get answers to the above questionnaires from the 180 participants, we will be able to compare the association of personality factors amongst alcoholics and non alcoholics and to study the impact of personality factors in outcome of alcohol related disorders\n\nBoth a presentation of the study and its publication in an index journal are planned for National Conference Proceedings.\n\nThe participant recruiting has not yet begun.\n\nInstitutional Ethical Committee approval was obtained from Datta Meghe.\n\nInstitute of Medical Sciences, Sawangi (Meghe) Wardha on 15th July 2022.\n\nIEC no. - DMIMS (DU)/IEC/2022/14\n\nWritten Informed consent will be taken from the targeted patients and their counterparts who will be participating in this study.", "appendix": "Data availability\n\nNo data is associated with this article.\n\nZenodo : STROBE checklist for 1. Apurva Bezalwar. Assessment Of Personality Factors Amongst Alcoholics And Non Alcoholics In Rural Part Of Central India : A Cross-Sectional Study. 10.5281/zenodo.8379312. 10\n\n\nReferences\n\nWorld Health Organization: Management of Substance Abuse Unit. Global status report on alcohol and health, 2014. World Health Organization; 2014.\n\nSachdeva S, Nagar M, Tyagi A, et al.: Alcohol consumption practices amongst adult males in a rural area of Haryana. Med. J. DY Patil Univ. 2014 Mar 12; 7(2): 128. Publisher Full Text\n\nGururaj G, Isaac MK: Psychiatric epidemiology in India: Moving beyond numbers. Mental health—an Indian perspective. 1946-2003.\n\nPeng MC, Chou WJ, Chen SS: Neurological problems in chronic alcoholics. Gaoxiong yixuekexue za zhi= The Kaohsiung Journal of Medical Sciences. 1991 Aug 1; 7(8): 404–412.\n\nBekman NM, Cummins K, Brown SA: Affective and personality risk and cognitive mediators of initial adolescent alcohol use. J. Stud. Alcohol. Drugs. 2010 Jul; 71(4): 570–580. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharma N, Sharma S, Ghai S, et al.: Living with an alcoholic partner: Problems faced and coping strategies used by wives of alcoholic clients. Ind. Psychiatry J. 2016 Jan; 25(1): 65–71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLittlefield AK, Sher KJ: The multiple, distinct ways that personality contributes to alcohol use disorders. Soc. Personal. Psychol. Compass. 2010 Sep; 4(9): 767–782. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeaudoin CM, Murray RP, Bond J Jr, et al.: Personality characteristics of depressed or alcoholic adult children of alcoholics.Pers. Individ. Differ.1997 Oct 1; 23(4): 559–67. Publisher Full Text\n\nMiller L: Personality Differences in Alcoholic and Nonalcoholic Brothers ( 1964). Master's Theses. 1889. https://ecommons.luc.edu/luc_theses/1889\n\nBezalwar A: Assessment Of Personality Factors Amongst Alcoholics And Non Alcoholics In Rural Part Of Central India: A Cross-Sectional Study. Zenodo. 2023. Publisher Full Text" }	[ { "id": "312294", "date": "12 Sep 2024", "name": "Johnson Pradeep Ruben", "expertise": [ "Reviewer Expertise Alcohol use disorders", "Community Psychiatry", "Digital innovations in managing depression in underserved rural areas" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary of the Protocol\nThe protocol is a research methodology that focusses on evaluating personality traits among rural Central India's alcoholics and non-alcoholics. The purpose of the study is to compare how personality traits affect people who abstain from drinking and those who suffer from alcohol dependence. A non-probability sampling technique was used to choose 180 participants for the cross-sectional comparison study, 90 of whom were alcohol use disorders and 90 of whom were not. The study is conducted in a hospital. Sociodemographic data and questionnaires such as the Alcohol Use Disorders Identification Test (AUDIT), CAGE Questionnaire, and Sixteen Personality Factor Questionnaire (16 PF) are used in the data collection process. The Institutional Ethics Committee has approved the trial, and participants' informed consent will be sought. The relationship between personality traits in alcohol use disorders and non-alcohol users will be evaluated using statistical analysis utilising SPSS software and a variety of tests. The study is still in the process of recruiting participants and intends to provide light on the role that personality variables play in alcohol-related diseases.\nMajor: The personality qualities of people with and without alcohol use disorders can be distinguished from this study. Finding these elements will support a therapeutic strategy that emphasises psychological input for characteristics more frequently seen in alcohol use disorders. But that is only one side of the tale; if they had been able to create an intervention based on their findings and give it a trial run on a few subjects, it might have been helpful. Some of the queries include: (1) what is the role of the CAGE questionnaire when you are using AUDIT. Better to use AUDIT. (2) Kindly mention the reference study for the sample size calculations. (3) Kindly give the rationale for using the 16 PF ; when you have newer and shorter personality scales available\nMinor queries (1) Be consistent with your terminologies in terms of alcohol dependence or Alcohol use disorders (Avoid the word “alcoholics” due to the discriminatory nature of the word. (2) The reference Sharma et al (2016) and Beaudoin et al. (1997) are irrelevant in this study. Kindly give more relevant references.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-397
https://f1000research.com/articles/13-396/v1	26 Apr 24	{ "type": "Study Protocol", "title": "Effect of high dietary fiber intake on insulin resistance, body composition and weight, among overweight or obese middle-aged women: study protocol for a double-blinded randomized controlled trail.", "authors": [ "Suvarna Hebbar", "Shashikiran Umakanth", "Latha Thimmappa", "Joniya Galbao", "Shashikiran Umakanth", "Latha Thimmappa", "Joniya Galbao" ], "abstract": "Background Obesity is a major consequence of malnutrition and significantly contributes to the global burden of chronic diseases. Currently, there are more overweight and obese individuals than underweight individuals. Increased fiber intake can increase insulin sensitivity and fat oxidation. According to research studies, the average dietary fiber consumption is below the recommended value, and the WHO anticipates that the worldwide obesity prevalence has increased in the past ten years.\n\nAim To evaluate the effect of high dietary fiber intake on insulin resistance, body composition, and weight in overweight and obese middle-aged women.\n\nMethod This hospital-based study evaluated 500 people during phase 1 to identify the prevalence of insulin resistance among overweight and obese middle-aged women. An RCT with intervention and control arms for 180 individuals is being conducted in Phase 2 to determine the effect of increased dietary fiber consumption on insulin resistance, body composition, and weight in overweight or obese middle-aged women. In the intervention group, women were counselled for 15 min and given a tailored food chart including 40 g of fiber. Women in the control arm will receive a typical food care plan with 25 g of fiber, based on their health status. Each engaged woman received fiber nutritional empowerment.\n\nDiscussion Increasing dietary fiber consumption can improve insulin resistance, body composition, and weight in middle-aged overweight and obese women.\n\nTrial registration The Clinical Trials Registry of India (CTRI/2022/01/039074) has registered this study as a clinical trial on January 3, 2022 http://ctri.nic.in", "keywords": [ "Middle Aged", "Women", "Insulin Resistance", "Overweight", "Obesity", "Body Composition", "Dietary Fiber", "Health Status." ], "content": "Background\n\nObesity is a major public health concern worldwide. Urbanization, economic growth, changing lifestyles, and dietary habits have posed a “double burden” of diseases in rapidly developing low- and middle-income countries, such as India.1 The average dietary fiber consumption was below the recommended value as per research studies, and the World Health Organization estimates that the incidence of obesity has increased worldwide in the last 10 years. Most people do not consume enough food with adequate amounts of fiber to meet the recommended level, and obese women report a lower intake of dietary fiber than normal-weight individuals.2 A rich source of dietary fiber in meals induces satiety, resulting in reduced hunger.3 The effect of dietary fiber was obvious in obese participants.4 According to a study led by Georgia State University, consumption of dietary fiber promotes the growth of beneficial bacteria in the colon, preventing obesity, metabolic syndrome, and adverse changes in the intestine.5\n\nThe decreased incidence of several diseases is associated with fiber-rich diets that have a positive impact on well-being. High-fiber foods can replace energy (calories), which provides low energy density against high-fat foods. The roughage and thickening properties of dietary fiber primarily influence satiation and fullness of the stomach. People who consume ample amounts of dietary fiber are at a low risk of developing coronary artery diseases, stroke, hypertension, diabetes, obesity, and certain gastrointestinal diseases compared to those who have minimal fiber intake. A significant improvement was observed in the values of serum lipoprotein and blood pressure, improvement in blood sugar for diabetic entities, and weight reduction by improving the consumption of elevated fiber foods or fiber supplements. Ingestion of soluble fiber enhances immune function.6\n\nAn increase in the consumption of dietary fiber from a variety of fruits, vegetables, legumes, and whole-grain products will provide various physiological benefits. Dietary fiber, if consumed in acceptable amounts, lowers the risk of several chronic disorders, such as cardiovascular diseases, type 2 diabetes mellitus, obesity, and certain types of cancer. Dietary fiber sources, along with functional fibers, have the additional benefit of organically occurring micronutrients and phytochemicals that may enhance human health. Health benefits of consuming dietary fiber must be actively communicated to the public.7 There are few studies on the utilization of dietary fiber in the treatment of obesity, but further research is required to confirm stronger associations between dietary fiber and obesity.8 The growth of beneficial bacteria in the gut is initiated by dietary fiber. Increased consumption of dietary fiber and whole grains helps normalize gut microbiota symbiosis. Dietary fiber improves the gut microbiota composition in individuals with obesity and other metabolic diseases. Nutritive fiber has different impacts on the gut microbiota because of the diverse compositions and structures of the fibers and whole grains.9 High-dietary fiber food is more satiating and has a significant role in establishing a sense of contentment, aids in reducing serum insulin secretion, helps in gastric emptying time, and reduces food intake. It also assists in increasing satiety levels, fat oxidation, decreasing energy intake, and lowering body fat content.10 Dietary fiber, upon fermentation, generates small chain fatty acids that alter eating forms by circulating peptides and gut hormones such as cholecystokinin and glucagon-like peptides, which reduce hunger and promote satiety.11 Insulin sensitivity and stimulation of fat oxidation can be improved by increasing fiber intake. Saliva and gastric juice secretions distend the stomach by promoting satiety by enhancing chewing limits.12\n\nThis study focuses on weight reduction by increasing fiber consumption. Recommended fiber intake of 40 2000 kcal is per the Indian Council of Medical Research and National Institute of Nutrition Guidelines.13 Dietary fiber has various health benefits, with a satiating role in establishing a sense of contentment, lowering cholesterol levels, and decreasing the rise in blood sugar and fat oxidation by lowering body fat content. Consumption of dietary fiber at the recommended amount will improve overall well-being.\n\n\nObjectives\n\n\n\n• To determine the effect of fiber intake on insulin resistance, body composition, and weight.\n\n\n\n• To determine the effect of fiber intake on biochemical parameters\n\n• To assess the opinions of women on modified fiber intake\n\n\nMethods\n\nThe present study will be conducted in the OPDs of the medicine, gynaecology, and endocrinology units of a tertiary care hospital in Karnataka, India. This study: 519/2021 was approved by Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee (IEC) on December 19, 2021. The data will be collected on the consent of the patients and the confidentiality will be strictly maintained. Women in the age group between 35-55 years will be screened for insulin resistance at Phase-1 and those women with no contraindication for high fiber consumption and abnormal HOMA-IR will be included in Phase-2. Baseline assessments will be performed for each woman in both the intervention and control groups. Demographic data will be collected, including age, religion, place of residence, type of family, number of family members, marital history, education, occupation, and income performance. Anthropometric data obtained using a stadiometer (for measuring height), weighing scale (for weight measurement), and measuring tape for waist circumference and hip circumference will be documented in the OPD. In the biochemical data, fasting blood glucose (hexokinase method) HbA1c (TINA), serum insulin (ECLIA) and lipid profile (triglyceride-GPO Trinder, HDL-direct homogenous, LDL enzymatic, total cholesterol-CE-CHOD-POD) will be checked. To assess dietary data, a 24-hr dietary recall and food frequency questionnaire was used. The data will be analysed using Diet Cal version 6.3. Physical activity data were assessed using the GPAQ (Global Physical Activity Questionnaire). Body fat analyzer was used to assess visceral fat, subcutaneous fat, and muscle mass. Clinical assessment (physical complaints such as bowel movement, satiety, leg pain, and backache) will be performed. Dietary advice was communicated to both the control and intervention groups. This study involves a minimal risk of drawing 10 ml blood thrice, discomfort related to high fiber diet and minimal physical examination. The study will help in increasing the awareness level of intake of fibre in women which will there by improve the nutritional status and quality of life.\n\nThis study was single-center, stratified, randomized, controlled, and double-blind. In the first phase, a cross-sectional study will be conducted to identify the prevalence of insulin resistance among overweight and obese middle-aged women. Two groups, with at least 166 in each group of overweight and obese will be screened and in second phase a randomized clinical trial will be conducted to find the effect of high dietary fiber intake on insulin resistance, body composition and weight, among overweight or obese middle-aged women. For this purpose, women with no contraindications for high fiber consumption or abnormal HOMA-IR were included. Simultaneously, an in-depth interview will be conducted telephonically for 45 min to understand the barriers of fiber intake among two equal groups of 20 each, consuming low fiber (< 20 g) and good fiber (= 20 g to 25 g) in phase 1.\n\nThis study will be carried out in the OPDs of the medicine, gynaecology, and endocrinology units of a tertiary care hospital in Karnataka, India.\n\nAt Phase 1, a total of 500 women will be screened to identify the prevalence of insulin resistance among overweight and obese middle-aged women. Two groups, with at least 166 in each group of overweight and obese will be screened. The sample size was calculated in accordance with insulin resistance and BMI.11 Simultaneously, in Phase 2, the sample size was 180 participants,12 who will be randomized into the study and control groups. Stratified Block Randomization,9 block with 20 in each (stratified based on overweight and obese with at least 60 participants in overweight and obese strata). Sequence generation of samples using online software and the Concealment-Opaque Envelope Method will be applied to identify the effect of high dietary fiber intake on insulin resistance, body composition, and weight among overweight or obese middle-aged women.\n\nSample size for repeated measures ANOVA.\n\nDrop out 15%\n\nWhere,\n\nn = sample size\n\nz1-α/2 = 1.96 at α = 0.05\n\nz1-β = 0.84 at 80% power\n\ns = anticipated population standard deviation of the outcome variable.\n\nd = clinically significant difference\n\nm = number of time points/follow-ups = 2\n\nρ = intraclass correlation = 0.4\n\nInsulin resistance\n\nn = 71\n\nAccounting for a dropout rate of 15%, n = 83 per group\n\nAs per BMI\n\nn = 77\n\nAccounting for a dropout rate of 15%, n = 90 per group\n\nThe final required sample size was 180 (90 each in the intervention and control groups).\n\nInclusion criteria – Phase-1\n\n• Women willing to give consent.\n\n• Middle-aged women of the age group 35-55 yrs.\n\n• Women with BMI ≥ 23 kg/m2 (Overweight- 23-24.9 kg/m2, Obese: ≥30 kg/m2)\n\nExclusion criteria – Phase-1\n\n• Women with any disorder that affects their nutritional status, such as tuberculosis, HIV, cancer, and organ failure.\n\n• Women with type 2 diabetes mellitus\n\n• Women with hypertension, thyroid disorders, or other medical conditions started on any medication that could affect body weight (including thyroxine, antithyroid medications, and diuretics) after enrolment in the study.\n\n• Pregnant or lactating women.\n\n• Women with contraindications for high fiber consumption, for example inflammatory bowel disease.\n\n• Women already following a weight loss regime.\n\n• Women consuming fiber more than the recommended dietary allowance.\n\nInclusion criteria – Phase-2\n\n• Abnormal HOMA-IR (>2) indicating insulin resistance.\n\n• Willingness to follow high fiber diet as recommended if randomized to intervention arm.\n\nExclusion criteria – Phase-2\n\n• Not willing to participate further in the study.\n\n• Not willing to follow the high fiber diet as recommended.\n\nSampling techniques: At baseline, 500 women will be screened to identify the prevalence of insulin resistance among overweight and obese middle-aged women.\n\nPhase-1, Two groups, with at least 166 in each group of overweight and obese will be screened and tested for insulin resistance.\n\nPhase-2, Overweight and obese participants with abnormal insulin resistance will be randomized into study and control groups.\n\nStratified Block Randomization consisted of 9 blocks with 20 participants each (stratified by overweight and obese, with at least 60 participants in each stratum). Sample sequence creation will be performed using online software. The Allocation Concealment-Opaque Envelope Method was applied.\n\nIntervention group\n\nAll women in the intervention arm will be counselled for about 15 min with a customized diet chart consisting of a high fiber of 40 g. Nutritional empowerment of fiber should be delivered to each enrolled woman. Necessary dietary advice on the modified diet plan and motivation to adhere to the diet plan will be communicated only to the intervention group. After the first counselling session, on the 15th day, women will be telephonically assessed on their 24hr recall dietary intake. On the 30th day, the women will be contacted telephonically again to record their 24hr recall of their dietary intake. Necessary dietary changes in the modified diet plan would be advised, and the motivation to adhere to the diet plan will be continued. On the 60th day, the women will be again telephonically contacted to record their 24hr recall on their dietary intake, necessary dietary changes on the modified diet plan will be advised, and motivation to adhere to the diet plan will be continued. On the 90th day, as an outcome-based assessment, women will be referred to the hospital for anthropometric data, biochemical data followed by dietary data, 24hr dietary recall, food frequency analyzed using Diet Cal version 6.3, physical activity data assessed using GPAQ, body fat analyzed using a body fat analyzer, and a questionnaire on patient opinion regarding modified diet plan. For motivation and adherence to fiber consumption, subjects will be communicated telephonically on the 135th day. From the 136th to 180th days, there was no conversation regarding dietary modifications. On the 180th day, as a compliance-checking, the women will be again called to the hospital for the anthropometric data, biochemical data followed by dietary data. 24hr dietary recall, food frequency analyzed using Diet Cal version 6.3, physical activity data assessed by using GPAQ, body fat analyzed using body fat analyzer and diet compliance on the modified diet plan shall be assessed.\n\nControl group\n\nWomen in the control arm will receive a traditional diet care plan with 25 g of fiber, according to their health condition. Necessary dietary advice was communicated to the control group during their first visit to the hospital. There was no telephonic communication with the control group until the 90th day. On the 90th day, as an outcome-based assessment, women will be referred to the hospital for anthropometric data, biochemical data, dietary data, 24hr dietary recall, food frequency analyzed using Diet Cal version 6.3, physical activity data assessed using GPAQ, and body fat analyzed using a body fat analyzer. On the 180th day, as a compliance-checking, the patient will be again called to the hospital for anthropometric data, biochemical data, dietary data, 24-hr dietary recall, food frequency analyzed using Diet Cal version 6.3, physical activity data assessed using GPAQ, and body fat analyzed using a body fat analyzer.\n\nThe intervention arm will be compared against the control arm for all the primary analysis. We will use the chi-square test for primary outcomes and the t-test for continuous outcomes.\n\nCurrently, participants have been recruited for phase-1 and 2, and follow-up for phase-2 is ongoing.\n\n\nDiscussion\n\nThere is limited evidence on the beneficial association between high dietary fiber intake and metabolic indicators, body composition, and weight in middle-aged women who are overweight or obese in the Indian population. This study will focus on improving insulin resistance, body composition, and weight, which will be recorded in participants with high dietary fiber intake. Dietary fiber has various health benefits, with a satiating role in establishing a sense of contentment, lowering cholesterol levels, and decreasing the rise in blood sugar and fat oxidation by lowering body fat content.\n\n\nArticle summary\n\n\n\n• An improvement in insulin resistance, body composition, and weight will be recorded in participants with high dietary fiber intake.\n\n• Good knowledge and practice regarding modified diet plans with high dietary fiber will be addressed to participants.\n\n• Knowledge regarding barriers/consequences/clinical hindrances in consuming a high-fiber diet will be addressed.\n\n• Drop out due to non-compliance\n\n• Patients adhering to follow the diet plan for a longer period\n\n• Limited resources are available to address the importance of inclusion of recommended fiber in the general public since we are only screening patients visiting hospitals.\n\nThe study protocol was reviewed and approved by the Institutional Research Committee (IRC) and Institutional Ethics Committee (IEC): 519/2021 was approved by Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee on December 19, 2021, registered under the Clinical Trials Registry- India (CTRI) (CRTI/2022/01/039074). The study will be carried out in compliance with Good Clinical Practice standards. These findings will be published in peer-reviewed journals and presented at international conferences.\n\nAll the participants signed a written informed consent form. All methods will be carried out in accordance with the relevant guidelines and regulations.\n\n\nData availability\n\nNo data are associated with this article.\n\nOpen Source Framework: Effect of high dietary fiber intake on insulin resistance, body composition, and weight among overweight or obese middle-aged women: Study protocol for a double-blind randomized controlled trial, DOI https://doi.org/10.17605/OSF.IO/HUW43.\n\nThe supplementary materials available are:\n\n‐ Questionnaire\n\n‐ SPIRIT checklist\n\n‐ Education Material\n\nOpen Source Framework: Checklist for Effect of high dietary fiber intake on insulin resistance, body composition, and weight among overweight or obese middle-aged women: Study protocol for a double-blinded randomized controlled trial, DOI https://doi.org/10.17605/OSF.IO/HUW43.", "appendix": "Acknowledgements\n\nWe are grateful to the funding agency IMCR-DHR, India.\n\n\nReferences\n\nNagarkar A, Kulkarni S: Obesity and its effects on health in middle-aged women from slums of Pune. J. Midlife Health. 2018; 9(2): 79–84. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNamazi N, Larijani B, Azadbakht L: Are Isolated and Complex Fiber Supplements Good Choices for Weight Management? A Systematic Review. Arch. Iran. Med. 2017; 20(11): 704–713. PubMed Abstract\n\nDelzenne NM, Cani PD: A place for dietary fibre in the management of the metabolic syndrome. Curr. Opin. Clin. Nutr. Metab. Care. 2005; 8(6): 636–640. PubMed Abstract \| Publisher Full Text\n\nHowarth NC, Saltzman E, Roberts SB: Dietary Fiber and Weight Regulation. Nutr. Rev. 2009; 59(5): 129–139. Publisher Full Text\n\nZou J, Chassaing B, Singh V, et al.: Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health. Cell Host Microbe. 2018; 23(1): 41–53.e4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSingh A, Singh SN: Dietary fiber content of Indian diets. Asian J. Pharm. Clin. Res. 2015; 58–61.\n\nPuri S, Krishnaswamy S, Joshi S, et al.: Position of the Indian dietetic association: dietary fibre and health. [Review of Position of the Indian dietetic association: dietary fibre and health.]. Indian Dietetic Association. Indian Dietetic Association; 2018; pp. 1–7.\n\nRuhee RT: Dietary fiber and its effect on obesity: A review article. Adv. Med. Res. 2018; 01(01). Publisher Full Text\n\nSnart J, Bibiloni R, Grayson T, et al.: Supplementation of the Diet with High-Viscosity Beta-Glucan Results in Enrichment for Lactobacilli in the Rat Cecum. Appl. Environ. Microbiol. 2006; 72(3): 1925–1931. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPereira MA, Ludwig DS: Dietary fiber and body-weight regulation. Pediatr. Clin. N. Am. 2001; 48(4): 969–980. Publisher Full Text\n\nDavis JN, Landry MJ, Vandyousefi S, et al.: Effects of a School-Based Nutrition, Gardening, and Cooking Intervention on Metabolic Parameters in High-risk Youth. JAMA Netw. Open. 2023; 6(1): e2250375. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHeaton KW: Food fibre as an obstacle to energy intake. Lancet. 1973; 302(7843): 1418–1421. PubMed Abstract \| Publisher Full Text\n\nAnderson JW, Baird P, Davis RH Jr, et al.: Health benefits of dietary fiber. Nutr. Rev. 2009; 67(4): 188–205. Publisher Full Text" }	[ { "id": "357073", "date": "05 Feb 2025", "name": "Gary Frost", "expertise": [ "Reviewer Expertise Nutrition and carbohydrate research" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI found the protocol somewhat confusing, primarily because the methods section combines both Phase 1 and Phase 2. It would be clearer if each phase were presented separately under distinct subheadings.\nIncluding a schematic diagram of the intervention would greatly aid in understanding the different phases and how they are structured.\nThe rationale for expecting sex-specific differences in response to the dietary fiber intervention is unclear. Additionally, the purpose of the intervention itself needs to be better justified. Is this study specifically designed for women’s health? If so, the justification for conducting a single-sex study should be clearly articulated.\nSome of the language used in the background section appears outdated and would benefit from revision. For example, terms like “roughage” should be updated to reflect current scientific terminology.\nThe study is described as stratified, randomized, controlled, and double-blind. However, given that the intervention involves dietary advice to achieve 40g of fiber intake compared to 20g, true double-blinding does not seem feasible. Clarification on how blinding is being implemented would be helpful. Additionally, why was a crossover design not considered, as it might have addressed some of these challenges?\nThere is confusion regarding the sample size. The power calculation suggests 90 participants per group, but the random allocation section mentions 60 per group. This discrepancy needs to be clarified.\nThe duration of the intervention is also difficult to determine. It appears to be 180 days for the intervention group, but this information is not presented clearly. Providing a concise summary of the study timeline would improve clarity.\nThere is limited justification for selecting a 20g difference in fiber intake between groups, as well as for the chosen length of the intervention. It would be useful to know if the research team has previously demonstrated success in increasing dietary fiber intake by 20g, as this can be challenging.\nRelying solely on 24-hour dietary recalls to assess compliance is concerning, given the known limitations of this method. Are there any plans to include additional compliance measures?\nLastly, will the composition of dietary fiber (i.e., soluble vs. insoluble) be consistent across participants? The metabolic effects of these fiber types can vary significantly, and this should be addressed.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] } ]	1	https://f1000research.com/articles/13-396
https://f1000research.com/articles/13-395/v1	26 Apr 24	{ "type": "Research Article", "title": "Efficacy of CEITA early intervention program for young children with autism spectrum disorders: A randomized controlled trial design", "authors": [ "Yung Lin Han", "Wan Shahrazad Wan Sulaiman", "Abdul Rahman Ahmad Badayai", "Wan Shahrazad Wan Sulaiman", "Abdul Rahman Ahmad Badayai" ], "abstract": "Background This study examined the efficacy of the Comprehensive Early Intervention for Toddlers with Autism (CEITA) program for children with autism spectrum disorders in Malaysia.\n\nMethods A randomized control trial design was adopted, in which 16 children (mean age= 34.25 months) were assigned to either the intervention group (n=8) or the control group (n=8). Children in the intervention group underwent three months of low intensity (2hrs/week) CEITA program intervention, whereas the control group received no treatment. Autism symptoms and developmental growth scores were measured at baseline, post-treatment, and 6-week follow-up to evaluate the efficacy of the CEITA program.\n\nResults Multivariate analysis of covariance results showed a significant intervention effect, whereby autism symptoms were significantly reduced (η2 = 0.36), and growth scores for all developmental domains (η2 = 0.20-0.66) were significantly increased.\n\nConclusion Hence, this study highlights the potential of the CEITA program’s clinical implications, and relevant future research is recommended.\n\nTrial registration Reg number: NMRR ID-22-00626-8LB, dated 29th April 2022.", "keywords": [ "autism spectrum disorder", "early intervention", "comprehensive early intervention for toddlers with autism", "malaysia" ], "content": "Early intervention for young children\n\nEarly interventions for young children with ASD are often recommended to build a comprehensive treatment model (Early Intervention Program for Infants and Toddlers with Disabilities, 2004; Reichow, 2012; Sandall et al., 2005) that aims to promote overall developmental growth through interventions across various domains (Hyman et al., 2020; McConachie & Diggle, 2007; Solomon et al., 2007). Nevertheless, a thorough review of the existing literature indicates a scarcity of interventional studies, specifically targeting toddlers and preschool-aged children diagnosed with ASD (Vismara & Rogers, 2008). Furthermore, only a few of these studies have implemented a comprehensive treatment model that holistically addresses many aspects of the disorder. Behavioral models, such as applied behavioral analysis (ABA) (Lovaas, 1987), and naturalistic developmental models, such as the Early Start Denver Model (ESDM) (Dawson et al., 2010), are, thus far, the most extensively researched approaches for treating ASD (Baril & Humphreys, 2017; MacDonald et al., 2014; Tiura et al., 2017; Velazquez & Nye, 2011; Vivanti & Dissanayake, 2016). However, both methods have been criticized for their limitations (Xu et al., 2018). On the one hand, the structured nature of ABA has faced criticism for its perceived limitations in promoting spontaneity and potential overreliance on prompts (Bradshaw et al., 2015; Schreibman et al., 2015). On the other hand, the widespread adoption of ESDM has been hindered by substantial qualification and training requirements, resulting in increased community costs (Boyd et al., 2010; Dawson et al., 2010).\n\nFurther, most early intervention studies have noticeably focused on samples comprising individuals who identify as white and monolingual English speakers (DuBay et al., 2018). Additionally, interventionists with the necessary qualifications are predominantly certified in Western countries. The lack of acknowledgment of cultural diversity when providing early intervention services may hinder the implementation and efficacy of treatment, as research (Buzhardt et al., 2016; Parra Cardona et al., 2012) has shown that the same interventions may not have similar efficacy across different populations. Moreover, interventions incongruent with a family’s culture, values, and expectations often lead to conflicts (Hwa-Froelich & Vigil, 2004), strained therapeutic relationships (Garcia et al., 2012), and higher rates of service discontinuation (Long et al., 2015).\n\n\nProblem statement\n\nThis phenomenon reflects the current situation in Malaysia. The exorbitant costs associated with obtaining the necessary training to become a proficient practitioner in administering early interventions can result in high treatment fees. According to published articles (Kamaralzaman et al., 2018; Md Jani et al., 2022), the estimated annual financial costs associated with intensive comprehensive treatment (10–40 hours per week) could range between RM36,000 and RM42,472. Consequently, a notable obstacle to the availability of therapy emerges, leading to a tendency toward more affordable options that may lack a foundation for empirical evidence (Ong, 2019; Yaacob et al., 2021). For instance, most alternative intervention strategies available in Malaysia, such as dietary supplements, hot-spring therapy, and religious practices, have not been tested empirically (Ong, 2019). Moreover, parents of children with ASD have reported facing difficulties in facilitating therapy at home, which often leads to strained adult-child relationships (Wetherby et al., 2014). Furthermore, vast differences in treatment approaches and outcomes pose difficulties in reaching a consensus as to which treatment strategies are the most effective (Strain et al., 2011; Warren et al., 2011).\n\nIn summary, based on several literature reviews, the current limitations of early intervention programs are as follows: (1) limited published studies (Vismara & Rogers, 2008); (2) not acknowledging cultural diversity (DuBay et al., 2018); (3) being overly time-consuming (Kasari et al., 2015); (4) poor transfer of acquired skills to daily life (Prizant et al., 2000); (5) extensive requirements for qualification or training (Boyd et al., 2010; Dawson et al., 2010).\n\nMoreover, with the emerging literature suggesting no relationship between the intensity or style of treatment and treatment outcomes (Rogers et al., 2021), as well as a significant effect of cultural values in early interventions (DuBay et al., 2018; Fong & Lee, 2017), there is an urgent need to develop interventions for young children with ASD specific to the targeted populations. As such, early interventions for young children should be comprehensive and low-intensity and implemented in community settings (Brian et al., 2015).\n\nA new comprehensive early intervention program, the Comprehensive Early Intervention for Toddlers with Autism (CEITA) program, was designed in this study to address the above issues. A group of Malaysian researchers developed the CEITA program for young children aged 4 years and below and who have ASD. It was built to complement the recommended guidelines (Early Intervention Program for Infants and Toddlers with Disabilities, 2004; Malaysian Health Technology Assessment Section [MaHTAS], 2014) for developing early intervention programs for young children in Malaysia.\n\nFigure 1 presents an overview of the CEITA theoretical model framework. According to previous research, manifestations of ASD symptoms correlate substantially with their impact on children’s developmental outcomes (Guralnick, 2020; Schertz et al., 2011). Drawing on the positive outcomes of several treatment strategies (Contaldo et al., 2020; Dawson et al., 2010; Kaale et al., 2012; Tiura et al., 2017), the CEITA intervention program was designed to utilize behavioristic strategies and naturalistic contingencies to teach developmentally appropriate pivotal skills. Additionally, thoughts were given to match treatment goals to appropriate values and perspectives culturally and maximize treatment outcomes, including overall developmental growth across various domains and reduction of ASD symptoms. The five key components or principles of the CEITA intervention program are as follows: (a) systematic developmental practices, (b) children’s active learning roles, (c) adult-child relationships, (d) natural settings and reinforcers, and (e) family involvement. Cultural considerations have been incorporated into the practical therapeutic practices of the CEITA program. For example, figurines of “Upin & Ipin,” famous Malaysian cartoon characters, were used in session to enhance social interaction. Another example would be incorporating elements of cultural celebration such as “Hari Raya,” Chinese New Year, and others to increase social communication, verbal expression, cognitive acquisition, and others.\n\nThis study used a randomized controlled trial design and proposed that children with ASD who received the CEITA program would show significant improvement across developmental domains and a reduction in ASD symptoms.\n\n\nMethods\n\nThis study was approved by the Faculty of Social Sciences and Humanities, University of Kebangsaan, Malaysia (UKM) (JEP-2021-871).\n\nThis research is registered under both the National University of Malaysia (reg number: JEP-2021-871, date: 14th February 2022, as well as under the Medical Research & Ethics Committee from the Ministry of Health Malaysia (reg number: NMRR ID-22-00626-8LB, dated 29th April 2022 Research Directory List \| National Medical Research Register (nmrr.gov.my) before commencement of the first trial.\n\nA randomized pre-post experimental design, with outcomes measured at baseline and after treatment, was used. A 6-week follow-up was also conducted to reduce bias, increase statistical power, and enhance the reliability of the results. Parents or caregivers completed the revised Malay version of the Modified Checklist for Autism in Toddlers (M-CHAT-R/F) to measure autism-related symptoms, whereas developmental growth was measured using the Developmental Profile-4 (DP-4) assessment completed by a therapist or clinician. All measured data were quantitatively collected, and statistical analysis was performed prospectively using SPSS version 27.\n\nAs this study was an extension of the authors’ previous study on validating the Malaysian M-CHAT-R/F, participants were recruited using a purposive sampling method. Malaysian children aged 18–48 months and diagnosed with ASD had participated in the previous study, and they were invited to participate in this study. Additional inclusion criteria were as follows: (a) having an identified caregiver, (b) absence of comorbidity with other neurological illnesses or physical handicap, and (c) capacity to commit to attending the CEITA program weekly for three months. The exclusion criteria were presence of comorbidity of neurological illnesses or physical disabilities, such as cerebral palsy, intellectual disabilities, Down syndrome, and other similar conditions. Further, parents who anticipated enrolling their children with ASD into other interventions throughout the research period were excluded from the study.\n\nBased on Kazdin’s (1994) review of clinical research and practice on the recommendation for sample size, the alpha was set at 0.05, with a power of 0.80, and an estimated effect size of 0.40. G Power (Faul et al., 2007) calculator was used to generate the required sample size and run a mixed Analysis of Variance (ANOVA) with two groups over three measurement time points. The minimum sample size needed was 12 participants. However, as research has documented a dropout rate of approximately 20% across most medical journals (Bell et al., 2013), this study recruited 16 participants in total and randomly assigned them to either the intervention or control group. Microsoft Excel’s randomization principles were executed for random assignment, with the RAND function used to assign random numbers to each participant. Subsequently, the function SMALL was used to divide the participants into two groups: the intervention group, comprising those with random values less than 0.5, and the control group, comprising the others. Thus, 16 participants were divided into two groups of eight individuals each.\n\nEach participants’ demographic characteristics are listed in Table 1, and the overall descriptive statistics of the intervention and control groups are shown in Table 2. Sixteen participants with an average age of 34.25 months (standard deviation = 7.12) were recruited for the study. The chi-square test was employed to evaluate the statistical significance between groups, considering that both children’s age and sex were categorical variables. No statistically significant differences were observed in terms of age (χ2 = 12.00, p = 0.29) or sex (χ2= 0.25, p = 0.59) among the various groups of participants.\n\nPrior to the data collection, the researcher obtained ethical approvals from the UKM institutional ethical board. Participants were recruited from the researcher’s previous validation study of M-CHAT-R/F Malay, which was approved by the UKM ethical board (JEP-2021-871) and Medical Research & Ethics Committee Malaysia (NMRR ID-22-00626-8LB). Sixteen participants from the previous study, who were diagnosed with ASD and aged 18–48 months, were identified. Figure 2 shows the overall procedure used in this study.\n\nThe parents or caregivers provided informed consent through their signature on the printed informed consent form, thereby granting their permission for their children’s participation in the study. Considering the age range, level of maturity and psychological condition of the prospective child who is diagnosed with ASD, the decision to withhold the child’s assent was made due to concerns over their comprehension of the potential risks and benefits associated with the research. All participants were informed of their right to withdraw or terminate their participation at any stage of the study. Next, parents or caregivers were asked to complete the M-CHAT-R/F, and the clinician or therapist completed the DP-4 assessment. The data obtained from these two measurements served as baseline values. Sixteen participants were randomly assigned to either the intervention (n=8) or control (n = 8) group. The therapists or clinicians appointed for each child were blinded to the measured data, and they declared no conflict of interest with any of the participants. The CEITA program intervention was administered to the participants assigned to the intervention group in two sessions per week, with each session lasting 60 minutes. This intervention was provided for approximately three months, equivalent to 24 sessions in total. The individuals assigned to the control group were not subjected to any form of intervention or therapy throughout the study period. All case data were recorded by the respective CEITA therapists and stored in hard or soft copies in the researchers’ cloud-based storage systems. Upon completion of the intervention or three months after baseline, parents, caregivers, and therapists were invited to complete the M-CHAT-R/F Malay and DP-4 again. The three measures were also obtained six weeks post-intervention. As no participant dropped out, all data were included in the analysis.\n\nPresence of autism symptoms or characteristic\n\nThe M-CHAT-R/F (Robins et al., 2009) is an ASD screening tool with 20 yes/no checklist items. This parent-administered questionnaire can be completed within 10 minutes. Translation, cultural adaptation, and validation of this screening tool in Malay for the Malaysian population were conducted prior to this study’s commencement (Han et al., 2023a). The Malaysian M-CHAT-R/F is documented to have high sensitivity (97%) and specificity (94%), with a satisfactory positive predictive value of 53.3% when used among young children aged 18–48 months.\n\nDevelopmental growth\n\nDP-4 (Alpern, 2020) is a 190-item checklist that measures five developmental domains (i.e., cognitive functioning, communication, social-emotional behavior, adaptive behavior, and physical development) for individuals from birth to 21 years and 11 months. For this study, a clinician-rated checklist was used and completed by the individual therapist or clinician in charge of each participant’s intervention. The scores were calculated by a different clinician who was blinded and had no conflict of interest with the child or the clinician who completed the checklist. Each subscale contained approximately 35 yes/no checklist items. The scores on each subscale were summed and converted into growth scores for comparison and monitoring of developmental progress over the intervention and follow-up periods.\n\nPrior to the study’s commencement, a feasibility analysis was conducted. A case study was conducted using semi-structured interviews with therapists, parents, and an expert panel in the field. Consequently, the case study revealed significant improvements in overall developmental growth and reduction of ASD symptoms. The expert panel advised on the adoption of a randomized controlled trial methodology when studying the CEITA intervention program’s efficacy to increase the results’ reliability and validity. Sample size calculation and randomization strategies were determined based on previous clinical research recommendations. The therapists surveyed suggested that having therapy sessions twice a week, with each session lasting about 60 minutes, would be feasible, and the commitment for 24 sessions, approximately three months, is reasonable. The decision regarding the frequency and duration of sessions was also inclusive of the parents’ willingness to commit and their financial capability. Outcomes were measured using the parent-administered Malaysian M-CHAT-R/F, as the tool had been validated, and the therapists and expert panel suggested that the DP-4 could measure developmental growth.\n\nAll participants were assessed at baseline, and descriptive statistics for each variable were calculated and listed. Considering the categorical nature of the demographic variables (age and sex), a chi-square test was performed to determine any significant differences between them. Subsequently, independent T-tests were performed to analyze the baseline differences between the intervention and control groups in the M-CHAT-R Malay and DP-4 scores. As this study aimed to examine the effectiveness of the CEITA program through changes in the measured data, analysis of covariance (ANCOVA) or Multivariate analysis of covariance (MANCOVA) statistical tests were performed, where relevant baseline scores were controlled as continuous covariates. As such, more reliable conclusions can be drawn, as the effect of the categorical independent variable (baseline scores) on the dependent variables (post-intervention and follow-up scores) was isolated. The post-hoc test results were then used for directional inferences.\n\n\nResults\n\nMultiple independent T-tests were performed, and the mean differences between the intervention and control groups were computed. Table 3 displays the Mean and Standard Deviation of each group’s M-CHAT-R/F and DP-4 measured variables. No significant differences were observed in any of the measured variables, p > 0.05.\n\nMANCOVA analysis was performed on the M-CHAT-R and DP-4 scores to examine the intervention effect. In these models, the relevant baseline scores were computed and controlled for as continuous covariates. Table 4 displays the descriptive statistics comparing the intervention and control groups at post-test and follow-up for all variables, whereas Table 5 displays the intervention effect based on partial eta squared and significance values for all variables.\n\n p<0.05.\n\n** p<0.01.\n\nAfter controlling for the baseline scores, the MANCOVA revealed a statistically significant difference between groups based on the M-CHAT-R/F scores at both time points: F(2, 12) = 12.60, p =.001, Wilks’ Λ =.323, partial η2 =.70. Post-hoc analysis of between-subjects effects utilizing MANCOVA (refer to Table 5) revealed a significant group difference at post-test, F(1,13) = 7.37, p =.018, partial η2 =.36, and at follow up, F(1,13)=14.51, p =.002, partial η2 =.53. As shown in Table 4 and Figure 3, participants in the intervention group had significantly lower M-CHAT-R/F scores at post-test (M=6.13, SD=3.00) and follow-up (M=4.88, SD=3.27) compared to participants in the control group at post-test (M=8.88, SD=2.23) and follow-up (M=9.00, SD=2.98).\n\nConversely, MANCOVA results for all DP-4 domains also showed a statistically significant difference between groups on the domain growth scores at both time points after controlling for baseline scores, with Wilks’ Λ ranging from 0.22 to.0.59 and partial η2 ranging from 0.41 to 0.79. Post-hoc analysis of between-subjects effects, using MANCOVA (refer to Table 5), revealed significant group differences in all developmental domains, with partial η2 effects spanning from 0.20 to 0.66. Table 4 and Figure 4 show significantly higher post-test and follow-up growth scores across all developmental domains for participants in the intervention group.\n\n\nDiscussion\n\nThe primary objective of this current randomized controlled study is to assess the effectiveness of the CEITA program as an early intervention program for children in Malaysia who have been diagnosed with ASD and are aged four years and below. The efficacy of the CEITA program was assessed by examining its impact on developmental domains and the existence of ASD symptoms in the participants. This program is designed to provide a comprehensive intervention, and it has been designed with a rigorous empirical foundation, aiming to optimize the intervention’s impact by employing low-intensity and culturally relevant delivery modalities. This approach was tailored to meet the requirements of a cost-effective yet highly successful intervention for a specific target demographic.\n\nIn this study, 16 Malaysian children aged 18–48 months had been diagnosed with ASD were recruited and randomly assigned to either the intervention or control groups. Children in the intervention group who participated in the CEITA program showed a statistically significant decrease in autism-related symptoms. The M-CHAT-R/F scores substantially declined immediately after the completion of the CEITA program. Furthermore, these scores decreased further even after six weeks post-intervention. Conversely, children in the control group did not demonstrate any noteworthy variations during the designated timeline. With the non-significant baseline scores between the intervention and control groups, the huge decrease in scores and significant difference between the groups further suggested the high efficacy of the CEITA program. Indeed, the average initial M-CHAT-R/F scores for both groups fell within the high-risk category. However, following the intervention, the children in the intervention group achieved significantly lower scores (M=6.13) and were classified as falling within the medium-risk range. Contrarily, children in the control group exhibited a consistent pattern of M-CHAT-R scores that fell within the high-risk category. The M-CHAT-R scores for children in the intervention group continued to decrease at even after six weeks post-intervention, further supporting the efficacy and validity of the CEITA program and its possible long-term benefits.\n\nThe findings of this study also showed a significant increase in almost all developmental domains among children in the intervention group immediately after the CEITA program completion. The growth scores exhibited a sustained and significant increase across all domains during the post-intervention and at the six-week follow-up, indicating that the effects of the intervention were substantial and enduring. In fact, the strong correlation observed in the post-intervention stage provides clear evidence of the interconnectedness and inter-relatedness of all developmental areas. Further, except for the physical domains, all other domains, such as adaptive behaviors, social-emotional, cognition, and communications, showed a large intervention effect (p<0.001) at post-intervention and follow-up. The consistent increase in growth scores across the measured timeline within the intervention group further validates the intervention effect of the CEITA program in this study. Compared to other intervention studies with control groups (Estes et al., 2015; Vivanti & Dissanayake, 2016) that did not show significant group difference immediately after the intervention, this research evidently presented a substantial intervention effect post-intervention. The immediate group differences observed in this study could be explained by several factors.\n\nCompared to intervention programs and studies conducted in Western countries, the current research highlights the inclusion of cultural values and traditions. Some of the cultural considerations were as follows: (a) the choice of language used in sessions was congruent with the family; (b) the choice of activities or reinforcements given were culturally appropriate; (c) cultural celebrations or events included were relevant to the local community; (d) the materials used were closely related to the local community. The integration of cultural values and traditions in the CEITA program may be one of the prominent factors in its succession. The importance of cultural differences and the need for adaptation to early intervention have also been documented in recent research (Xu et al., 2018), which found a significant intervention effect immediately after treatment. In their study, the authors also claimed that the cultural adaptation steps were necessary to ensure successful implementation of the intervention. Therefore, the findings of this study further support the importance of acknowledging cultural diversity among populations. In line with the widespread use of screening tools globally (Han et al., 2023b; Soto et al., 2015), future studies should explore the potential of modifying efficacious interventions to cater to diverse populations with varying cultural backgrounds.\n\nApart from the cultural factors, the use of appropriate measures could also have contributed to the success of this study. As noted in previous studies (Fulton et al., 2014; Vivanti & Dissanayake, 2016), different instruments and methodologies have been used to measure intervention efficacy. Although a consensus is reached that the efficacy of an ASD intervention is reflected in the decreased autism symptoms, the data obtained from different instruments may not accurately reflect the severity of symptoms, given the highly complex nature of the disorders. Additionally, young children diagnosed with ASD often exhibit impairments beyond communication and behavioral deficits (Brian et al., 2015). Hence, This study assessed the effectiveness of the intervention by documenting the alterations in symptoms associated with autism and examining the changes in growth scores across various developmental domains. Specifically, the high correlation between developmental domains and autism symptoms further supports the inter-relatedness of the domains. This finding provides additional support for the fundamental theoretical underpinnings of the CEITA program, which is designed to prioritize comprehensive developmental growth rather than solely address the symptoms associated with ASD. Nonetheless, predictive analysis could not be performed in this study because the sample size of the intervention group was small. Future research could gather more data to analyze which developmental domains could be significant predictors of a reduction in ASD symptoms.\n\nOverall, the findings of this study provide preliminary evidence that the CEITA program may be an effective early intervention for young children with ASD. The development-based approach in this model analytically assesses a child’s functioning level across many developmental domains, enabling therapists and parents to establish goals that are more attainable and aligned with the child’s current ability level. Therefore, the implementation and utilization of the CEITA program in this study align with the concept of early intervention for young children (Dunst, 2000), which refers to the provision of assistance and services to young children and their families regardless of whether the child has a diagnosed disability or is at risk of developing a disability. In fact, the current findings provide initial support for further studies on evidence-based early intervention to enhance overall developmental growth as a primary method for mitigating symptoms related to ASD. Consequently, the stigmatization linked to ASD could be alleviated, and the effectiveness of treatments could be conveyed in a more optimistic and encouraging manner to parents. From a practical standpoint, the adoption of the CEITA program is anticipated to be more cost-effective and less time-consuming because of its delivery in low-intensity and brief sessions.\n\nHowever, this study has several limitations. First, despite the significant intervention effects observed across measures, significant predictors among the developmental domains of autism symptoms could not be pinpointed, as the number of participants was too small for regression analysis. Second, although the CEITA program noted the importance of parental involvement, the analysis or findings on how parental involvement moderated the findings were not discussed. Third, as this study was designed to be quantitative, the qualitative nature that offers insights into other possible key explanations for the efficacy of the CEITA program might have been missed. Therefore, the current research findings are preliminary and should be interpreted cautiously.\n\n\nConclusion\n\nIn summary, this study makes a significant contribution to the field of early intervention services for young children with ASD, particularly considering the limited number of existing comparable papers. Furthermore, the CEITA program examined in this study was designed to recognize the significance of cultural diversity. This study’s findings suggest that the inclusion of cultural values in early interventions may have a beneficial moderating effect on their efficacy. Furthermore, the CEITA program’s design and methodology were emphasized as being of significant relevance. The developmental trajectory of a child with ASD is highlighted as comparable to that of a neurotypical child, in which the growth of all developmental domains is interwoven during the early years (Hyman et al., 2020). These results emphasize the importance of complete and holistic early interventions.", "appendix": "Data availability\n\nFigshare: DataSet_CEITA Early Intervention Program, https://doi.org/10.6084/m9.figshare.24125091.v2.\n\nThis project contains the following underlying data:\n\n- Random formular.xlsx\n\n- Dataset_excel.xlsm\n\n- DataSet_final.sav\n\nRepository: Consort checklist and flow chart for ‘Efficacy of CEITA early intervention program for young children with autism spectrum disorders: a randomized controlled trial design’, https://doi.org/10.6084/m9.figshare.25445962.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAlpern GD: (DPTM-4) Developmental Profile 4.2020. Reference Source\n\nAmerican Psychiatric Association: Diagnostic and statistical manual of mental disorders: DSM-5. 5th ed.American Psychiatric Association; 2013. Publisher Full Text\n\nBaril EM, Humphreys BP: An Evaluation of the Research Evidence on the Early Start Denver Model. J. Early Interv. 2017; 39(4): 321–338. Publisher Full Text\n\nBell ML, Kenward MG, Fairclough DL, et al.: Differential dropout and bias in randomised controlled trials: when it matters and when it may not. BMJ. 2013; 346. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoyd BA, Odom SL, Humphreys BP, et al.: Infants and toddlers with autism spectrum disorder: Early identification and early intervention. J. Early Interv. 2010; 32(2): 75–98. Publisher Full Text\n\nBradshaw J, Steiner AM, Gengoux G, et al.: Feasibility and effectiveness of very early intervention for infants at-risk for autism spectrum disorder: A systematic review. J. Autism Dev. Disord. 2015; 45(3): 778–794. PubMed Abstract \| Publisher Full Text\n\nBrian JA, Bryson SE, Zwaigenbaum L: Autism spectrum disorder in infancy. Curr. Opin. Neurol. 2015; 28(2): 117–123. Publisher Full Text\n\nBuzhardt J, Rusinko L, Heitzman-Powell L, et al.: Exploratory evaluation and initial adaptation of a parent training program for Hispanic families of children with autism. Fam. Process. 2016; 55(1): 107–122. PubMed Abstract \| Publisher Full Text\n\nCheong SK: Increasing number of autism cases. The Star Online. 2009, September 20.\n\nCidav Z, Lawer L, Marcus SC, et al.: Age-related variation in health service use and associated expenditures among children with autism. J. Autism Dev. Disord. 2013; 43(4): 924–931. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nContaldo A, Colombi C, Pierotti C, et al.: Outcomes and moderators of Early Start Denver Model intervention in young children with autism spectrum disorder delivered in a mixed individual and group setting. Autism. 2020; 24(3): 718–729. PubMed Abstract \| Publisher Full Text\n\nDawson G, Rogers S, Munson J, et al.: Randomized, controlled trial of an intervention for toddlers with autism: The Early Start Denver Model. Pediatrics. 2010; 125(1): e17–e23. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDuBay M, Watson LR, Zhang W: In search of culturally appropriate autism interventions: Perspectives of Latino caregivers. J. Autism Dev. Disord. 2018; 48(5): 1623–1639. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDunst CJ: Revisiting “Rethinking early intervention.”. Top. Early Child. Spec. Educ. 2000; 20(2): 95–104. Publisher Full Text\n\nElsabbagh M, Divan G, Koh YJ, et al.: Global prevalence of autism and other pervasive developmental disorders. Autism Res. 2012; 5(3): 160–179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElsabbagh M, Johnson MH: Autism and the social brain: The First-Year Puzzle. Biol. Psychiatry. 2016; 80(2): 94–99. PubMed Abstract \| Publisher Full Text\n\nEstes A, Munson J, Rogers SJ, et al.: Long-term outcomes of early intervention in 6-year-old children with autism spectrum disorder. J. Am. Acad. Child Adolesc. Psychiatry. 2015; 54(7): 580–587. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFaul F, Erdfelder E, Lang A-G, et al.: G*Power 3: A flexible statistical power analysis program for the social, behavioral, and biomedical sciences. Behav. Res. Methods. 2007; 39(2): 175–191. PubMed Abstract \| Publisher Full Text Reference Source\n\nFong EH, Lee H: Sociocultural perspective on autism intervention. Autism: Paradigms, Recent Research and Clinical Applications. IntechOpen; 2017; 291–300. Publisher Full Text\n\nFulton E, Eapen V, Črnčec R, et al.: Reducing maladaptive behaviors in preschool-aged children with autism spectrum disorder using the Early Start Denver Model. Front. Pediatr. 2014; 2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarcia EF, Breslau J, Hansen R, et al.: Unintended consequences: an ethnographic narrative case series exploring language recommendations for bilingual families of children with autistic spectrum disorders. Journal of Medical Speech - Language Pathology. 2012; 20(2): 10.\n\nGlynne-Owen R: Early intervention and autism: The impact of positivism and the call for change. Int. J. Child. Rights. 2010; 18(3): 405–416. Publisher Full Text\n\nGuralnick MJ: Applying the developmental systems approach to inclusive community-based early intervention programs: Process and practice. Infants Young Child. 2020; 33(3): 173–183. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHan YL, Wan Sulaiman WS, Ahmad Badayai AR, et al.: Validating the Malaysian modified checklist for autism in toddlers, revised with follow-up (M-CHAT-R/F): a cross-cultural adaptation. Frontiers in Child and Adolescent Psychiatry. 2023a; 2. Publisher Full Text\n\nHan YL, Wan Sulaiman WS, Ahmad Badayai AR, et al.: Systematic Review of Translation and Cultural Adaptations of Autism Spectrum Disorder’s Screening Tool: The Modified Checklist for Autism in Toddlers, Revised (M-CHAT-R). F1000Res. 2023b; 12: 471. Publisher Full Text\n\nHwa-Froelich DA, Vigil DC: Three aspects of cultural influence on communication: A literature review. Commun. Disord. Q. 2004; 25(3): 107–118. Publisher Full Text\n\nHyman SL, Levy SE, Myers SM, et al.: Identification, evaluation, and management of children with autism spectrum disorder. Pediatrics. 2020; 145(1). Publisher Full Text\n\nEarly Intervention Program for Infants and Toddlers with Disabilities: 2004. 60139. Reference Source\n\nKaale A, Smith L, Sponheim E: A randomized controlled trial of preschool-based joint attention intervention for children with autism. J. Child Psychol. Psychiatry Allied Discip. 2012; 53(1): 97–105. PubMed Abstract \| Publisher Full Text\n\nKamaralzaman S, Toran H, Mohamed S, et al.: The economic burden of families with autism spectrum disorders (ASD) children in Malaysia. Journal of ICSAR. 2018; 2(1): 71–77. Publisher Full Text\n\nKasari C, Gulsrud A, Paparella T, et al.: Randomized comparative efficacy study of parent-mediated interventions for toddlers with autism. J. Consult. Clin. Psychol. 2015; 83(3): 554–563. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKazdin AE: Methodology, design, and evaluation in psychotherapy research.Bergin AE, Garfield SL, editors. Handbook of psychotherapy and behavior change. John Wiley & Sons; 1994; pp. 19–71.\n\nKhan NZ, Gallo LA, Arghir A, et al.: Autism and the grand challenges in global mental health. Autism Res. 2012; 5(3): 156–159. PubMed Abstract \| Publisher Full Text\n\nKitzerow J, Hackbusch M, Jensen K, et al.: Study protocol of the multi-centre, randomised controlled trial of the Frankfurt Early Intervention Programme A-FFIP versus early intervention as usual for toddlers and preschool children with autism spectrum disorder (A-FFIP study). Trials. 2020; 21(1): 1–17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLavelle TA, Weinstein MC, Newhouse JP, et al.: Economic burden of childhood autism spectrum disorders. Pediatrics. 2014; 133(3): e520–e529. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLong KA, Kao B, Plante W, et al.: Cultural and child-related predictors of distress among Latina caregivers of children with intellectual disabilities. Am. J. Intellect. Dev. Disabil. 2015; 120(2): 145–165. PubMed Abstract \| Publisher Full Text\n\nLovaas OI: Behavioral treatment and normal educational and intellectual functioning in young autistic children. J. Consult. Clin. Psychol. 1987; 55(1): 3–9. PubMed Abstract \| Publisher Full Text\n\nMacDonald R, Parry-Cruwys D, Dupere S, et al.: Assessing progress and outcome of early intensive behavioral intervention for toddlers with autism. Res. Dev. Disabil. 2014; 35(12): 3632–3644. PubMed Abstract \| Publisher Full Text\n\nMaenner MJ, Warren Z, Williams AR, et al.: Prevalence and characteristics of autism spectrum disorder among children aged 8 years — Autism and Developmental Disabilities Monitoring Network, 11 Sites, United States, 2020. MMWR Surveill. Summ. 2023; 72(2): 1–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMalaysian Health Technology Assessment Section (MaHTAS): Clinical practice guidelines: Management of ASD in children & adolescence. Malaysian Health Technology Assessment Section; 2014.\n\nMcConachie H, Diggle T: Parent implemented early intervention for young children with autism spectrum disorder: A systematic review. J. Eval. Clin. Pract. 2007; 13(1): 120–129. PubMed Abstract \| Publisher Full Text\n\nMd Jani SH, Salleh N, Mohd Ali NA, et al.: Adapting Public-Private Partnership as Strategic Collaboration between Government and Philanthropy-Based Autism Spectrum Disorder Centre. International Journal of Academic Research in Business and Social Sciences. 2022; 12(1). Publisher Full Text\n\nNeik T, Lee LW, Low HM, et al.: Prevalence, diagnosis, treatment and research on autism spectrum disorders (ASD) in Singapore and Malaysia. International Journal of Special Education. 2014; 29: 1–10.\n\nOng JJ: Parental satisfaction and perception of progress in influencing the practice of complementary health approaches in children with autism: A cross sectional survey from Negeri Sembilan, Malaysia. BMC Complement. Altern. Med. 2019; 19(1): 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nParra Cardona JR, Domenech-Rodriguez M, Forgatch M, et al.: Culturally Adapting an Evidence-Based Parenting Intervention for Latino Immigrants: The Need to Integrate Fidelity and Cultural Relevance. Fam. Process. 2012; 51(1): 56–72. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrizant B, Wetherby A, Rydell P: Communication intervention issues for children with autism spectrum disorders.Wetherby M, Prizant BM, editors. Autism spectrum disorders - a transactional development perspective. Paul H. Brookes; 2000.\n\nReichow B: Overview of meta-analyses on early intensive behavioral intervention for young children with autism spectrum disorders. J. Autism Dev. Disord. 2012; 42(4): 512–520. PubMed Abstract \| Publisher Full Text\n\nRobins DL, Fein D, Barton M: Modified Checklist for Autism in Toddlers, Revised, with Follow-Up (M-CHAT-R/F) TM.2009. Reference Source\n\nRogers SJ, Yoder P, Estes A, et al.: A multisite randomized controlled trial comparing the effects of intervention intensity and intervention style on outcomes for young children with autism. J. Am. Acad. Child Adolesc. Psychiatry. 2021; 60(6): 710–722. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSandall SR, Hemmeter ML, Smith BJ, et al.: DEC recommended practices. A comprehensive guide for practical application in early intervention/early childhood special education. Division for Early Child-hood (DEC), Council for Exceptional Children; 2005.\n\nSchertz HH, Baker C, Hurwitz S, et al.: Principles of early intervention reflected in toddler research in autism spectrum disorders. Top. Early Child. Spec. Educ. 2011; 31(1): 4–21. Publisher Full Text\n\nSchreibman L, Dawson G, Stahmer AC, et al.: Naturalistic developmental behavioral interventions: Empirically validated treatments for autism spectrum disorder. J. Autism Dev. Disord. 2015; 45(8): 2411–2428. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShumway S, Wetherby AM: Communicative acts of children with autism spectrum disorders in the second year of life. J. Speech Lang. Hear. Res. 2009; 52(5): 1139–1156. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSolomon R, Necheles J, Ferch C, et al.: Pilot study of a parent training program for young children with autism. Autism. 2007; 11(3): 205–224. Publisher Full Text\n\nSoto S, Linas K, Jacobstein D, et al.: A review of cultural adaptations of screening tools for autism spectrum disorders. Autism. 2015; 19(6): 646–661. PubMed Abstract \| Publisher Full Text\n\nStrain PS, Schwartz IS, Barton EE: Providing interventions for young children with autism spectrum disorders: What we still need to accomplish. J. Early Interv. 2011; 33(4): 321–332. Publisher Full Text\n\nSullivan K, Stone WL, Dawson G: Potential neural mechanisms underlying the effectiveness of early intervention for children with autism spectrum disorder. Res. Dev. Disabil. 2014; 35(11): 2921–2932. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTiura M, Kim J, Detmers D, et al.: Predictors of longitudinal ABA treatment outcomes for children with autism: A growth curve analysis. Res. Dev. Disabil. 2017; 70: 185–197. PubMed Abstract \| Publisher Full Text\n\nVelazquez R, Nye C: Systematic review offers cautious support for positive effects from ABA-based early intervention programs for children with autism spectrum disorder. Evid. Based Commun. Assess. Interv. 2011; 5(2): 1–4. Publisher Full Text\n\nVismara LA, Rogers SJ: The Early Start Denver Model: A case study of an innovative practice. J. Early Interv. 2008; 31(1): 91–108. Publisher Full Text\n\nVivanti G, Dissanayake C: Outcome for children receiving the early start Denver model before and after 48 months. J. Autism Dev. Disord. 2016; 46(7): 2441–2449. Publisher Full Text\n\nWarren Z, McPheeters ML, Sathe N, et al.: A systematic review of early intensive intervention for autism spectrum disorders. Pediatrics. 2011; 127(5): e1303–e1311. Publisher Full Text\n\nWetherby AM, Guthrie W, Woods J, et al.: Parent-implemented social intervention for toddlers with autism: An RCT. Pediatrics. 2014; 134(6): 1084–1093. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXu Y, Yang J, Yao J, et al.: A pilot study of a culturally adapted early intervention for young children with autism spectrum disorders in China. J. Early Interv. 2018; 40(1): 52–68. Publisher Full Text\n\nYaacob WNW, Yaacob LH, Muhamad R, et al.: Behind the scenes of parents nurturing a child with autism: A qualitative study in Malaysia. Int. J. Environ. Res. Public Health. 2021; 18(16): 8532. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "284849", "date": "01 Jul 2024", "name": "Eleni Gkiolnta", "expertise": [ "Reviewer Expertise ASD", "autism", "autism treatment", "early intervention", "educational technology", "robotics", "assistive robotics", "assistive technology", "STEM", "AAC", "autism communication" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, this is a very interesting and well-written manuscript. The data provided are very sufficient in order to provide comprehensive results and conclusions and the statistical analysis is quite thorough. The only issue is that no sufficient description is given regarding the content of the intervention sessions. To be more specific, readers cannot be sure of what the activities comprising the sessions were, therefore any researcher cannot reproduce this research if no further details are given. Also, a detailed description of the content of the intervention sessions should be provided in order to avoid bias. Sufficient details of methods and analysis are partly provided, therefore they do not allow full reproducibility andÂ replication by others.Â Otherwise, the manuscript is worthy and is giving readers a comprehensive view about an innovative early intervention program for young children with autism.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-395
https://f1000research.com/articles/13-394/v1	26 Apr 24	{ "type": "Research Article", "title": "Efficacy of sweet orange peels (citrus sinensis l.) 0.1% extract cream on improvement of axillary postinflammatory hyperpigmentation", "authors": [ "Felicia Oei", "Imam Budi Putra", "Nelva Karmila Jusuf", "Imam Budi Putra", "Nelva Karmila Jusuf" ], "abstract": "Background Postinflammatory hyperpigmentation (PIH) is not harmful but can affect appearance and quality of life. It occurs due to increased melanin production after cutaneous injury or inflammation. Axillary hyperpigmentation, one of the commonly acquired hypermelanosis, raises concern, and treatment regarding this condition is still evolving. Sweet orange contains several components that can improve pigmentation through tyrosinase inhibition and antioxidant mechanisms. The objective was to determine the efficacy of sweet orange peel extract cream on axillary hyperpigmentation.\n\nMethods This quasi-experimental study is a pretest-posttest design on 32 subjects with axillary hyperpigmentation. Diagnosis is established through history taking and clinical evaluation. Evaluation of melanin index using Mexameter® MX18 was carried out at weeks 0, 2, 4, 6, and 8. Clinical evaluation improvement made using Physician Global Assessment. Side effects and satisfaction during the study are also recorded. The data is processed using the Friedman test, with p <0.05 considered significant.\n\nResults There was a statistically significant decrease in melanin index on axillary hyperpigmentation (p<0.01) after eight weeks of administration of 0.1% sweet orange peel extract cream. In this study, there were clinical improvements and no side effects in the subjects. All subjects were satisfied with the result of the application of 0.1% sweet orange peel extract cream.\n\nConclusions The use of 0.1% sweet orange peel extract cream can improve axillary postinflammatory hyperpigmentation.", "keywords": [ "postinflammatory hyperpigmentation", "axilla", "melanin index", "sweet orange peel", "Citrus sinensis L." ], "content": "Introduction\n\nThe trend of having even and bright skin was considered attractive and widely known as a sign of beauty and youth in several countries.1 Skin hyperpigmentation was usually a complaint, and 8.5% of dermatologic consultation was because of it. Hyperpigmentation is defined as an increasing accumulation and production of melanin or increasing in melanocytes amount.2 Axillae are one of the common areas to experience hyperpigmentation.3,4 Hyperpigmentation in the skin fold, such as the axilla, is known as acquired hyperpigmentation due to trauma and repeated irritation from hair plucking, shaving, the cleaning method, tight clothes, or the use of deodorant and antiperspirant.4,5\n\nCurrently, the treatment of axillary hyperpigmentation often does not give satisfactory results and becomes a challenge in its implementation. The target treatments for hyperpigmentation are photoprotection and using agents that can disrupt melanogenesis and reduce excessive melanin. Several therapies that have been introduced to treat hyperpigmentation include topical whitening agents, chemical peeling, oral agents, microdermabrasion, microneedle, and laser therapy.6,7\n\nExtract from plants as skin whitening has been used in traditional medicine in Indonesia. Orange was one of the most common fruits cultivated in Indonesia. Berastagi Highland located in North Sumatera, Indonesia was well known as the center of oranges commodity and sweet orange was a flagship product. Sweet orange (Citrus sinensis L.) has a chemical composition of ascorbic acid, vitamin E, vitamin A, and polyphenols. The whitening effect of sweet orange, one of which is the ascorbic acid, was due to the mechanism that decreases oxidized dopaquinone, suppression of NF-kß and TNF-α, and photoprotection.6,8 Sweet orange peel extract also contains components that have antioxidant, antiinflammation, and anti-tyrosinase effects. Tyrosinase was a key enzyme in melanogenesis. Its function is to catalyze a reaction in melanin biosynthesis from tyrosine in melanin. Nobiletin, one of the sweet orange peel components, is a tyrosinase inhibitor.8–10 Melanogenesis inhibition can also happen because sweet orange peel extract contains flavonoids.11 Yoshizaki, Hashizume and Masaki found that polymethoxyflavones extracted from orange peel can suppress the localization from tyrosinase to melanosome and simultaneously inhibition of melanogenesis due to organelle cell acidification, including melanosome.12,13 This study aimed to determine the efficacy of sweet orange peel extract cream on axillary hyperpigmentation.\n\n\nMethods\n\nThis study is a quasi-experimental study with a pretest–posttest design group carried out from August 2022 to December 2022 at the Department of Dermatology and Venereology, Prof. Dr. Chairuddin Panusunan Lubis, Universitas Sumatera Utara Hospital. All subjects had signed informed consent prior to participating in this study and consent for publication was obtained, which was conducted in accordance with the Declaration of Helsinki. This study was conducted after approval from the health research ethics committee No: 658/KEPK/USU/2022 on 25 July 2022 obtained from the University of North Sumatera Research Ethics Committee.\n\nSweet orange fruit is obtained from Brastagi Highland, North Sumatera, then the process of 0.1% sweet orange peel extract cream is carried out at the Medicinal Plant Research and Development Laboratory of Indonesian Herbal Traditional Medicine Association, Medan.\n\nThis study subjects were axillary hyperpigmentation patients, 32 of them were female, aged 18-35 years, who came to the outpatient clinic of the Department of Dermatology and Venereology, Prof. Dr. Chairuddin Panusunan Lubis, Universitas Sumatera Utara Hospital, Indonesia. All participants were evaluated through anamnesis and dermatological examination. Participants were omitted if they were pregnant or breastfeeding, had received topical care products containing retinoids and their derivatives, hydroquinone, azelaic acid, kojic acid, antioxidants, vitamin C, other depigmenting agents, had received oral products such as carotenoid, glutathione, melatonin or tranexamic acid, had received interventions such as chemical peeling, microneedle or laser within the past month. Patients were excluded from the study if they did not use the cream for three consecutive days and the total use of the cream was less than seven weeks.\n\nIn this study, subjects were asked to apply one fingertip unit of cream on each axilla every morning and night and evaluated every two weeks. The melanin index was assessed before and after using the 0.1% sweet orange peel extract cream, and clinical evaluation was assessed with Physician Global Assessment (PGA). In addition, this study evaluated side effects, including dry skin, desquamation, erythema, burning, and itching, and the participants’ satisfaction.\n\nAll data collected from weeks 0, 2, 4, 6, and 8 were analyzed using SPSS version 22.0 software. They were analyzed using the Shapiro-Wilk normality test. The Friedman test was used to compare the melanin index before and after the application of 0.1% sweet orange peel extract cream because the data were not normally distributed. A p-value <0.05 was considered significant.\n\n\nResults\n\nIn this study, all participants were females, and most were in the age range of 18-25 years (65.6%) (Table 1).26 The mean age of the subjects was 25.31 years, with the youngest at 19 and the oldest at 34. After the data were collected, the Shapiro-Wilk normality test was carried out, which showed that the data had an abnormal distribution, so it was continued with the Friedman test to assess the comparison of lesions before and after the application of 0.1% sweet orange peel extract cream. At the beginning of the study, the average value of the melanin index was 349.04±109.84 AU. After using sweet orange peel extract cream for eight weeks, a significant decrease in melanin index was found to be 253.06±96.36 AU. The p-value obtained through the Friedman test is <0.001 (Table 2).\n\n* p value using the Friedman test.\n\nPhysician Global Assessment (PGA) was carried out to evaluate the clinical improvement at the end of the study. It was scored as poor (0–25%), mild (26–50%), good (51-75%), or excellent (>75%). The majority of the subjects had mild improvement (68.8%), followed by good improvement (25%) (Table 3). In this study, no side effects were noted in all participants, and all were satisfied with the application of 0.1% sweet orange peel extract cream.\n\n\nDiscussion\n\nThe subjects in this study were all female, the majority aged 18-25 years. This study was in accordance with a study conducted by Castanedo-Cazares et al., which shown that the mean of subjects with axillary hyperpigmentation was 21.7±1.6 years.5 In a study by Jusuf reported that skin hypermelanosis conditions such as postinflammatory hyperpigmentation is a cosmetic complaint that can affect patients’ quality of life, and females are most likely to come and seek treatment.14\n\nThere has been no single therapy that is truly satisfactory in getting rid of axillary hyperpigmentation. This research is a preliminary study on sweet orange peel extract’s use to improve axillary hyperpigmentation. The result of this study indicates that 0.1% sweet orange peel extract cream can improve the pigmentation seen through decreasing in melanin index from 349.04 AU to 253.06 AU at the end of the study. Improvement of hyperpigmentation can occur due to several components from sweet orange peel extract.\n\nMelanin is an essential component in skin, eye and hair color, synthesized in melanosomes that transfer from melanocytes. Hyperactivity and abnormal synthesis in melanocytes, as well as melanin accumulation, can cause hyperpigmentation in the skin.15–17 Potential targets of skin depigmentation agents include melanocyte stimulation inhibitors, tyrosinase enzyme inhibitors, melanosome transfer inhibitors, and degradation of melanin formed in keratinocytes.18\n\nFlavonoids, a bioactive component in sweet orange peel, can act as a promising whitening agent through tyrosinase enzyme inhibition that controls melanin production.15,19 All flavonoids inhibit tyrosinase enzymes by their ability to chelate copper from active sites. Badria and el Gayyar also found that flavonoid contains a keto group that had potent tyrosinase inhibition activity. So that it can explain the similarity between the dihydroxyphenyl group in L-DOPA and the keto group in flavonoid.20 Hesperidin, a bioflavonoid in citrus peels, showed potent anti-tyrosinase activity in melanoma cell B16 that causes melanin synthesis inhibition without cytotoxicity.21 Yoshizaki, Hashizume and Masaki found that polymethoxyflavone extracted from orange peel can suppress the localization from tyrosinase to melanosome and simultaneously inhibit melanogenesis.13\n\nCellular oxidative stress was formed because of toxic hydrogen peroxide (H2O2) and reactive oxygen species (ROS) on the skin. As a result, ROS will accumulate and induce the melanogenesis process through interaction with the tyrosinase enzyme. Antioxidants’ role in controlling and minimizing the formation of free radicals in the skin by neutralizing, decreasing harmful radicals, and stimulating free radical degradation. The antioxidant also has the potential to improve hyperpigmentation by interaction with o-quinones, thus avoiding the oxidative polymerization of melanin intermediates or with copper at the active site of tyrosinase. In addition, antioxidant agents can regulate the signaling process by scavenging ROS in the skin.22\n\nAll study subjects did not experience side effects such as dry skin, desquamation, erythema, burning, or itching after eight weeks of using the 0.1% sweet orange (Citrus sinensis L.) peel extract cream. According to the current study, Dosoky and Setzer showed that sweet orange essential oil neither causes irritation nor sensitizing in the skin at an 8% concentration.23 In addition, there was noted clinical improvement, and all study subjects were satisfied with the pigmentary changes in axillary hyperpigmentation. Postinflammatory hyperpigmentation can cause emotional stress, so subjective evaluation of treatment efficacy is essential.24,25 From this result, we concluded that using a 0.1% sweet orange (Citrus sinensis L.) peel extract cream was safe, well tolerated, and provided a good satisfaction.\n\nThis study still has limitations, whereas the preliminary study cannot exclude confounding factors from study subjects. Nevertheless, the data in this study can be used as primary data for further study, and further study with a randomized controlled trial design is needed to further evaluate the efficacy of sweet orange peel extract against axillary hyperpigmentation.\n\n\nConclusion\n\nThe 0.1% sweet orange (Citrus sinensis L.) peel extract cream can improve pigmentation in axillary hyperpigmentation. This current study shows that sweet orange peel was effective and has the potential to be used as axillary hyperpigmentation therapy.\n\n\nEthics and consent\n\nThis study was conducted after approval from the health research ethics committee No: 658/KEPK/USU/2022 on 25 July 2022 obtained from the University of North Sumatera Research Ethics Committee. All subjects had signed informed consent prior to participating in this study and consent for publication was obtained, which was conducted in accordance with the Declaration of Helsinki.\n\n\nAuthor contributions\n\nAll authors contributed to the entire process of this study, from the preparation, data collection, and analysis, as well as drafting until the approval for publication of this manuscript.", "appendix": "Data availability\n\nZenodo: Data, Side effects and satisfaction. https://doi.org/10.5281/zenodo.10775090. 26\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe would like to express our gratitude to the Head of Cosmetic Division, Department of Dermatology and Venereology, Faculty of Medicine Universitas Sumatera Utara and to Prof. Dr. CPL Universitas Sumatera Utara Hospital.\n\n\nReferences\n\nSaade DS, Maymone MBC, De La Garza H, et al.: Trends in use of prescription skin lightening creams. Int. J. Environ. Res. Public Health. 2021; 18(11). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaufman BP, Aman T, Alexis AF: Postinflammatory Hyperpigmentation: Epidemiology, Clinical Presentation, Pathogenesis, and Treatment. Am. J. Clin. Dermatol. 2018; 19(4): 489–503. PubMed Abstract \| Publisher Full Text\n\nWardhani PH: Pilihan Terapi Hiperpigmentasi Pascainflamasi pada Kulit Berwarna (Treatment Options for Postinflammatory Hyperpigmentation in Color Skin). Berk Ilmu Kesehat Kulit dan Kelamin. 2016; 28: 1–8.\n\nRobredo IGC: Q-Switched 1064nm Nd: YAG Laser in Treating Axillary Hyperpigmentation in Filipino Women With Skin Types IV-V. J. Drugs Dermatol. 2020; 19(1): 66–69. PubMed Abstract \| Publisher Full Text\n\nCastanedo-Cazares JP, Lárraga-piñones G, Ehnis-pérez A, et al.: Topical niacinamide 4% and desonide 0.05% for treatment of axillary hyperpigmentation: a randomized, double-blind, placebo-controlled study. Clin. Cosmet. Investig. Dermatol. 2013; 6: 29–36. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCheng J, Vashi NA: Dermatoanthropology of Ethnic Skin and Hair. Dermatoanthropology Ethn Ski Hair. 2017; 417–436. Publisher Full Text\n\nMeys R: Skin pigmentation. Med (United Kingdom). 2017; 45(7): 438–443. Publisher Full Text\n\nRoska TP, Sahati S, Fitrah AD, et al.: Efek Sinergitas Ekstrak Kulit Jeruk (Citrus sinensis L) Pada Patch Bioselulosa Dalam Meningkatkan Penyembuhan Luka Bakar. J. Farm. Galen (Galenika J Pharmacy). 2018; 4(2): 87–92. Publisher Full Text\n\nWuttisin N, Boonmak J, Thaipitak V, et al.: Anti-tyrosinase activity of orange peel extract and cosmetic formulation. Int. Food Res. J. 2017; 24(5): 2128–2132. Corpus ID: 52231490.\n\nSingh AP, Kandpal JB, Sharma RK, et al.: Nobiletin a Biologically Active Phytoconstituent: Systematic Review. J. Biol. Act. Prod. Nat. 2021; 11(3): 204–211. Publisher Full Text\n\nAllgisna KN, Hindun S, Rantika N: Review: Comparison of Fruit Skin Extract as Anti-hyperpigmentation. J. Sains dan Kesehat. 2020; 3(2): 335–342. Publisher Full Text\n\nSasaki K, Yoshizaki F: Nobiletin as a tyrosinase inhibitor from the peel of Citrus fruit. Biol. Pharm. Bull. 2002; 25(6): 806–808. PubMed Abstract \| Publisher Full Text\n\nYoshizaki N, Hashizume R, Masaki H: A polymethoxyflavone mixture extracted from orange peels, mainly containing nobiletin, 3,3’,4’,5,6,7,8-heptamethoxyflavone and tangeretin, suppresses melanogenesis through the acidification of cell organelles, including melanosomes. J. Dermatol. Sci. 2017; 88(1): 78–84. PubMed Abstract \| Publisher Full Text\n\nJusuf NK: Pattern of pigmentation disorder in Cosmetic Dermatology Clinic H. Adam Malik General Hospital, Medan, 2012-2015. J. Gen. Dermatol. Venereol. Indones. 2017; 2(1): 1–6. Publisher Full Text\n\nAddi M, Elbouzidi A, Abid M, et al.: An Overview of Bioactive Flavonoids from Citrus Fruits. Appl. Sci. 2022; 12(1): 1–15. Publisher Full Text\n\nD’Alba L, Shawkey MD: Melanosomes: Biogenesis, properties, and evolution of an ancient organelle. Physiol. Rev. 2019; 99(1): 1–19. PubMed Abstract \| Publisher Full Text\n\nMaranduca MA, Branisteanu D, Serban DN, et al.: Synthesis and physiological implications of melanic pigments (review). Oncol. Lett. 2019; 17(5): 4183–4187. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNautiyal A, Wairkar S: Management of hyperpigmentation: Current treatments and emerging therapies. Pigment Cell Melanoma Res. 2021; 34(6): 1000–1014. PubMed Abstract \| Publisher Full Text\n\nEl-Nashar HAS, Gamal El-Din MI, Hritcu L, et al.: Insights on the inhibitory power of flavonoids on tyrosinase activity: A survey from 2016 to 2021. Molecules. 2021; 26(24): 1–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nParavez S, Kang M, Chung H-S, et al.: Naturally Occurring Tyrosinase Inhibitors: Mechanism and Applications in Skin Health, Cosmetics and Agriculture Industries. Phyther. Res. 2007; 21(9): 805–816. PubMed Abstract \| Publisher Full Text\n\nAli SA, Choudhary RK, Naaz I: Understanding the Challenges ofMelanogenesis: Key Role of Bioactive Compounds in the Treatment of Hyperpigmentory Disorders. J. Pigment. Disord. 2015; 2(11). Publisher Full Text\n\nKim H, Choi HR, Kim DS, et al.: Topical hypopigmenting agents for pigmentary disorders and their mechanisms of action. Ann. Dermatol. 2012; 24(1): 1–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDosoky NS, Setzer WN: Biological activities and safety of citrus spp. Essential oils. Int. J. Mol. Sci. 2018; 19(7): 1–25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoggenkamp D, Dlova N, Mann T, et al.: Effective reduction of post-inflammatory hyperpigmentation with the tyrosinase inhibitor isobutylamido-thiazolyl-resorcinol (Thiamidol). Int. J. Cosmet. Sci. 2021; 43(3): 292–301. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYadav A, Garg T, Mandal AK, et al.: Quality of life in patients with acquired pigmentation: An observational study. J. Cosmet. Dermatol. 2018; 17(6): 1293–1294. PubMed Abstract \| Publisher Full Text\n\nOei F: Data, Side effects and satisfaction. [Dataset]. Zenodo. 2024. Publisher Full Text" }	[ { "id": "277639", "date": "08 Jun 2024", "name": "Nomakhosi Mpofana", "expertise": [ "Reviewer Expertise Melasma", "QoL", "Lasers and Lights", "Skin rejuvenation", "Indigenous Knowledge." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nINTRODUCTION\nIt is not clear why the axillary hyperpigmentation is a concern/problem, the prevalence is not clear too.\n\nThe authors do acknowledge that currently, the treatment of axillary hyperpigmentation often does not give satisfactory results and becomes a challenge in its implementation, however they do not not explicitly explain the shortfalls or ineffectiveness of the current, cited, treatments.\n\nThe authors should briefly explain the science behind the PIH which includes inflammation as well as oxidation. Currently they only described the melanogenesis/tyrosinase process, as such there is a no clear link between the anti-oxidant and anti-inflammatory properties of of the orange peel used.\n\nAuthors conducted the clinical evaluation with with PGA, it is not clear how the melanin index and side effects will be measured and recorded.\n\nMETHODS\nIt is not clear how the sample size was decided/calculated. Please justify the enrolment of female participants and exclusion of the males. The application of \"apply one fingertip unit of cream\" is not a very accurate measurement tool. Please provide exact measures eg 5 ml.\n\nRESULTS\nThe melanin index before the treatment should be provided for a comparison. It would add value to the results to conduct a correlation analysis between the melanin index values and the PGA. The authors used PGA to evaluate the clinical improvement at the end of the study did they measure the baseline. It is challenging to make conclusive results as the authors have provided no baseline measurement data for comparison.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "297574", "date": "14 Aug 2024", "name": "Asha Thomas", "expertise": [ "Reviewer Expertise Phytochemical Research", "Natural Product Development" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nScientific names should be in italics. Explain in detail the role of tyrosinase in melanogenesis and how its inhibition will prevent hyperpigmentation. Please explain the drawback of current treatments. Please justify the advantage 0.1% sweet orange peel extract cream of over other available solutions. Add details about extraction procedure. Will you please add more details about the formulation of 0.1% sweet orange peel extract cream. Will you please justify why only female participants are included and exclusion of the males. Study limitations are not discussed. Study has not involved any standard for comparison, so it is difficult to draw conclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-394
https://f1000research.com/articles/12-104/v1	27 Jan 23	{ "type": "Review", "title": "Technological innovation for workload allocation in nursing care management: an integrative review", "authors": [ "Maria Alejandra Galiano", "Maria Elisa Moreno Fergusson", "William J. Guerrero", "Maria Francisca Muñóz", "Germán A. Ortiz Basto", "Juan Sebastián Cardenas Ramírez", "Maryory Guevara Lozano", "Ana Larraín Sundt", "Maria Alejandra Galiano", "Maria Elisa Moreno Fergusson", "Maria Francisca Muñóz", "Germán A. Ortiz Basto", "Juan Sebastián Cardenas Ramírez", "Maryory Guevara Lozano", "Ana Larraín Sundt" ], "abstract": "Background: Technology reduces the nursing workload, improve the quality care processes, patient's safety, and avoid staff burnout. Innovative technologies are disrupting healthcare systems by improving the efficiency of processes and management. There is a discussion on the benefits, challenges, and barriers of these technologies and considering human factors of nursing management. Methods: To analyse the nursing workload models, the predictors of nursing burnout and outcomes, the new technologies and its acceptance for nursing care management based on the literature. An integrative literature review is performed. Scopus, Scielo, PUBMED, and CINALH databases were searched to perform an integrative review following PRISMA guidelines. Articles published from January 2016 to December 2020 were included. Quality appraisal was performed using the Crowe Critical Appraisal Tool version 1.4 (CCAT). Two reviewers independently examined the title and abstract for eligibility according to the inclusion and exclusion criteria. Quality appraisal was performed using the Crowe Critical Appraisal Tool version 1.4 (CCAT). Results: Initially 2,818 articles were potentially relevant. After following the PRISMA Guidelines, 35 studies were included in the review. Four themes appeared: Nursing workload models; Predictors of nursing burnout and outcomes; Information technologies and technological means for management; Technology acceptance. Conclusions: Technology has the potential to improve care management by estimating nurse workload in ICUs and non-critical units, but scientific evidence is more detailed in the former type of services. The literature provides insights about the factors that factors and the barriers that promote the technology acceptance and usability. We did not find studies comparing technologies and no scientific evidence proving improvements in care.", "keywords": [ "Health Information Management", "Nursing Care Management", "Workload", "Personnel Staffing", "Scheduling Information Systems" ], "content": "Introduction\n\nThe nursing staff contribution is essential to guarantee quality and access to health services, as well as the outcomes of care for patients and their families. New technologies should support nursing management and decrease workload to meet the needs of the patients. This aspect is relevant since nursing care is essential for the patient recovery and safety (Moreno-Monsiváis et al. 2015).\n\nAccording to the World Health Organization, there is a relationship between the nursing workload, the morbidity, and mortality of hospitalized patients (Ball et al., 2018) and after discharged (Kim et al., 2020). Nevertheless, the evidence is not strong to determine the best nurse-to-patient ratio and the effects on the nursing workload and patient outcomes (Coster et al., 2018).\n\nThe nursing workload is the amount of time, physical and cognitive effort needed to provide nursing care, in addition to activities related to service management and professional development (Pedroso et al., 2020). Excessive nursing workload goes against the values of humanization of care, patient outcomes, patient safety (Arango et al., 2015), quality of care (Romero-Massa et al., 2011), omitted care (Moreno-Monsiváis et al., 2015) and nurses’ health (Harvey et al., 2020). There is interest in creating technology to integrate scientific evidence and nursing expertise to reveal the relationship between nurse workload, burnout, and care quality (Farid et al., 2020). Thus, an interdisciplinary research team, including nurses and engineers, working together is required to understand this relationship.\n\nThe aim was to analyse the nursing workload models, the predictors of nursing burnout and outcomes, the new technologies and its acceptance for nursing care management. The following research questions (RQ) were addressed:\n\n• How to calculate the nursing workload referred on the literature?\n\n• What approaches are considered for the nursing workload?\n\n• What factors influence nursing care management technology acceptance by nursing professionals?\n\n\nMethods\n\nAn integrative literature review was performed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Studies were retrieved from SCOPUS, Scielo, PUBMED, and CINAHL in January 2021. The search strategy was: (“analytics” OR “operations research” OR digital* OR “IT” OR technolog*) AND (“nursing workload” OR “nurse-patient ratio” OR “nursing workforce planning” OR “nursing algorithm” OR “nursing personnel staffing and scheduling” OR “nursing staff”)). Inclusion criteria considered studies published in full text in English, Spanish or Portuguese classified as scientific articles or reviews, in the areas of nursing, medicine, social sciences, engineering, published between January 2016 and December 2020. This date range was considered to focus on the recent technologies. Articles related with technology that didn’t analyze the impact on nursing workload or didn’t present technologies were excluded.\n\nFor all research, this must include a final section including details of ethical approval, informed consent and, where relevant registration.\n\nInitially 2,818 articles were potentially relevant, of these 21 that were duplicates were eliminated and 129 were discarded by automation tools because they didn’t meet the inclusion criteria. In the second phase, the titles of 2668 articles were screened and 2486 were excluded since they didn’t meet the inclusion criteria. Later, the abstracts of 182 articles were analyzed. In the third phase, two independent reviewers read the full texts and discarded 96 articles because they didn’t contribute to the RQ and 46 because they obtained a low score in the CCAT. Ultimately, 35 studies were included (Figure 1).\n\nQuality review of each article was independently reviewed by two members of the research team/authors using the CCAT, that has shown to have high reliability to rate research papers (Crowe et al., 2011). This tool is divided into eight categories and 22 items; each category receives a score on a 6-point scale from 0 (the lowest score) to 5. The total score is expressed as a percentage, and we arbitrarily considered acceptable a score above 60%. When there were differences in the quality assessment of an article, team consensus was achieved by comparing the arguments and evidence.\n\nData extraction was performed identifying the purpose, the design, participants and context of the study, the type of information collected, and the results. The interdisciplinary work between engineers and nurses made it possible to resolve doubts about technological and nursing concepts. For data synthesis, we performed an inductive content analysis. The information was collected in our database, and then grouped into categories that responded the RQ.\n\n\nResults\n\n35 studies from 18 countries were included, 18 observational studies, two quasi-experimental, five qualitative, three mixed methods, four literature reviews and three project evaluations. 57.1% were assessed as high quality, 42.9% as medium quality (Table 1).\n\nThe studies were classified into four categories: 1. Nursing workload models; 2. Predictors of nursing burnout and outcomes; 3. Information technologies and technological means for management; 4. Technology acceptance. Figure 2 presents a concept map of the categories discussed in the results.\n\n\n\n- Nursing workload models\n\nThe challenge for workload estimation and prediction systems is having adequate information about the time and effort needed for nursing care activities, considering the interactions and iterations of the day-to-day care process, in physical, cognitive, organizational, and emotional dimensions (Redley et al., 2020). The variability in the patient care process usually has significant skewness. There are methodologies for estimating nursing care requirements, which are classified into those based on expert opinion, benchmarking, nurse-patient relationship, patient prototyping, multifactorial indicators, and task time-based approaches (Griffiths et al., 2020).\n\nThere is literature about nurse-to-patient ratios, but the validity and reliability of the studies is weak (Griffiths et al., 2020). In practice, legislation on minimum nurse staffing levels varies. In California (USA), law 394 of 1999 stipulates a 1:6 ratio. In Australia, the Safe Patient Care Act 2016 stipulates a 1:4 ratio. In Queensland, the daytime ratio is 1:4, and nighttime 1:7. In Wales (United Kingdom) the law stipulates a daytime ratio 1:5, and nighttime 1:7. Other countries, such as Colombia (South America), do not have legislation. The methodological proposals on how to calculate the nursing care requirements, nurse staffing, and skill mix, are based on local observations, which don’t allow generalization.\n\nLow staffing levels negatively affect safety indicators and staff performance (Simonetti et al., 2020), but estimating the nursing workload, considering emergent care, for decision making, is still an unsolved challenge (Griffiths et al., 2020). There are no systems that estimate workload beyond ad hoc methodologies, based on average measurements that ignore the variability. The most currently used systems are:\n\n• GRASP (Grace-Reynolds Application and Study of PETO) (Clark & Poland, 1976).\n\n• TOSS (Time Oriented Score System dedicated to intensive care patients) (Italian Multicenter Group of ICU Research, 1991).\n\n• NAS (Nursing Activities Score dedicated to intensive care patients) (Miranda et al., 2003).\n\n• The Safer Nursing Care Tool SNCT (The Shelford Group, 2014).\n\n• RAFAELA Patient Classification System including the Oulu Patient Classification instrument and the Professional Assessment of Optimal Nursing Care Intensity Level (PAONCIL) (Aschan et al., 2009).\n\n• Safecare by Allocate Software.\n\nComparisons of these systems show significant differences in the results (Griffiths et al., 2020), and there is no evidence that one outperforms the others. In addition, the professional judgement-based approaches are popular and relatively reliable.\n\nCommercial software computes staffing levels, coordinates nursing shifts, and plans nursing activities in case of unexpected staff absences. Tuominen et al. (2020) show that such tools reduce operating costs, the time required by nurse managers during the rescheduling process, the number of understaffed shifts, and unexpected changes in shift assignments.\n\nThe impact of technology for predicting nurse workload and deciding optimal staffing levels includes factors such as quality of care, patient safety, staff turnover and satisfaction, and process efficiency. Understanding nurses work is essential to assessing how technologies contribute to quality of care (Redley et al., 2020). There has been insufficient discussion of how technologies can be used to correlate operational cost with quality of care (Griffiths et al., 2020).\n\n- Predictors of nursing burnout and outcomes\n\nPatient and nursing staff outcomes are affected by nursing burnout and workload, which is significantly higher in ICUs than in other units (Youn et al., 2020). Burnout is a problem that originates in individuals and organizations (Maslach & Leiter, 2017). High nursing workload and poor skill mix are correlated with higher levels of burnout (Assaye et al., 2020; Simonetti et al., 2020), as does a poor work environment (Pekince & Aslan, 2020). In turn, burnout is associated with lower patient safety and omitted patient care (Dall’Ora et al., 2020).\n\nHigh nurse workload is associated with higher rates of mortality (Assaye et al., 2020; Aiken et al., 2021), hospital-acquired infections, pressure ulcers, medication administration errors (de Oliveira et al., 2016; Kang et al., 2016), falls (Carlesi et al., 2017), treatment dropout (Assaye et al., 2020), increased length of stay (Magalhães et al., 2017) and readmissions (Assaye et al., 2020; Aiken et al., 2021). It is also related to needlestick injuries, intent to leave, and absenteeism (Assaye et al., 2020).\n\nHarris et al. (2018) found a correlation between technology use and nursing burnout. The study showed that nurses experienced stress, burnout, and frustration with the use of EMRs and they reported insufficient amount of time for documentation.\n\nThe most studied technologies in ICUs (intensive care unit) were electronic medical records (EMR) and electronic medication management (Redley et al., 2020). Nursing-specific information systems, general computer, communication technologies and electronic data analysis being less often studied. Time savings are proven with the use of technology, but the impact on clinical decision making, interpersonal relationships, and work stress that underpin nursing care quality is unproven with respect to direct benefits. These systems could fail to record legitimate reasons for missing data, which can reduce patient safety (Hope et al., 2019).\n\n- Information technologies and technological means for management\n\nHuman and compassionate relationship between patients and nurses requires a meticulous synchronization between patients, healthcare staff, suppliers, processes, technologies, and information. The studies show that information technologies (IT) and technological means can support nursing care (Vorakulpipat et al., 2019; Zhou et al., 2019).\n\nIT include EMR and systems for: online data input, tracking patients, detect changes in the patient condition and workload reallocation, trace patient’s calls, hands-free communication between nurses, detecting falls, barcode technologies for medicine management, data mining on nursing flows, among others (Massarweh et al., 2017; Respicio et al., 2018; Vorakulpipat et al., 2019; Yu et al., 2019; Zhou et al., 2019; Moon, 2019).\n\nFor effective IT implementation in nursing, change management and communication are determinants (Giraldo et al., 2018) as well as technology skills training (Farzandipour, 2020). It’s also recommended to follow workflows, multiplicity of task and patient care plans (Vorakulpipat et al., 2019).\n\nCurrent technology to assess the nursing workload doesn’t capture the complexity or quality of care, and doesn’t recognize the concurrent, iterative, and interrelated nature of cognitive processes and activities in nursing. Therefore, there is a gap in the literature on how technology affects the quality of nursing care and how to measure it (Redley et al., 2020).\n\nThe patient’s condition has a significant effect on the workload (Sato et al., 2016). The development of early warning systems for patient deterioration (systolic blood pressure, pulse, respiratory rate, and oxygen saturation), using analytics, shows a significant decrease in nursing care time (Mau et al., 2019). These findings could be used to build a model for staffing (Leary et al., 2016).\n\n- Technology acceptance\n\nThe factors that influence technology acceptance are the perceive usefulness, the ease-of-use (Berg et al., 2017; Holden et al., 2016), and the participation of nurses in its design (Redley et al., 2019; Pendon et al., 2020). The human and organizational dimensions influence acceptance more than the technological dimensions (Handayani et al., 2018). The use of technology is beneficial when it promotes productivity and nurses’ empowerment, patient safety (Beaney et al., 2019), and quality of care (Higgins et al., 2017). Also, there is a positive correlation between the perception of usefulness and ease-of-use of EMR, the scanner to record the medication administration, and the use of lifts to mobilize patients and nurses’ technology acceptance (Tubaishat, 2018). These technologies contribute to reducing nursing staff fatigue (Steege & Dykstra, 2016) and nurses’ stress, while increasing their ability to focus on patient care (Ozan & Duman, 2020).\n\nTubaishat (2018) and Zhou et al. (2019) found that nurses age, sex, experience level and willingness to use the technology, are moderating variables of technology usage behavior, and predictors of perceived usability of EMR. On the other hand, the interface design of software functions plays a crucial role in technology implementation (Tu et al., 2018).\n\nIn contrast, the lack of confidence by professionals, past experiences, heavy workloads, and the time needed to learn are barriers to use technology (Wood et al., 2019). Additionally, nursing staff tend to use “informal workarounds” to deal with exceptional situations in administrative processes that have technology. These practices are a risk for patient safety (van der Veen et al., 2020) and information reliability.\n\n\nDiscussion\n\nTechnology in health services has benefits for streamlining processes, improving the quality of care, improving communication by supplying real-time information related to patient management and having data for decision making, process evaluation and results. The implementation success depends on the acceptance of technology.\n\nNurses have significant interaction with technology to monitor and manage patient care. Most studies look at the interaction of ICU nurses, but the technology requirement should extend to all health services, at all levels of complexity. Hence, an essential aspect in the implementation of technology is to enhance its acceptance (Phillips, 2019).\n\nIT and care management systems in nursing should allow effective planning of nursing workload. These tools should promote patient safety, quality of care, and staff satisfaction. This is achieved when technology allows staff to spend more time with the patient and less time doing administrative processes. Although the usefulness of technology for nursing practice and clinical decision making has been demonstrated, the study on the impact of these is incipient and there is no evidence on the best way to plan workload allocation in nursing (Griffiths et al., 2020).\n\nThere are opportunities for research in this topic because the conclusions in the literature are contradictory. While some studies conclude that technology can increase staff productivity, empowerment, and improve nursing care outcomes, other’s show that technology can increase nursing staff stress and burnout. In addition, it is unknown how these technologies contribute to promote compassionate nursing care.\n\nFurther, the literature recognizes that studies analyzing the effect of technology use in nursing care is not free of bias (Redley et al., 2020). In these cases, although observational practices do not allow us to see cause-effect relationships, it is feasible to think of methodologies that resolve these questions (Griffiths et al., 2020).\n\nMost of the software is limited because they don’t use real-time information. Instead, they work under the assumption that a sample is sufficient to generalize the needs of the patient population in the future. Furthermore, these solutions assume that once the contracted staffing level has been found, a fixed nurse-to-patient ratio and fixed number of hours will satisfy nursing care requirements (Griffiths et al., 2020). The strongest assumption relies on average care requirement times and allocating the load assuming that individual variations can be accommodated (Griffiths et al., 2020), ignoring the staff experience levels. Further, information systems should consider the scientific evidence showing that understaffing, low levels of skilled staffing, burnout, and high levels of intent to quit negatively affect clinical outcomes and increase turnover costs (Simonetti et al., 2020). Simultaneously, user-friendly systems are needed to allow nurse managers to make better decisions quickly and efficiently without creating staff burnout and stress (Harris et al., 2018).\n\nThe discipline of operational research techniques has proposed techniques to optimize staffing decisions using mathematical models or computer simulations, known as the “nurse rostering problem” and how to reassign staff to units with high demand. These algorithms have been able to prove that allocation based on averages may not be best in the face of variability in patient requirements and that this variability usually means more staffing to meet peak demand. However, how to calculate workload has not been discussed in depth (Griffiths et al., 2020), and how to use IT to estimate and predict workload including all the physical, cognitive, organizational, and emotional dimensions still is a major unsolved question.\n\nFinally, in this research we have not taken into consideration sex and gender differences in the results since the reviewed papers do not clearly conclude on how the associated factors and barriers that promote the technology acceptance and usability is different for different sex and gender.\n\nDespite having a rigorous protocol for identifying scientific articles, there are few studies performed in non-critical services. The studies found have heterogeneous methodologies, which made it difficult to compare the evidence in the studies.\n\n\nConclusions\n\nBased on the literature analysis, we conclude that IT has the potential to improve care management. There are several technological platforms that propose solutions to manage nurse workload and shift management. Further, the existing models use approaches based on expert opinion, benchmarking, nurse-patient relationship, patient prototyping, multifactorial indicators, and approaches based on task-based time requirements. These approaches differ importantly in how workload is assigned and the variables that are considered. It is equally important to analyze the technology and nursing workload in ICUs and non-critical units, but scientific evidence is more detailed in the former type of services.\n\nThe factors that promote the technology acceptance and usability of these models include the satisfaction for an increased time for direct care, a perception of improved patient safety, quality of care, and reduction of workload and staff burnout. The identified barriers for these technologies are the lack of knowledge of the technological tools, long times needed for their use, and low perceived ease of use. Thus, it is important to involve nursing professionals in the technological design process.\n\nOur study reveals that most of the models and technologies are focused on intensive care units, and few studies for other types of care units. Also, all the considered studies are performed in developed economies, none of them are performed in economies in transition or developing economies. In addition, there is no scientific evidence to compare the technologies between each other and we found no scientific evidence showing improvements in care processes provided after using them. Further, with the proliferation of nursing workforce management systems, a review to evaluate efficacy is warranted. One key contribution of this study is that the conclusions are obtained from the analysis of a multidisciplinary research team, including nurses with expertise in management and engineers with expertise in healthcare systems.\n\n\nSummary\n\n\n\n• Evidence shows that the patient condition modifies the nursing workload. There is a relationship between the nursing workload, the morbidity, and mortality of hospitalized patients.\n\n• Excessive nursing workload goes against the values of humanization of care, patient outcomes, patient safety, and quality of care.\n\n• There is interest in creating technology to integrate scientific evidence and nursing expertise to reveal the relationship between nurse workload, burnout, and care quality.\n\n\n\n• Current information technology for managing nursing workload partially contemplates evidence on nursing workload models, the predictors of nursing burnout and outcomes, and the theories of acceptance of technology. Existing technological platforms for nursing care management that propose solutions to manage nurse workload and shift management, each with different methodologies.\n\n• Further, these technologies need to assess the nursing workload to capture the complexity or quality of care, and to recognize the concurrent, iterative, and interrelated nature of cognitive processes and activities in nursing. Evidence is needed to compare technologies and provide scientific evidence proving improvements in care.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nOSF: PRISMA checklist for “Technological innovation for workload allocation in nursing care management: an integrative review”, https://doi.org/10.17605/OSF.IO/JXFYK\n\nPRISMA checklist is available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Universal (CC0 1.0) Public Domain Dedication).\n\n\nAcknowledgements\n\nThe authors thank Clínica Universidad de Los Andes (Chile) for the support to the project. Also, we thank Professor Beatriz Sanchez-Herrera for the support provided to the project.\n\n\nReferences\n\nAiken LH, Simonetti M, Sloane DM, et al.: Hospital nurse staffing and patient outcomes in Chile: a multilevel cross-sectional study. Lancet Glob. Health. 2021; 9(8): e1145–e1153. PubMed Abstract \| Publisher Full Text\n\nArango GL, Peña B, Vega Y: Relación de la asignación de personal de enfermería con indicadores de resultado de la calidad de la atención en unidades de cuidados intensivos de adultos. Aquichan. 2015; 15(1): 90–104. Publisher Full Text\n\nAschan H, Junttila K, Fagerstrôm L, et al.:RAFAELA™ patient classification system as a tool for management. Connecting Health and Humans. IOS Press;2009; (pp. 478–482).\n\nAssaye AM, Wiechula R, Schultz TJ, et al.: The impact of nurse staffing on patient and nurse workforce outcomes in acute care settings in low-and middle-income countries: a quantitative systematic review. JBI Evidence Synthesis. 2020.\n\nBall JE, Bruyneel L, Aiken LH, et al.: Post-operative mortality missed care and nurse staffing in nine countries: a cross-sectional study. Int. J. Nurs. Stud. 2018; 78: 10–15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeaney P, Hatfield R, Hughes A, et al.: Creating digitally ready nurses in general practice. Nurs. Manag. 2019; 26(3): 27–35. PubMed Abstract \| Publisher Full Text\n\nBerg GM, LoCurto J, Lippoldt D: Stages of adoption concern and technology acceptance in a critical care nursing unit. J. Nurs. Adm. 2017; 47(9): 441–447. Publisher Full Text\n\nCarlesi KC, Padilha KG, Toffoletto MC, et al.: Patient Safety Incidents and Nursing Workload. Rev. Lat. Am. Enfermagem. 2017; 25: e2841. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nClark EL, Poland M: GRASP: Grace-Reynolds application and study of PETO. Morganton, N.C:Kate B. Reynolds Health Care Trust to Grace Hospital;1976.\n\nCoster S, Watkins M, Norman IJ: What is the impact of professional nursing on patients’ outcomes globally? An overview of research evidence. Int. J. Nurs. Stud. 2018; 78: 76–83. PubMed Abstract \| Publisher Full Text\n\nCrowe M, Sheppard L, Campbell A: Comparison of the effects of using the Crowe Critical Appraisal Tool versus informal appraisal in assessing health research: a randomised trial. Int. J. Evid. Based Healthc. 2011; 9(4): 444–449. PubMed Abstract \| Publisher Full Text\n\nDall’Ora C, Ball J, Reinius M, et al.: Burnout in nursing: a theoretical review. Hum. Resour. Health. 2020; 18: 1–17. Publisher Full Text\n\nde Oliveira AC , Garcia PC, Nogueira L d S: Nursing workload and occurrence of adverse events in intensive care: A systematic review. Rev. Esc. Enferm. 2016; 50: 683–694. PubMed Abstract \| Publisher Full Text\n\nFarid M, Purdy N, Neumann WP: Using system dynamics modelling to show the effect of nurse workload on nurses’ health and quality of care. Ergonomics. 2020; 63: 952–964. PubMed Abstract \| Publisher Full Text\n\nFarzandipour M: Self-assessment of nursing informatics competencies in hospitals. Online J. Nurs. Inform. 2020; 24(2).\n\nGiraldo L, Schachner B, Luna D, et al.:Exploring nurses’ perceptions and expectations toward a BCMA implementation using a mobile app and workstations as a change management strategy. Nursing Informatics 2018. IOS Press;2018; (pp. 134–138).\n\nGriffiths P, Saville C, Ball J, et al.: Nursing workload, nurse staffing methodologies and tools: A systematic scoping review and discussion. Int. J. Nurs. Stud. 2020; 103: 103487. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHandayani PW, Hidayanto AN, Pinem AA, et al.: Hospital information system user acceptance factors: User group perspectives. Inform. Health Soc. Care. 2018; 43(1): 84–107. PubMed Abstract \| Publisher Full Text\n\nHarris DA, Haskell J, Cooper E, et al.: Estimating the association between burnout and electronic health record-related stress among advanced practice registered nurses. Appl. Nurs. Res. 2018; 43: 36–41. PubMed Abstract \| Publisher Full Text\n\nHarvey C, Thompson S, Otis E, et al.: Nurses’ views on workload, care rationing and work environments. J. Nurs. Manag. 2020; 28(4): 912–918. PubMed Abstract \| Publisher Full Text\n\nHiggins LW, Shovel JA, Bilderback AL, et al.: Hospital Nurses’ Work Activity in a Technology-Rich Environment. J. Nurs. Care Qual. 2017; 32(3): 208–217. PubMed Abstract \| Publisher Full Text\n\nHolden RJ, Asan O, Wozniak EM, et al.: Nurses’ perceptions, acceptance, and use of a novel in-room pediatric ICU technology: testing an expanded technology acceptance model. BMC Med. Inform. Decis. Mak. 2016; 16(1): 110–145. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHope J, Griffiths P, Schmidt PE, et al.: Impact of using data from electronic protocols in nursing performance management: A qualitative interview study. J. Nurs. Manag. 2019; 27(8): 1682–1690.\n\nItalian Multicenter Group of ICU Research (GIRTI)., Iapichino, G: Time oriented score system (TOSS): A method for direct and quantitative assessment of nursing workload for ICU patients. Intensive Care Med. 1991; 17: 340–345. Publisher Full Text\n\nKang JH, Kim CW, Lee SY: Nurse-Perceived Patient Adverse Events depend on Nursing Workload. Osong. Public Health Res. Perspect. 2016; 7: 56–62. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim Y, Kim HY, Cho E: Association between the bed-to-nurse ratio and 30-day post-discharge mortality in patients undergoing surgery: a cross-sectional analysis using Korean administrative data. BMC Nurs. 2020; 19: 17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeary A, Cook R, Jones S, et al.: Mining routinely collected acute data to reveal non-linear relationships between nurse staffing levels and outcomes. BMJ Open. 2016; 6(12): e011177. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMagalhães AMMD, Costa DGD, Riboldi CDO, et al.: Association between workload of the nursing staff and patient safety outcomes. Rev. Esc. Enferm. U.S.P. 2017; 51.\n\nMaslach C, Leiter MP: New insights into burnout and health care: Strategies for improving civility and alleviating burnout. Med. Teach. 2017; 39(2): 160–163. PubMed Abstract \| Publisher Full Text\n\nMassarweh LJ, Tidyman T, Luu DH: Starting the Shift Out Right: The Electronic eAssignment Sheet Using Clinical Decision Support in a Quality Improvement Project. Nurs. Econ. 2017; 35(4): 194–200.\n\nMau KA, Fink S, Hicks B, et al.: Advanced technology leads to earlier intervention for clinical deterioration on medical/surgical units. Appl. Nurs. Res. 2019; 49: 1–4. PubMed Abstract \| Publisher Full Text\n\nMiranda DR, Nap R, de Rijk A , et al.: Nursing activities score. Crit. Care Med. 2003; 31(2): 374–382. Publisher Full Text\n\nMoon WH: Development and evaluation of NRMIS (Nursing Resources Management Information System) for managing healthcare resources. Technol. Health Care. 2019; 27(5): 557–565. PubMed Abstract \| Publisher Full Text\n\nMoreno-Monsiváis MG, Moreno-Rodríguez C, Interial-Guzmán MG: Missed nursing care in hospitalized patients. Aquichan. 2015; 15(3): 318–338. Publisher Full Text\n\nOzan Y, Duman M: Nurses’ Perceptions Regarding the Use of Technological Devices in Nursing Care Practices. Int. J. Caring Sci. 2020; 13(2): 901–908.\n\nPedroso TG, Pedrão LJ, Perroca MG: Approaches to workload in psychiatric and mental health nursing. Rev. Bras. Enferm. 2020; 73: e20190620. PubMed Abstract \| Publisher Full Text\n\nPekince H, Aslan H: Determining the Work-Related Strain Levels of Nurses and Influencing Factors. Int. J. Caring Sci. 2020; 13(1): 135–142.\n\nPendon RC, Bitencourt JV d OV, Haag FB, et al.: Evaluation of care technology applied to the nursing process in the light of best practices. Rev Rene. 2020; 21: e44420. Publisher Full Text\n\nPhillips J: Complex Patient Care Technology. AACN Adv. Crit. Care. 2019; 30(1): 23–24. Publisher Full Text\n\nRedley B, Douglas T, Botti M: Methods used to examine technology in relation to the quality of nursing work in acute care: A systematic integrative review. J. Clin. Nurs. 2020; 29(9-10): 1477–1487. PubMed Abstract \| Publisher Full Text\n\nRedley B, Richardson B, Peel C, et al.: Co-development of “BRAIN-TRK”: Qualitative examination of acceptability, usability, and feasibility of an App to support nurses’ care for patients with behavioural and psychological symptoms of neurocognitive disorders in hospital. J. Clin. Nurs. 2019; 28(15-16): 2868–2879. PubMed Abstract \| Publisher Full Text\n\nRespicio A, Moz M, Pato MV, et al.: A computational application for multi-skill nurse staffing in hospital units. BMC Med. Inform. Decis. Mak. 2018; 18(53): 53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRomero-Massa E, Lorduy-Bolívar JP, Pájaro-Melgar C, et al.: Relación entre la carga laboral de enfermería y la gravedad del paciente en unidades de cuidado intensivo de adultos. Aquichan. 2011; 11(2): 173–186. Publisher Full Text\n\nSato K, Yamashita K, Goshima M, et al.: An Analysis of the Factor Model on the Workload of Nursing Staff Using a Hospital Management Tool. Nursing Informatics. 2016; 58–62.\n\nSimonetti M, Soto P, Galiano A, et al.: Dotaciones, skillmix e indicadores laborales de enfermería en Hospitales Públicos chilenos. Rev. Med. Chil. 2020; 148(10): 1444–1451. PubMed Abstract \| Publisher Full Text\n\nSteege LM, Dykstra JG: A macroergonomic perspective on fatigue and coping in the hospital nurse work system. Appl. Ergon. 2016; 54: 19–26. PubMed Abstract \| Publisher Full Text\n\nThe Shelford Group: Safer nursing care tool implementation resource pack.2014.\n\nTu MH, Chang P, Lee YL: Avoiding obsolescence in mobile health: Experiences in designing a mobile support system for complicated documentation at long-term care facilities. Comput. Inform. Nurs. 2018; 36(10): 501–506. Publisher Full Text\n\nTubaishat A: Perceived usefulness and perceived ease of use of electronic health records among nurses: Application of Technology Acceptance Model. Inform. Health Soc. Care. 2018; 43(4): 379–389. PubMed Abstract \| Publisher Full Text\n\nTuominen O, Lundgren-Laine H, Teperi S, et al.: Comparing the two techniques for nursing staff rescheduling to streamline nurse managers’ daily work in finland. CIN. Comput. Inform. Nurs. 2020; 38(3): 148–156. PubMed Abstract \| Publisher Full Text\n\nvan der Veen W , Taxis K, Wouters H, et al.: Factors associated with workarounds in barcode-assisted medication administration in hospitals. J. Clin. Nurs. 2020; 29(13-14): 2239–2250. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVorakulpipat C, Rattanalerdnusorn E, Sirapaisan S, et al.: A mobile-based patient-centric passive system for guiding patients through the hospital workflow: design and development. JMIR Mhealth Uhealth. 2019; 7(7): e14779. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWood C, Chaboyer W, Carr P: How do nurses use early warning scoring systems to detect and act on patient deterioration to ensure patient safety? A scoping review. Int. J. Nurs. Stud. 2019; 94: 166–178. PubMed Abstract \| Publisher Full Text\n\nYoun SH, Son H, Kim J, et al.: Trauma Versus Nontrauma Intensive Care Unit Nursing: A Workload Comparison. J. Trauma Nurs. 2020; 27: 346–350. PubMed Abstract \| Publisher Full Text\n\nYu M-H, Lee T-T, Mills ME: The Effect of Barcode Technology Use on Pathology Specimen Labeling Errors. AORN J. 2019; 109: 183–191. PubMed Abstract \| Publisher Full Text\n\nZhou LL, Owusu-Marfo J, Antwi HA, et al.: Assessment of the social influence and facilitating conditions that support nurses’ adoption of hospital electronic information management systems (HEIMS) in Ghana using the unified theory of acceptance and use of technology (UTAUT) model. BMC Med. Inform. Decis. Mak. 2019; 19(1): 1–9. Publisher Full Text" }	[ { "id": "178447", "date": "12 Jul 2023", "name": "Lorena Chaparro-Diaz", "expertise": [ "Reviewer Expertise Chronic illness", "Research", "Caregiver", "Care Policy", "Nursing", "Qualitative research", "Nursing care", "Education", "Health Policy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract This article is an integrated review of the scientific literature produced in 3 languages (Spanish, English, and Portuguese) that sought to analyze nursing workload models, predictors of overload and outcomes, and new technologies in nursing care management. The authors used as a methodological framework PRISMA elements that allowed them to analyze 35 articles in full text, was conducted by an interdisciplinary team integrating nurses and engineers, to understand the phenomenon adequately. The results showed the potential of technology in care management, but there is a lack of systems and validated technology that would allow usable nursing workload models. Barriers to the use of technology that could be associated with work overload were identified; however, there is more evidence of the effects of burnout on patient outcomes and adverse events. Their findings are located more in critical care settings.\nStrengths Among the strengths of the review is that it contributes to a need for summative evidence on aspects of nursing care management that had not been identified as influential, such as nursing workload. It recognizes current elements such as the use of technologies for nursing care and concludes that nurses need to work collaboratively with software programmers for the development of new technologies.\nAnother important aspect is the identification of at least some existing systems, especially in critical care, which could be taken up again to compare their use in future studies.\n\nThe review also validates with more evidence that excessive nursing workload has negative impacts on the health of the people cared for, which is a useful manuscript for nurse managers to justify institutional changes.\n\nIn nursing, real-time patient assessment has always been key, which would allow the development of schemes with technology; however, it highlights that causality is not the only way of nursing care, and qualitative aspects of care that are performed with humanization and compassionate care should be contemplated; this gives a comprehensive paradigm to the reader of the nursing role.\n\nWeaknesses The article could improve its presentation of aspects that may be justifiable from the methodology used, such as answering the question: Why did not they use the new PRISMA 2020 scheme? For an integrative review, it should not necessarily be used, but in the methodology, this methodology is used, but it is not mentioned what is or is not used and why. It is not possible to identify the elements suggested in the PRISMA 2020 parameters, regarding aspects such as the date on which each resource was last consulted. It is not clear whether the authors were involved in the screening stages in the selection or only in the phase of reading abstracts.\n\nTable 1 has very valuable information for readers; however, one could be more assertive in the presentation by having more heterogeneity in the presentation of the results in the Data Collection Methods and Results column; it may be that having been elaborated by different authors of the article or supporting persons, the presentation of the information varies too much. Now, it may have been the effect of the limitation they presented in the manuscript that it was too heterogeneous, which they could specify there and cite as an example in Table 1, where this can be seen.\nImprovements to the article The manuscript can also be improved with aspects such as updated references. In the introduction, they have a citation from 2011 (12 years’ difference), on a topic that could have more recent references.\n\nThe discussion could include aspects of recently published discussions (last two years until 2023) since they were limited to the same studies of the review.\n\nI suggest being more precise in stating the research gaps identified, which may guide readers on topics of research interest, lacking this specification.\n\nFinally, from origin of the article, I suggest reviewing if the word \"innovation\" is pertinent in the article, since it relates it to the topic of technologies that is in the research questions; however, not necessarily when talking about technology it is associated to an innovation, a technology can be an artifact or a technique; while innovation is to create or modify a product, but it is not what was sought in the review nor was it what was found in the studies.\nFinal conclusion of the concept The manuscript is very good in its content, richness, rigorous work, concise, and useful for care management. It can be improved with precisions and updates typical of literature reviews. I congratulate the authors for the phenomenon addressed and the possibility of having this type of review.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [ { "c_id": "10272", "date": "29 Sep 2023", "name": "William Guerrero", "role": "Author Response", "response": "We thank the reviewer for the valuable comments made on version 1 of the manuscript. We answer the reviewers’ comments as follows: Why did not they use the new PRISMA 2020 scheme? For an integrative review, it should not necessarily be used, but in the methodology, this methodology is used, but it is not mentioned what is or is not used and why. It is not possible to identify the elements suggested in the PRISMA 2020 parameters, regarding aspects such as the date on which each resource was last consulted. It is not clear whether the authors were involved in the screening stages in the selection or only in the phase of reading abstracts. Answer: The first paragraph of the Methods section provides the details of the methodology used that corresponds to the PRISMA 2020 guidelines as suggested by the reviewer. The corresponding paragraph is as follows: An integrative literature review was performed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. Studies were retrieved from SCOPUS, Scielo, PUBMED, and CINAHL in January 2021. The search strategy was: (\"analytics\" OR \"operations research\" OR digital* OR \"IT\" OR technolog) AND (\"nursing workload\" OR \"nurse-patient ratio\" OR \"nursing workforce planning\" OR \"nursing algorithm\" OR \"nursing personnel staffing and scheduling\" OR \"nursing staff\")). The authors were involved in the identification, screening, and analysis stages. Inclusion criteria considered studies published in full text in English, Spanish or Portuguese classified as scientific articles or reviews, in the areas of nursing, medicine, social sciences, engineering, published between January 2016 and December 2020. This date range was considered to focus on the recent technologies. Articles related with technology that didn’t analyse the impact on nursing workload or didn’t present technologies were excluded. For all research, this must include a final section including details of ethical approval, informed consent and, where relevant registration. Table 1 has very valuable information for readers; however, one could be more assertive in the presentation by having more heterogeneity in the presentation of the results in the Data Collection Methods and Results column; it may be that having been elaborated by different authors of the article or supporting persons, the presentation of the information varies too much. Now, it may have been the effect of the limitation they presented in the manuscript that it was too heterogeneous, which they could specify there and cite as an example in Table 1, where this can be seen. Answer: we have improved table 1. We included more information about references Redley et al. (2019), Hope et al. (2019), Kang, Kim, Lee (2016), Sato et al. (2016), Vorakulpipat et al. (2019), Zhou et al. (2019), Higgins et al. (2017), Tu et al. (2018), Van der Veen et al. (2020), Handayani et al. (2018), De Oliveira, Garcia, Nogueira (2016). The records on this new table are more homogeneous. Nevertheless, we still acknowledge the study limitation about the heterogeneous methodologies in the retrieved studies and we cite the example in the limitations. In the introduction, they have a citation from 2011 (12 years’ difference), on a topic that could have more recent references. Answer: To update the references, we have included the following citation: Chang, L. Y., Yu, H. H., & Chao, Y. C. (2019). The Relationship Between Nursing Workload, Quality of Care, and Nursing Payment in Intensive Care Units. The journal of nursing research : JNR, 27(1), 1–9. https://doi.org/10.1097/jnr.0000000000000265 The discussion could include aspects of recently published discussions (last two years until 2023) since they were limited to the same studies of the review. Answer: It is true that our discussion section is built upon the studies that were retrieved by the proposed systematic review. In fact, we aimed to draw conclusions appropriate in the context of the current research literature and minimize bias and lack of rigor (Hopia et al., 2016). In fact, we aimed to avoid common pitfalls in integrative literature reviews that are described by Toronto and Remington (2020) the document entitled: “A Step-by-Step Guide to Conducting an Integrative Review”. The pitfalls are: Drawing conclusions or formulating implications that cannot be supported by the literature, Inserting new information/citations in the conclusion section of the review Hopia, H., Latvala, E., & Liimatainen, L. (2016). Reviewing the methodology of an integrative review. Scandinavian journal of caring sciences, 30(4), 662-669. Toronto, C. E., & Remington, R. (Eds.). (2020). A step-by-step guide to conducting an integrative review (pp. 1-9). Cham: Springer International Publishing. I suggest being more precise in stating the research gaps identified, which may guide readers on topics of research interest, lacking this specification. Answer: We conclude that “The main research gap that we identify is the lack of studies showing evidence of the impact of technology measured as the correlation between the nursing outcomes and staff well-being with the use of workload estimation and the strategies for planning workload allocation”. This conclusion is presented in the final section of the paper. I suggest reviewing if the word \"innovation\" is pertinent in the article, since it relates it to the topic of technologies that is in the research questions; however, not necessarily when talking about technology it is associated to an innovation, a technology can be an artifact or a technique; while innovation is to create or modify a product, but it is not what was sought in the review nor was it what was found in the studies. Answer: We declare as a limitation of the study that the literature review did not focus on studying the concept of innovation in nursing practice or workload management as in Rylee and Cavanagh (2022) for nursing practice. We thank the reviewer for the valuable comments made on version 1 of the manuscript. We answer the reviewers’ comments as follows: Why did not they use the new PRISMA 2020 scheme? For an integrative review, it should not necessarily be used, but in the methodology, this methodology is used, but it is not mentioned what is or is not used and why. It is not possible to identify the elements suggested in the PRISMA 2020 parameters, regarding aspects such as the date on which each resource was last consulted. It is not clear whether the authors were involved in the screening stages in the selection or only in the phase of reading abstracts. Answer: The first paragraph of the Methods section provides the details of the methodology used that corresponds to the PRISMA 2020 guidelines as suggested by the reviewer. The corresponding paragraph is as follows: An integrative literature review was performed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. Studies were retrieved from SCOPUS, Scielo, PUBMED, and CINAHL in January 2021. The search strategy was: (\"analytics\" OR \"operations research\" OR digital OR \"IT\" OR technolog*) AND (\"nursing workload\" OR \"nurse-patient ratio\" OR \"nursing workforce planning\" OR \"nursing algorithm\" OR \"nursing personnel staffing and scheduling\" OR \"nursing staff\")). The authors were involved in the identification, screening, and analysis stages. Inclusion criteria considered studies published in full text in English, Spanish or Portuguese classified as scientific articles or reviews, in the areas of nursing, medicine, social sciences, engineering, published between January 2016 and December 2020. This date range was considered to focus on the recent technologies. Articles related with technology that didn’t analyse the impact on nursing workload or didn’t present technologies were excluded. For all research, this must include a final section including details of ethical approval, informed consent and, where relevant registration. Table 1 has very valuable information for readers; however, one could be more assertive in the presentation by having more heterogeneity in the presentation of the results in the Data Collection Methods and Results column; it may be that having been elaborated by different authors of the article or supporting persons, the presentation of the information varies too much. Now, it may have been the effect of the limitation they presented in the manuscript that it was too heterogeneous, which they could specify there and cite as an example in Table 1, where this can be seen. Answer: we have improved table 1. We included more information about references Redley et al. (2019), Hope et al. (2019), Kang, Kim, Lee (2016), Sato et al. (2016), Vorakulpipat et al. (2019), Zhou et al. (2019), Higgins et al. (2017), Tu et al. (2018), Van der Veen et al. (2020), Handayani et al. (2018), De Oliveira, Garcia, Nogueira (2016). The records on this new table are more homogeneous. Nevertheless, we still acknowledge the study limitation about the heterogeneous methodologies in the retrieved studies and we cite the example in the limitations. In the introduction, they have a citation from 2011 (12 years’ difference), on a topic that could have more recent references. Answer: To update the references, we have included the following citation: Chang, L. Y., Yu, H. H., & Chao, Y. C. (2019). The Relationship Between Nursing Workload, Quality of Care, and Nursing Payment in Intensive Care Units. The journal of nursing research : JNR, 27(1), 1–9. https://doi.org/10.1097/jnr.0000000000000265 The discussion could include aspects of recently published discussions (last two years until 2023) since they were limited to the same studies of the review. Answer: It is true that our discussion section is built upon the studies that were retrieved by the proposed systematic review. In fact, we aimed to draw conclusions appropriate in the context of the current research literature and minimize bias and lack of rigor (Hopia et al., 2016). In fact, we aimed to avoid common pitfalls in integrative literature reviews that are described by Toronto and Remington (2020) the document entitled: “A Step-by-Step Guide to Conducting an Integrative Review”. The pitfalls are: Drawing conclusions or formulating implications that cannot be supported by the literature, Inserting new information/citations in the conclusion section of the review Hopia, H., Latvala, E., & Liimatainen, L. (2016). Reviewing the methodology of an integrative review. Scandinavian journal of caring sciences, 30(4), 662-669. Toronto, C. E., & Remington, R. (Eds.). (2020). A step-by-step guide to conducting an integrative review (pp. 1-9). Cham: Springer International Publishing. I suggest being more precise in stating the research gaps identified, which may guide readers on topics of research interest, lacking this specification. Answer: We conclude that “The main research gap that we identify is the lack of studies showing evidence of the impact of technology measured as the correlation between the nursing outcomes and staff well-being with the use of workload estimation and the strategies for planning workload allocation”. This conclusion is presented in the final section of the paper. I suggest reviewing if the word \"innovation\" is pertinent in the article, since it relates it to the topic of technologies that is in the research questions; however, not necessarily when talking about technology it is associated to an innovation, a technology can be an artifact or a technique; while innovation is to create or modify a product, but it is not what was sought in the review nor was it what was found in the studies. Answer: We declare as a limitation of the study that the literature review did not focus on studying the concept of innovation in nursing practice or workload management as in Rylee and Cavanagh (2022) for nursing practice." } ] }, { "id": "178450", "date": "10 Aug 2023", "name": "Angela María Salazar Maya", "expertise": [ "Reviewer Expertise Epistemology of nursing", "perioperative care", "family caregivers", "qualitative research" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is a relevant issue for nursing as a discipline and profession, since evidence is required on how the workload influences the results of the patients cared for.\nThe search was only carried out until the year 2020, it would be pertinent to extend the search until at least 2022 or the first half of 2023 so that the integrative review is more up-to-date.\nThe paper presents the 4 categories that emerge from the analysis: workload models, burnout predictors, and outcomes; information technology and the meaning of technology for management; technology acceptance. develop each category.\nI consider the discussion and conclusions pertinent.\nIn a brief search carried out in PubMed, I find articles on the subject.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-104
https://f1000research.com/articles/12-543/v1	24 May 23	{ "type": "Research Article", "title": "Youth political participation and digital movement in Indonesia: the case of #ReformasiDikorupsi and #TolakOmnibusLaw", "authors": [ "Sri Lestari Wahyuningroem", "Rheinhard Sirait", "Uljanatunnisa Uljanatunnisa", "Dudy Heryadi", "Rheinhard Sirait", "Uljanatunnisa Uljanatunnisa", "Dudy Heryadi" ], "abstract": "The younger generations have always been at the forefront of and contributed significantly to social movements that are critical of state policies or respond to socio-political situations. This is also what happened in large movements involving young people in Indonesia, conventionally in the form of demonstrations and digital movements. This study seeks to explore the relationship between youth political participation, digital media, and the development of youth political identity by analyzing young people’s engagement in some of the most significant political protests in Indonesia during the mass protests of #ReformasiDikorupsi, a movement opposing the amendments of several important bills, and #TolakOmnibusLaw, a movement opposing the establishment of a new single bill related to labor and investment, between 2019 and 2020. By analyzing quantitative data through data mining from Twitter from October 2019 to November 2020 with the social network analysis method, this study discusses online youth participation in social movements and the way they shape their political identity. Our research found that young people play an active and central role in building online and offline movements. In particular, the online movement contributes to the growth of the offline protest movement, and vice versa, because of concerns about the practice of illiberal democracy.", "keywords": [ "youth", "political participation", "digital movement", "democracy" ], "content": "Introduction\n\nThe Internet and social media have greatly affected the participation of student movements in digital democracy in Indonesia; numerous protests have been carried out against corruption, and changes in democratic patterns (Saud & Margono, 2021), as seen in the #ReformasiDikorupsi movement in 2019 and #TolakOmnibusLaw movement in 2020. #ReformasiDikorupsi (Corrupted Reform) was a protest against the ratification of the Draft Law (RUU) of the Corruption Eradication Commission (KPK), which is considered likely to curb civil liberties and freedom of expression (Sastramidjaja, 2020), while #TolakOmnibusLaw was a 2020 movement of students, trade unions, and civil society groups fighting against or rejecting the Omnibus Law on Job Creation, which was considered detrimental to workers (Sastramidjaja & Rasidi, 2021). This study will focus on the relationship between youth political participation, digital media, and the development of youth political identity by analyzing young people’s experiences of participation in Indonesia, especially during the mass protests of #ReformasiDikorupsi in 2019 and #TolakOmnibusLaw in 2020.\n\nRecent studies indicate that the state of democracy in Indonesia has experienced ups and downs in a situation that some scholars call illiberal democracy (Hadiz, 2017; Diprose et al., 2019). This condition is characterized as blocking citizens from obtaining knowledge about the activities of power holders due to the lack of civil liberties, despite holding elections. Closed legislation processes against various laws that are considered detrimental to general society have triggered large-scale demonstrations, primarily attended by workers, university students, high school students, and other various groups of youth. The protests came in distinct waves. The first wave was seen in late 2019 when the government and parliament revised the criminal code and passed a law that reduced the independency of the Corruption Eradication Commission (KPK), an Indonesian institution that had revealed a number of high-profile corruption cases. The second and much larger wave was observed in October 2020, protesting against the Omnibus Law on Job Creation.\n\nIn these political events, the role of young citizens was not only participants but also core actors who mobilized these protest movements to become so large-scale. We refer to young people as a diverse and heterogeneous societal group showing various complex identities—psycho-social, politico-economic, and educational. Indeed, young people are not a monolithic group whose members all feel and want the same or have convergent interests. This study particularly focuses on young people between the ages of 15 and 30 years. The UN Secretariat uses the terms “youth” and “young people” interchangeably to mean people aged 15–24 years with the understanding that member states and other entities use different definitions. In the Indonesian context, the category of young people is legally defined according to the 2009 Law of Youth; “youth” (Pemuda) as “Indonesian citizens who are entering an important period of growth and development and are aged between 16 and 30 years.” The 2020 national census reported that the number of youth is 75.49 million, or around 27.94 percent of the population (BPS, 2021).\n\nMany scientists have carried out studies on youth participation and digital society in the last two decades. Social and political dynamics in several countries are influenced by youth participation in the digital world; not infrequently, youth have been the driving force behind many social movements in various parts of the world. In this context, youth activism in the digital world is a consequence of the increasing loss of young people’s trust in conventional political models such as political parties and elections. In the United States, for example, a poll conducted by the Harvard Institute of Politics indicated consistently declining levels of trust in government institutions among Americans aged 18- to 29-year-olds between 2010 and 2015 (Graeff, 2016, p. 95). In Europe, in 2013, the London School of Economics (LSE) Enterprise conducted a study on young people aged 16- to 26-year-olds who participated in voting and institutional politics. They reflect that “the political ‘offer’ does not match their concerns, ideas, and ideals of democratic politics.” At the same time, high levels of youth participation in issue-oriented activism, boycotting and buycotting, and protest activities were observed (Graeff, 2016: 95). W. Lance Bennett describes this new generation of young people as “actualizing citizens,” “who favor loosely networked activism to address issues that reflect personal values,” in contrast with “dutiful citizens,” who maintain more collective and government-centered practices (Bennet, quoted in Graeff, 2016, p. 96)\n\nAccording to Mei (2021), youth involvement in digital activism is generally influenced by three factors: social identity, a desire to be heard, and an increase in online activism. Youth derive their social identity from their group membership and eating outside, and with protests, their identity becomes politically potent, as in the case of the 2010 Arab Spring protests. Furthermore, they are attracted to political action because they desire to be adequately recognized in the political environment. If not, the youth will find a unique method to express their voice. Moreover, the rise of online activism through social media has dramatically influenced young people to become more politically involved and aware, as demonstrated in the #BlackLivesMatter movement in the United States, the #UmbrellaMovement in Hong Kong, and the #TeaMilk in Thailand.\n\nSimilar global research has considered Afghan youth’s political participation on Facebook (Orfan, 2021). This study examines the effects of Facebook use on youth political involvement or participation in the 2019 presidential election. The results show that many Afghan youths needed to actively participate in Facebook. Another study by Sairambay (2021) examines the contributions of new media to young people’s political participation in Russia and Kazakhstan, showing that new media contributed to political participation in Russia and Kazakhstan among young people both online and offline through raising awareness as a prerequisite for political participation, and supporting communication, interaction, advocacy as political participation, mobilization, organization, and coordination.\n\nIn the local context, research on the rise of digital democracy and youth’s political participation in Indonesia by Saud and Margono (2021) is noteworthy. The study focuses on the influence of digital media on young people’s political involvement through digital platforms during the student movement in 2019 as a response to the ratification of the Corruption Law (KPK). This study demonstrates that social media platforms increase the influence of young people in politics in Indonesia. Sastramidjaja (2020) studied the #ReformasiDikorupsi protest, claiming it to have opened a path for digital activism in Indonesia. The Internet, especially social media, has broken down communication barriers, and, accordingly the dissemination of information has become rapid and inclusive. Indonesian society has seen increased involvement of millennials and generation Z in digital activism because these two generations grew up with advanced technology. The corrupted reform movement has given a rise to a new “generation” of activism in Indonesia. This suggests that conventional activism in Indonesia has succeeded in shifting to digital activism, which holds new hope for democracy in Indonesia.\n\nIn another article, Sastramidjaja and Rasidi (2021) discuss conflicts centered around the Omnibus Law or the Job Creation Act (#TolakOmnibusLaw), both in direct action and virtual action, between mainstream media and social media, and between physical repression and control over cyberspace. Resistance to the Omnibus Law continued as of May 2020 in the public sphere, with direct action against the law and the trending hashtag #TolakOmnibusLaw on social media. The collective action against the Omnibus Law spread the issue and popularized several hashtags so that the discourse on Omnibus Law was not limited to netizens involving social media. Several mainstream media also reported the rejection of the Omnibus Law by referring to Twitter trends as an indicator of public voices. The community’s immediate rejection of the Omnibus Law has prompted the government to react by promoting several hashtags, such as #RUUCiptakerLindungiPekerja, through buzzers and several influencers. Buzzers are not only mere buzzers on social media but also have been persecuting netizens who are vocal about the Omnibus Law issue. This caused fear among netizens to raise their opinions in social media.\n\nBoth articles (Sastramidjaja, 2020; Sastramidjaja & Rasidi, 2021) show the importance and relevance of looking at the trends of digital social movements, especially in the context of Indonesia, and in particular at the two movements that are the focus of this article. However, they did not specifically address the involvement of young people in the movement, nor did they capture the relevance of their participation in the analysis of weakened democracy in Indonesia. In this study, we will fill this gap and examine how their movements contribute to the political identity of young people.\n\nWithin the two movements featured in this study, the central part of the strategy adopted by young people is to take advantage of digital media platforms. While governments, technology, and forms of technology and participation change over time, this study finds that increasingly mediated, connected, and participatory social lives occur in countries where democracy is challenged. The study seeks to identify the basic features and implications of youth politics—illiberal practices. The key questions posed in this study are: What is the involvement and role of young people in digital-based social movements, and how are they related to conventional (offline) protests? How does weakening democracy, characterized by non-transparent and violent practices in handling criticism, contribute to youth engagement on social media?\n\n\nLiterature review\n\nTo better understand political participation in social media, Paskarina (2020) explored digital activism and democracy, identifying six main points of digital activism practices standard in Indonesia: 1. Strategies to mobilize support or form social or political movements; 2. public spaces to discuss marginalized issues; 3. criticism and control of the government; 4. “hoaxtivism” and counter-hoaxtivism; 5. hacktivism; and 6. the process of building identity. According to the author, these six digital activism practices reflect how technology shapes the breadth of activism. This explains that advances in media technology are shaped by social, political, and economic needs and practices that drive digital activism. The digital activism we discuss in this paper, therefore, concerns the four forms of activism: 1. strategies to mobilize support or to form social or political movements, 2. creating a public space to discuss marginalized issues, 3. criticism and control of the government, and 4. the process of building identity. For the context of the two movements in Indonesia that we examine, the strategies and approaches are adopted from a similar movement in Hong Kong called the Umbrella Movement in 2014.\n\nAgur and Frisch (2019) discuss how activists used social media as a component of digital activism during the 2014 Hong Kong protests and the extent to which social media influenced the success of these actions. Social media play a role in mobilizing, organizing, and inviting the public to be involved in the action. Agur and Frisch argue that social media played a role in measuring the sentiments of activists and the public and as a place to plan strategies to increase pressure on the government. Social media are also crucial in gathering protesters from various regions, as well as a place to avoid police accusations and facilitate rescue and advocacy if participants are arrested by the police. However, this study does not explicitly discuss the role of youth in the movement.\n\nWong (2021) examines, more specifically, youth involvement in the movement to explain how social media affects youth participation and outlines four key findings. First, the dichotomy between loyal and materializing citizens is an oversimplified description of the impact of social media on youth participation. Second, its actual impact depends on many mediating and contextual factors. Third, media use, particularly reliance on social media to receive and share news and information about public affairs, creates an echo chamber effect that significantly separates the opinions of young people engaged in social media from the rest of the population. Fourth, while changing the nature of traditional social movements, social media emphasizes personalization, blurs the lines between leaders and advocates, and bridges the connections between institutions and participants. The weakening of the traditional structures has created a new logic of cohesive behavior in political participation.\n\nIn the current study, we examined youth participation in digital activism and conventional (offline) activism. In this case, online activism is not a substitute for offline activism, for as Baybars-Hawks explains, the two can go hand in hand to create a more significant impact (Baybars-Hawks, 2015). Cammaerts (2015) assumes that the use of information and communication technology, which includes activist communicative practices, can be divided into two categories: practices supported by social media and practices based on social media. As explained by Cammaerts (2015), in communicative practices supported by internet communication technology and social media, social media support many activities such as internal organization, recruitment, building networks, and mobilizing efforts, as well as coordinating direct actions that activists will carry out. Social media are independently capable of disseminating a range of movements without relying on mainstream media, as well as affording space for discussions, debates, and deliberation in decision-making as a forum for activists (Cammaerts, 2015).\n\nAccording to Cammaerts (2015), social media have a more constitutive nature. The Internet and social media are used by activists to fight ideological enemies, facilitate the surveillance of supervisors (sousveillance), and store protest artifacts (Cammaerts, 2015). Meanwhile, the function and role of external social media, as Cammaerts (2015) puts, can involve three activities: First, mobilization and recruitment for direct offline action are more flexible and have a lower cost. Second, the establishment of independent alternative communication channels via social media allows activists to carry out self-mediation by distributing goals and framing movements more easily. As explained by Cammaerts (2015), self-mediation is done by distributing the framing and interpretation of the movement toward an issue through independent communication channels such as social media. Social media have given activists the ability to transmit text and visual discourses. They are also considered to have the potential to provide opportunities for communities and subordinate groups to build alternative collective identities. An essential part of the self-mediation process, according to Cammaerts (2015), is the production of protest artifacts by participants documenting their protest actions and distributing them through social media to expand the archives and self-representation of the protest actions carried out. The third activity is the practice of resistance, as activists use the Internet and social media as weapons against the enemy. Social media serve as an instrument for direct action such as sousveillance—supervision of supervisors or management from the bottom up.\n\n\nMethods\n\nThis study used a mixed-method approach to comprehensively collect and analyze case study data by integrating complementary quantitative and qualitative approaches (Tashakkori & Creswell, 2007). The research data were digital conversations produced and mobilized by netizens on Twitter within the conversation period from October 2018, when the #ReformasiDikorupsi started, until the end of November 2019, after the #TolakOmnibusLaw movement ended. Conversations on Twitter are a form of cross-geographical dissemination of microblog information that is useful for researchers as a source of research data whose context can be seen (Letierce et al., 2010) and helps in predicting the dynamics of the data to some extent (Eysenbach, 2011). This research quantitatively used text mining, machine learning word clouds, and social network analysis (SNA) through Gephi open-source software (www.gephi.org) with specific computational configurations to produce quantified text data. Open source software (OSS) is a public good and alternative programming operating system that users can use, modify and develop mutually according to their respective data processing needs (Kollock & Smith, 1999; Grodzinsky et al., 2003). The quantified data are checked and re-verified by human-led annotation or manual data classification by humans.\n\nThis research started with a preliminary study in October 2018 that determined the accounts and hashtags relevant to the research needs of analyzing and describing the conversations of netizens on the Twitter platform about the issue of the Job Creation Law (Omnibus Law). This process also identified certain representative accounts and hashtags to produce conversations about the issues to be researched. These representative hashtags constituted the source of text-based data crawled by machine learning Python programming language conducted from October 2018 until September 2019. The following data processing technique were consisted of three processes: data filtering, classification, and visualization of data collected through text mining. The results of this data processing were visualized via SNA (social network analysis), a technique for analyzing relationships between individuals through a collection of relationships or ties between nodes to establish the pattern of relationships between social actors (Williams & Durrance, 2008). This study used SNA to visualize the network of conversations and hashtags produced by content creators (actors). These processes are part of a digital research method that can filter and verify digital data that are varied, dynamic, and interconnected (Rogers, 2015).\n\nSpecifically, data processing in this research underwent data filtering, classification, and visualization to produce contextual digital data findings that can visualize findings objectively. The filtering process took place in two stages. In the first stage, filtering takes place by classifying conversations into irrelevant, unstructured, and structured conversations and eliminating irrelevant conversations. This process also collected the conversation metadata, such as date, time, account, and hashtags. The first filtering process was carried out on the Microsoft Excel application.\n\nIn the second stage, filtering was conducted by processing structured conversations. This process grouped conversations with similar meanings into categories of specific narrative types in separate Microsoft Excel documents. This produced a structured dataset of categorized conversations.\n\nThe following process is data classification, which was divided in two stages. In the first stage, similar conversations (also known as structured datasets) were grouped based on specific predetermined attributes, after which the categorization of conversations based on these attributes was grouped again based on the exact attributes. Furthermore, unstructured conversations underwent processing through machine-learning word clouds to produce word cloud visualizations. The resultant keywords were also verified to identify the meaning and context of the conversation, which are helpful in describing the research findings.\n\nThe final process was data visualization, which takes three forms: timeline visualization (chronology of conversations about the research topic), graphical visualization (distribution of hashtags), and SNA visualization (informal networks and hashtags that connect actors through SNA).\n\nThis research was reviewed for ethics clearance by the Universitas Pembangunan Nasional Veteran Jakarta’s internal research ethics commission and authorized by the Vice Chancellor for Academic Affairs at the University, numbered 3/UN61/PT.01.06/2022, dated April 1, 2021. The request for ethics clearance was made later after data collection with the research team’s extensive data method. Given that using data from personal accounts on social media, in this case, Twitter, also requires ethical conformity, we have proposed ethical clearance for this data requirement and received the approval on April 1, 2021.\n\n\nThe emergence of the #ReformasiDikorupsi and #TolakOmnibusLaw movements\n\nIn 2019, the Indonesian Parliament (Dewan Perwakilan Rakyat, DPR), on the recommendation of the executive, amended Law No. 19 of 2019 concerning the KPK Law (KPK Law) and discussed the Draft Criminal Code (RKUHP). Many elements in civil society view the revision of the KPK law and the discussion of the RKUHP as betraying the ideals of the 1998 Reformasi (Reformation) when the economic and political crisis finally brought mass protests and ousted Suharto, the president of 32 years. Many believe revising the KPK Law will weaken the Commission by reducing several of its powers to investigate corruption. At the same time, the RKUHP has the potential to limit the rights of citizens.\n\nThis decision was opposed by many elements of society, especially students. Tens of thousands of students in almost all cities flooded the streets in September 2019 with seven demands, including the cancellation of the revision of the KPK Law. They also urged the DPR to immediately pass the Bill on the Elimination of Sexual Violence and the Domestic Workers Protection Bill. Academics in the country and abroad also supported the student movement through an open letter stating their rejection of the revised KPK Law.\n\nFollowing the escalation of protests in various cities, many experts suggested that the president immediately issue a Government Regulation Law Substitute as a solution. The pressing urgency was increasingly felt due to the wave of demonstrations, which were increasingly considered unstoppable. The action, which was triggered by public disappointment, immediately turned to anger after two students in Kendari, Southeast Sulawesi, La Randi, and Muhammad Yusuf Qardhawi, were killed by a police projectile during a demonstration (Gabrilin, 2019). Thousands of others were arrested without a valid reason, and journalists were victimized by police brutality according to the recapitulation of the Indonesian Journal Alliance (AJI) recorded 14 cases of violence against journalists in various regions including Jakarta, Maksaaar, Palu and Jayapura (Madrim, 2019). In this action, students had broad sympathy from various national and international groups, especially for the victims and in light of the severe repression of students. This sympathy resulted in support in the digital space, in this case, on social media. Public figures with large followings on social media, such as singer Ananda Badudu, also expressed sympathy and even invited the public to help and show solidarity. In his tweet, Badudu invited anyone who felt that the students’ demands were justified to help students in action in front of the DPR Building. Moreover, Badudu helped raise funds on the Kitabisa citizen funding platform to help with food and student logistics. Badudu was later arrested by the police as a result (Persada, 2019).\n\nIn parallel, movement mobilization occurred both offline and online. When repression strengthens against the offline movement, the online movement in social media strengthens simultaneously. For example, the tweet from the Center for Anti-Corruption Studies Universitas Gadjah Mada @PUKAT_UGM, which became the top tweet #1, created a thread that briefly and quickly explained the problems in the Job Creation Bill, including the process, method of formation, and contents. The thread helps to understand the main problems of the Law in systematic and easy-to-read by common public.\n\nSeveral students who took part in the action stated that their attitude was also extended to social media by using their accounts and delivering unique messages (Adam, 2019). With public pressure on the government in response to various repressions over the student demonstrations, President Jokowi promised to delay revising the bills, particularly the amendments to the KPK Law. One year later, the government made a new policy that once again invited a strong reaction from the public, including university students. President Jokowi initiated an Omnibus Law compiling approximately 76 laws in 1,200 articles to avoid overlapping rules to make a less complex and more favorable environment for investors to enter Indonesia. However, drafting this law seemed hasty, without extensive consultation with the public. The president targeted the passage of this policy within 100 days. This raised public doubts, especially regarding the interests of several elite oligarchs in the current government, as stated by Wijayanto, the government’s motivation in passing the Job Creation Law quickly was because there are common interests, namely political economy among the oligarchic elite (Dzulfaroh, 2020). The participation of young people, especially students, on social media in opposing the labor law is also widely reported through the mass media. As reported by Kompas, the biggest newspaper in Indonesia, the wave of rejection of the omnibus law has become a trending topic on Twitter. Their report is based on observations through social media analysts, and several hashtags dominate the conversations of netizens on Twitter, such as #TolakOmnibusLaw. While the conversation map on Twitter shows an exciting pattern, dominated by counter omnibus law clusters, even accounts from academics, BEM (Universitas Indonesia student union), NGOs, activists, and K-popers unite to support each other #MosiTidakPercaya and #DPRKhianatiRakyat. While the conversation map on Twitter shows an exciting pattern, dominated by counter omnibus law clusters, even accounts from academics, BEM, NGOs, activists, and K-popers unite to support each other (Mulyana, 2022). CNN Indonesia also reported that there were many rejections of the omnibus law, such as “Failure of the Omnibus Law Echoing in Social Media, Support Action on the Road” or “The Beginning of the Omnibus Law Protest to Noise on Social Media” similar to the Kompas Media coverage. CNN Indonesia emphasized that the action of rejecting the omnibus law not only directly participated in the demonstration, but the demonstrators also echoed on Twitter social media by highlighting popular hashtags such as #GagalkanOmnibusLaw.\n\nThis bill was passed in a plenary meeting of the DPR on October 5, 2021. A day after the passage, simultaneous demonstrations involving tens of thousands of people were held in at least 18 provinces of Indonesia on October 6–8. The police again resorted to violence and repression, resulting in chaos and many victims, including high school and vocational high school students. Amnesty International Indonesia reported at least 51 videos showing 43 violent incidents in 15 provinces between October 6 and 10, 2021. In these videos, the police are seen brutally using blunt objects to disperse demonstrations, injuring at least 402 people and arresting 6,658 demonstrators (Saputra, 2020).\n\nIn this protest, the participants of the demonstration were not predominantly students but included several others, including workers and activists. Labor was involved in large numbers, dominating the organizations in various regions of Indonesia. Students were less involved in numbers as extensively as the previous year Rahmah et al. (2020). This is also partly due to the COVID-19 pandemic that hit Indonesia in March 2020, imposing limitations on the recruitment and mobilization of protest movements. However, the pandemic has conversely afforded more excellent and broader online recruitment and mobilization opportunities. However, student organizations still voiced their support for the passage of the law through social media, such as the Student Executive Board of Universitas Indonesia (BEM UI). This organization has been opposed to ratification of the Job Creation Law from the beginning because considered to be able to harm the people. Not only through tweets but also, BEM UI said that the Job Creation Law since it was mentioned in the initial speech of the President of the Republic of Indonesia, reaped many problems, many rejections caused by product defects both ‘formally’ and ‘materially’.\n\nIn the next section, we will show the expansion of the digital movement on social media, which involves youth elements previously considered apolitical, such as K-Poppers. We collected data and information presenting the dominant narratives of the groups of young people involved in both movements. We divide the period into (1) the #ReformasiDikorupsi event, and (2) the #TolakOmnibusLaw event.\n\n\nThe #ReformasiDikorupsi movement\n\nIn the #ReformasiDikorupsi movement, students started to build and mobilize support and participation through social media at least two weeks before any action took place. The hashtag #ReformasiDikorupsi first appeared on September 16 at 00:00:50 West Indonesia Time (WIB). Before that, the hashtag #RKUHPNgawur had already appeared on September 1 at 19:20:55 WIB.\n\nOur study found the four most used hashtags: #ReformasiDikorupsi, or Corrupted Reform (18,460 lines); #TolakRKUHP, or Reject KUHP (53,922 lines); #RKUHPNgawur, or Inconsequent KUHP (1,099 lines); and #MahasiswaBergerak, or Students Move (53,922 lines). Hashtag #ReformasiDikorupsi shows that #Mahasiswa (college students) dominated the conversation. This shows that the most active or widely discussed segment of the youth groups involved in the movement were students.\n\nIn Figure 1, #Students is the most talked-about term, showing students as the main subject in the movement. Student entities are described as #us, or us, and the targets of criticism as #them or them. Those who fall into the “our” category in this movement besides students are #pelajar or secondary students, #labor or labor, and #activists or activists. Several student entities were also discussed, including #BEM, the executive student organization in universities, and #gejayan, which refers to a student mobilization initiative in Yogyakarta. Meanwhile, tweets are addressed to parties such as #Jokowi, #President, #Government or government, #penguasa or rulers, #representasi or representatives, #polisi or police, and #buzzers, namely the influencers on social media who create narratives that defend government policies. The criticisms and concerns raised are the most common conversations, such as #KPK, Indonesia, #Democracy, #reject or reject, #revision or amendment, #UU or Law, and #korupsi or corruption.\n\nSimilarly, the pattern for the hashtag #TolakRKUHP also shows students as the most talked-about hashtag. #Indonesia and #RKUHP or the Criminal Law draft were also extensively discussed in the movement, and as the previous figure shows, the binary opposition between them and us also existed. Figure 2 shows the pattern.\n\nThe movement more specifically inspired the involvement of students with the hashtag #MahasiswaBergerak. The hashtag was first mentioned on September 6, 2019, at 03:49:07 WIB, and was involved in 53,922 lines of conversation. The picture below shows these conversations on Twitter.\n\nIn Figure 3, #student and #demo, an abbreviation for demonstration, were the two most common words. The rest, as in the two previous hashtags conversations, show the position of “us” and “them” in this widespread movement, and the form of criticism of the government and its apparatus.\n\nIn the conversations shown in the three figures, students were the predominant parties, and the conversations mainly concerned the revision of the Indonesian Criminal Law (KUHP), which held significant implications for the lives of young people, including threats to privacy, safety, and freedom of expression. The movement also echoed the protests for revision of the Anti-Corruption Law, and the readings find concern over this issue in the movement. What links these two concerns are the students’ assessment of a decline or setback in Indonesian reformation (reformasi) and democracy in general. The criticisms were addressed to the government, represented by #Jokowi as president and #DPR as parliament, and the state apparatus involved in legal reform such as #polisi or police.\n\nIn social media, parties who support this policy amendment also build a narrative. In our dataset, hashtags of those supporting the amendments to the KPK Law include #KPKcengeng or whining over the KPK, #belistepjokowi or trust Jokowi steps, and #revisiuukpkfornkri or revising KPK Law for the unitary state of Indonesia. The number of conversations using this hashtag is much smaller than those rejecting the law revision. The hashtag #kpkcengeng, for example, only appeared in 1,503 conversations. In comparison, #beliefstepjokowi appeared in 2,572 conversations, and #revisiuukpkfornkri appeared in 739 conversations, in strong contrast with the four hashtags against the amendments to the law described above. In addition, conversations supporting the revision of the law, most by buzzers’ accounts, also show trash hashtags or those that have no meaning other than to enliven the conversation, such as tribal hashtags like #sunda, #betawi, and #baduy, and hashtags whose relevance to this movement is not clear, such as #bakso and #biru.\n\n\nThe #TolakOmnibusLaw movement\n\nOur readings for the #TolakOmnibusLaw show some unique differences from the #ReformasiDikorupsi movement. The four most used hashtags in this movement are #tolakomnibuslaw (425,461 lines), #GagalkanOmnibusLaw (120,537 lines), #JegalOmnibusLaw (21,516 lines), and #JegalSampaiGagal (36,848 lines). In this movement, students did not dominate the conversation, as many more different groups of society were involved, including mostly labor groups.\n\nThe most mentioned hashtag, #TolakOmnibusLaw, first appeared on October 6, 2020, at midnight. In Figure 4, we can see that the words #student and #mahasiswa were less widely used than words such as #pembohong (liar), #penghianat (traitor), or #Omnibus. This shows that the conversation was dominated by the substance of the criticism and did not focus on the actors as in #ReformasiDikorupsi. Apart from #Omnibus, #liar, and #traitor, criticism was expressed in a strong language such as #reject, #annul, #freedom, #fight, #right, and #justice.\n\nThe readings for #GagalkanOmnibusLaw involved 120,537 lines of conversation as shown in Figure 5, initially mentioned on October 6, 2020, at 06:59:59. Similar to #tolakomnibuslaw, the lines were dominated by words such as “liar,” “traitor,” and “omnibus.” Other words included #keamanan or “security,” #usul or “initiative,” #subversif or “subversion,” #dituduh or “accused,” #dibungkam or “silenced,” #ditimbang or “considered,” #mengganggu or “disturb,” and #batalkan or “cancel.”\n\nWe found a similar pattern for #jegalomnibuslaw, also first appearing on October 6, 2020, at 21:59:57, as shown in Figure 6.\n\nTwo days after the initial mention of #jegalomnibuslaw, another hashtag, #jegalsampaigagal was first mentioned at 00:00:16. In Figure 7, we see that conversations with this hashtag were dominated by the word “fight” (lawan), a word often quoted from a poem by Widji Thukul, a pro-democracy activist who disappeared in 1997 for his “subversive” and critical poems. The words Widji, Wiji, Thukul, and #lawan were used repeatedly and dominated conversations during the Tolak Omnibus Law movement.\n\nThe active roles of K-Poppers in the movement indicated youth involvement. K-Poppers are a community of young people. Generally, Generation Z means people who were born between 1997 and the 2000s and are devoted fans of popular Korean products, including movies and songs. The top hashtags first appear on accounts representing K-Poppers that not only use the names of Korean artists or popular Korean words but whose stories and main pages generally relate to K-Pop. K-Poppers’ intense involvement in this movement (Mulyana, 2022) can be observed from the SNA shown in Figure 8.\n\nCN-01: @CNNIndonesia, DP-02: @DPR_RI.\n\nK-Poppers, academic accounts, BEM, NGOs, and activists presented the main opposition to the Omnibus Law. These accounts united and supported each other to form a large cluster (Fahmi, 2020), showing the significant role of K-Poppers as a solid and influential group in the #TolakOmnibusLaw movement on Twitter. Drone Emprit’s research identified an extraordinary increase in conversations on Twitter after the Omnibus Law was passed (Fahmi, 2020). K-Poppers’ presence can be seen in the number of profile photos in the conversation about the Omnibus Law (Fahmi, 2020).\n\nOur dataset includes many accounts with K-Pop terms and names of artists. The most retweeted can be seen in Figure 8. We identify K-Popper accounts using Korean terms or elements of idol and group names in the Twitter account name, as well as profile photos and tweets discussing various K-Pop matters.\n\nFrom our SNA mappings, we identified many K-Poppers accounts that were involved in the #TolakOmnibusLaw movement. If we look more specifically at the SNA in the middle position, which occupies the most central position in the movement, we obtain Figure 9.\n\nCN-01: @CNNIndonesia, DP-02: @DPR_RI.\n\nTo see how important the role of K-Poppers is in the movement, we looked at the most referenced account (LA-03), and saw that for #TolakOmnibusLaw, this account was followed and retweeted by various other accounts, including the Indonesian Parliament (@dpr_ri) and public figures such as Najwa Shihab (@najwa_shihab), a famous senior journalist and TV host, NGOs such as LBH Yogyakarta (@LBHYogya), and mainstream media like CNN (Figure 10).\n\nLB-05: @LBHYogya, DP-02: @DPR_RI.\n\nAnother account (DO-04) that is also heavily referenced in conversations on #TolakOmnibusLaw also had many followers and was often retweeted, especially by fellow K-Popper accounts, as shown in Figure 11.\n\nFrom the information above, we see the vital role of young people in these two movements which present criticism towards the state policies. This study aims to provide a snapshot and explanation of the political participation of young people in digital activism, both online and offline, criticizing government policies. Furthermore, we observe different patterns for the two movements. In #ReformasiDikorupsi, students dominate the protests. The repression and violence of the security forces ultimately led to digital activism that focused on topics related to students.\n\nConversely, in the #TolakOmnibusLaw protests, students, along with other elements of society, especially workers, took to the streets and protested state policies that were not transparent and participatory. Digital activism started to grow when offline action started (Rahmah et al., 2020). This was also conditioned by the COVID-19 pandemic, causing students to participate in smaller numbers than the previous year. Although young K-Poppers were involved in #ReformasiDikorupsi, their role in the #RejectOmnibusLaw movement was more active and significant from the beginning.\n\nThe extensive data analysis method we chose in this study has several weaknesses. First, quantitatively using big data, we can only analyze patterns and interpret them to get answers to research questions. However, we needed the opportunity to investigate in depth and verify what motivates Twitter users to engage in digital activism and their experiences in that activism. The second, which is also very principal, is the limitation in verifying the owners of these accounts. In this case, we focus on the criteria of young people who are, among other things, limited by age, but this is precisely what needs to be verified from the hundreds of thousands of accounts included in our analysis. However, two of the students on our team involved in this study conducted their studies with a specific focus on investigating specific accounts. The first research focuses on the role of k-poppers in the #TolakOmnibusLaw movement, and the second is the role of pro-democracy activists in mobilizing the #TolakOmnibusLaw movement.\n\n\nConclusion\n\nThroughout this article, we provided an overview and understanding of the phenomenon of youth involvement in two critical movements in Indonesia since the Reformation began in 1998, namely the 2019 #ReformasiDikorupsi and the 2020 #TolakOmnibusLaw. Specifically, we focused our investigation on youth engagement in digital-based social movements on Twitter. Using data mining techniques, we confirmed that youth groups, especially students and millennial K-Poppers, actively participated in the movement and mobilized it by generating hashtags and expanding conversations on Twitter. The emergence of a digital society allows for mutual connection and expansion of the venue for freedom of expression as well as a form of active participation in political developments at the state level. Thus, this group of youth provided a valuable contribution to the development of democracy in Indonesia. Although the activism of young people on social media is massive, this movement is inseparable from the large-scale demonstrations that took place offline in many large cities in Indonesia. In this case, the two movements, online and offline, influenced each other. The online medium constituted a recruitment space for building, framing, and mobilizing the offline movement. As Cammaerts (2015) highlights, activism in social media can involve three activities: mobilization and recruitment, channeling communication, and direct action opposing the government’s policies. Mobilization and recruitment took place before and during the offline movement. One example is #gejayanmemanggil, or gejayan calling, referring to Gejayan, a meeting point in Yogyakarta where students gather and consolidate offline. As alternative communication channels, social media facilitate activists’ self-mediation by distributing goals and framing movements more efficiently and enable activists to transmit text and visual discourse, as well as afford opportunities for communities and subordinate groups to build alternative collective identities. Direct actions were communicated effectively in social media, helping construct the binary opposition of “Us” (#Kita) and “Them” (#Mereka).\n\nConversely, the repression of demonstrators, especially university students and secondary school students, strengthened the movement with broader forms of solidarity and mobilization. As in Hong Kong (Wong, 2021), young people’s reliance on social media to receive and share news and information on public affairs created an echo chamber effect that significantly divided social media-engaged youth from the rest of the population.\n\nThe massive size of this movement, online and offline, of course, cannot be separated from the context of its emergence. In this case, illiberal democratic practices, such as non-transparency and exclusivity in policy making by certain elites, policy inconsistencies, or responses to criticism with violence and repression, are alarms for young people to express their concerns and voice their aspirations. Diaz, a student who joined in an offline demonstration and later went viral in social media for a tweet on cosmetic brands suitable for a demonstration, stated in a media interview: “Yesterday’s demo proved many things, but what should be highlighted the most is that our situation means that it is severe. That is why students protested in large numbers” (Adam, 2019). This statement shows the concern of young people for the socio-political conditions in Indonesia, and their participation in voicing these concerns is a separate part of the meaning of their political identity.", "appendix": "Data availability\n\nThe underlying data to this research cannot be shared due to the ethical and copyright restrictions surrounding social media data. The Methods section also contains detailed information to allow replication of the study. Any queries about the methodology should be directed to the corresponding author.\n\n\nAcknowledgement\n\nWe would like to thank Anandha Rizky and Tiara Alya, who assisted the team with preparation and data processing. We also would like to thank Bimo, Andrew, Ambrosius, Alif, Ammar, and Rifaldi for assisting with data cleaning and categorizing more than 650,000 lines of Twitter conversations, and Sardo Hutauruk and the team from Bhinneka Kultura, who assisted with data mining. This paper is an extended version of a paper on preliminary research finding presented in the 3rd Jakarta International Conference on Social Sciences and Humanities (JICoSSH) 2021. The paper (https://doi.org/10.18502/kss.v7i12.11516) was published in the Conference proceeding, and was looked over by the conference organiser but not peer reviewed.\n\n\nReferences\n\nAdam A: Memahami Peran Gen Z dalam Aksi #ReformasiDikorupsi di DPR. Tirto.id. 2019 26 September. accessed on 24 April 2022. Reference Source\n\nAgur C, Frisch N: Digital Disobedience and the Limits of Persuasion: Social Media Activism in Hong Kong’s 2014 Umbrella Movement. Social Media + Society. January 2019; 5: 205630511982700. Publisher Full Text\n\nBadan Pusat Statistik: Statistik Kependudukan 2020. Jakarta: BPS; 2021. Reference Source\n\nBaybars-Hawks B: New Media Politics: Rethinking Activism and National Security in Cyberspace. Cambridge: Cambridge Scholar Publishing; 2015.\n\nCammaerts B: Social Media and Activism.Mansell R, Hwa P, editors. The International Encyclopedia of Digital Communication and Society. Oxford, UK: Wiley-Blackwell; 2015; 2015. : pp. 1027–1034. Publisher Full Text\n\nDiprose R, McRae D, Hadiz VR: Two Decades of Reformasi in Indonesia: Its Illiberal Turn. J. Contemp. Asia. 2019; 49: 5.\n\nDzulfaroh AN: Tiga Catatan Kritis untuk Omnibus Law UU Cipta Kerja.7 September 2020. Accessed on 7 August 2022. Reference Source\n\nEysenbach G: Can Tweets Predict Citations? Metrics of Social Impact Based on Twitter and Correlation with Traditional Metrics of Scientific Impact. J. Med. Internet Res. 2011; 13(4): e123. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFahmi I: RUU Omnibus Law Disahkan K-Popers Strike Back.2020 6 October. Reference Source\n\nGabrilin A: 2 Mahasiswa Universitas Halu Oleo Jadi Korban Tewas Demo di Kendari.27 September, 2019. Accessed on 24 April 2022. Reference Source\n\nGraeff E: Youth Digital activism. United Nations World Youth Report, Youth Civic Engagement. New York: the United Nations; 2016; 95–107.\n\nGrodzinsky FS, Miller K, Wolf MJ: Ethical Issues in Open Source Software. J. Inf. Commun. Ethics Soc. 2003; 1(4): 193–205. Publisher Full Text\n\nHadiz VR: Indonesia’s Year of Democratic Setbacks: Toward a New Phase of Deepening Illiberalism? Bull. Indones. Econ. Stud. 2017; 53: 3.\n\nKollock P, Smith M: Communities in Cyberspace. Routledge; 1999.\n\nLetierce J, Passant A, Breslin J, et al.: Understanding How Twitter is Used to Spread Scientific Messages. Proceedings of the WebSci10: Extending the Frontiers of Society On-Line. Raleigh, NC: US; 2010. Reference Source\n\nMadrim S: 10 Jurnalis Jadi Korban Kekerasan Saat Demo Mahasiswa.29 September 2019. Accessed on 24 April 2022. Reference Source\n\nMei E: Youth-Led Social Identity and Movements: A Case Study of Youth Activism in Hong Kong. Aleph, UCLA Undergraduate Research Journal for the Humanities and Social Sciences. 2021; 18. Publisher Full Text Reference Source\n\nMulyana T: Aktivitas Digital Politik K-Popers dalam Gerakan Menolak Omnibus Lawdi Media Sosial Twitter. Research Seminar of Political Science Department. Jakarta: Universitas Pembangunan Nasional Veteran Jakarta; 2022. not published.\n\nOrfan SN: Political participation of Afghan Youths on Facebook: A case study of Northeastern Afghanistan. Cogent Soc. Sci. 2021; 7(1): 1857916. Publisher Full Text\n\nPaskarina C: Digital Activism and Democracy in Indonesia Learning from the Foregoing Research Issues (2014–2020). Indonesian Journal of Political Research (IJPR). 2020; 1: 43–57.\n\nPersada S: Galang Dana Aksi Mahasiswa, Ananda Badudu Ditangkap Polisi.27 September 2019. Accessed on 24 April 2022. Reference Source\n\nRahmah FE, Ma’rufah LP: Di Balik Aksi Mahasiswa Menolak UU Omnibus Law Cipta Kerja.6 November 2020. Accessed on 10 February 2023. Reference Source\n\nRogers R: Digital Methods for Web Research.Scott RA, Buchman MC, Kosslyn SM, editors. Emerging Trends in the Social and Behavioral Sciences. California: Sage Publication; 2015; pp. 1–22.\n\nSairambay Y: The contributions of new media to young people’s political participation in Russia and Kazakhstan. Centr. Asian Surv. 2021; 41: 571–595. Publisher Full Text\n\nSaputra MG: Usman Hamid: 402 Orang Jadi Korban Kekerasan Polisi saat Demo UU Cipta Kerja. Merdeka.com. 2020 2 December. Accessed on 27 April 2022. Reference Source\n\nSastramidjaja Y: Indonesia: Digital Communications Energising New Political Generation’s Campaign for Democracy. ISEAS Perspective. Singapore: 2020; 16(March 31).\n\nSastramidjaja Y, Rasidi PP: The Hashtag Battle over Indonesia’s Omnibus Law: From Digital Resistance to Cyber-Control. ISEAS Perspective. Singapore: 2021; 95(July 21).\n\nSaud M, Margono H: Indonesia’s rise in digital democracy and youth’s political participation. J. Inform. Tech. Polit. 2021; 18: 443–454. Publisher Full Text\n\nTashakkori A, Creswell JW: Editorial: The New Era of Mixed Methods. J. Mix. Methods Res. 2007; 1: 3–7. Publisher Full Text\n\nWilliams K, Durrance JC: Social Networks and Social Capital: Rethinking Theory in Community Informatics. J. Community Inform. 2008; 4: 1–20.\n\nWong W: Youth Participation and Social Media: Evidence from the Youth Activism and Social Movement of Hong Kong (September 14, 2021).2021. SSRN. Publisher Full Text Reference Source" }	[ { "id": "178191", "date": "15 Jun 2023", "name": "M. Zaenul Muttaqin", "expertise": [ "Reviewer Expertise Policy Communication" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper raises a comprehensive theme, paying attention to political participation and youth digital movements in Indonesia. Overall, this study uses the right method to answer what is the research problem formulation. It's just that there is no clear focus. In every part of the writing, apart from lack of consistency.\nAbstract\nThe younger generation has always been at the forefront and made a significant contribution to social movements that are critical of state policies. The purpose of this research is to explore the relationship between youth political participation, digital media, and the development of youth political identity. The political identity of young people needs to be emphasized in the concluding part of this section.\nIntroduction\nThere is no explanation regarding the platform that is the focus of research in the background section. The author can ensure the focus of his explanation, is it the role of the younger generation or the role of social media? In addition, this study describes too many problem formulations, so the authors lose focus. For that the author must explore a topic that is urgent.\nAnswering this, will provide an explanation regarding the unclear structure and contribution of this research in a consistent and systematic manner.\nLiterary Review\nIn this section, paragraph four, the statement that online activism has no substitute for offline activism needs to be clarified.\nMethods\nThe keywords used need to be explained by the author, so as not to confuse the withdrawal of the keywords used in this reader's research.\nIn this section sufficient detail of the methods and analysis is provided to allow replication by others as it combines both quantitative and qualitative research for a comprehensive problem\nResults\nThe author needs to add a discussion section. Because the results of this study look partial without adequate focus\nConclusion\nIn this section, the authors need to align with the objectives and results of this study\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "11169", "date": "09 Apr 2024", "name": "Sri Lestari Wahyuningroem", "role": "Author Response", "response": "1. We’ve revised the introduction, main analysis and conclusion, to make it clear that the focus of this article is to look on the roles of young people in social movement through digital platform, and to discuss their engagement and mobilization that contribute significantly in the larger movement. We’ve revised the introduction, main analysis and conclusion, to make it clear that the focus of this article is to look on the roles of young people in social movement through digital platform, and to discuss their engagement and mobilization that contribute significantly in the larger movement. 2. We've revised the Abstract as suggested. 3. We've revised the Introduction to be more focus as suggested by the Reviewer. 4. We've made the clarification as suggested. 5. Discussion was added to include the focus if the paper. 6. We've revised to align with objectives of the study." }, { "c_id": "11173", "date": "09 Apr 2024", "name": "Sri Lestari Wahyuningroem", "role": "Author Response", "response": "Thank you for comments and feedbacks from the Reviewer." } ] }, { "id": "191178", "date": "17 Aug 2023", "name": "Oluyinka Osunkunle", "expertise": [ "Reviewer Expertise Political Communication", "Media and Society", "new/social media efficacies and Stakeholder Relations." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nContribution of Article to Knowledge The paper no doubt contributes to knowledge in the field and especially looking at youth political participation in digital-based social movements.\nIntroduction The author/s gave a very good background to the study by looking at Internet and social media and how they have influenced the participation of youths inter alia student movements in digital democracy in Indonesia. The article also made reference to certain protests against corruption, and changes in democratic patterns by citing protests such as the #ReformasiDikorupsi movement in 2019 and #TolakOmnibusLaw movement in 2020. #ReformasiDikorupsi and also #TolakOmnibusLaw, which was a 2020 movement of students, trade unions, and civil society groups.\nThis paper is unique and should contribute to knowledge in the sense that it focuses on the relationship between youth political participation, digital media, and the development of youth political identity while also analyzing young people’s experiences of participation in Indonesia, especially during the mass protests of #ReformasiDikorupsi in 2019 and #TolakOmnibusLaw in 2020.\nAlso noteworthy is the fact that the paper highlights the role of young citizens not only as participants, but also core as actors who mobilized these protest movements to become so large-scale. Interestingly, the study also made reference to other youth political participations around the world as the Indonesia cases were discussed.\nLiterature Review The author/s have reviewed current/recent literature, which is a page and a half, which in my view, I deemed to be too little unless if the Journal allows it. Adding a paragraph of discussion on another key issue would do the paper a lot of good. Also, the author/s only had a single long discussion under Literature Review without any heading or subheading to show or demarcate the issues or literature being reviewed. Separating discussions under suitable heading/subheading helps to ensure clarity and better understanding to guide the readers. The author/s should revise and ensure this to improve the quality of the paper.\nMethod The study design is good as the paper/study has made use of suitable research method for data collection and analysis with a mixed-method approach employed to collect and analyze case study data by integrating complementary quantitative and qualitative approaches. The data considered or analysed in this study were digital conversations produced and mobilized by netizens on Twitter within the conversation period from October 2018, when the #ReformasiDikorupsi started, until the end of November 2019, after the #TolakOmnibusLaw movement ended. This research quantitatively used text mining, machine learning word clouds, and social network analysis (SNA) with specific computational configurations to produce quantified text data.\nData Analysis/Findings/Discussion I see that data was analysed but for the sake of the readers and to ensure clarity in this paper, the author/s need to clearly show us where data analysis, findings and discussions are in this paper. After a good discussion on ‘Methods’, the author/s went on to discuss ‘Ethical Approval’ and after this, there is a discussion titled ‘The emergence of the #ReformasiDikorupsi and #TolakOmnibusLaw movements’. The question here is, could this the beginning of the section on Data Analysis or Findings? Or is it focused on reviewing literature or just discussing about the movements under study?\nIt therefore becomes very important for the author/s to properly demarcate the writings to ensure clarity. If the discussion after ‘Ethical Approval’ is Data Analysis or Discussion of Findings etc, then they should put a suitable heading/subheading there to show this to ensure clarity and also help the readers to have a good understanding of key issues discussed.\nStyle and Clarity There are no grammatical or spelling glitches and the author’s writing style is clear to some extent.\nConclusion The author/s have come up with a very good conclusion in relation to the study.\nRecommendation The paper is well written and very relevant to contemporary society considering the several global cases of youth political participation in digital-based social movements. Documenting the use of the Internet and social media and how they have influenced the participation of youths inter alia student movements in digital democracy in Indonesia is noteworthy. There is evidence of good data analysis and conclusion too. In light of this, I recommend that the paper be accepted with minor correction – the author/s need to clearly demarcate / identify the Data Analysis section. They need to read through the paper again to ensure it is clean and well edited and that there is a good flow across the sections and headings therein.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11172", "date": "09 Apr 2024", "name": "Sri Lestari Wahyuningroem", "role": "Author Response", "response": "The focus was adjusted as suggested by the Reviewer. The literature review has been shortened as suggested by the Reviewer. We made clear the discussion into context and data analysis and findings sections. This is to make clear of the structure and focus as commented by the Reviewer." }, { "c_id": "11174", "date": "09 Apr 2024", "name": "Sri Lestari Wahyuningroem", "role": "Author Response", "response": "Thank you for the comments and feedbacks from the Reviewer." } ] } ]	1	https://f1000research.com/articles/12-543
https://f1000research.com/articles/13-389/v1	25 Apr 24	{ "type": "Research Article", "title": "Demand for digital skills, skill gaps and graduate employability: Evidence from employers in Malaysia", "authors": [ "Poh Kiong Tee", "Ling Chai Wong", "Morakinyo Dada", "Bee Lian Song", "Chee Pung Ng", "Ling Chai Wong", "Morakinyo Dada", "Bee Lian Song", "Chee Pung Ng" ], "abstract": "Background A major workforce inadequacy and the change in skill demanded have been observed due to the digital transformation. This study aims to identify the digital skills demanded by employers, focusing on exploring the skills gaps among the graduates that impact graduate employability.\n\nMethods A cross sectional online survey was conducted among the companies registered with the Malaysian Productivity Corporation (MPC). Demand for digital skills was assessed using descriptive analysis of mean scores of the employers’ rating in digital skills at present and in future. A pair sample t-test was performed to explore the existence of skill gaps, by comparing the demand versus competencies of the graduates’ digital skills in the workplace.\n\nResults Of the 393 responses collected, 376 responses were used for final analysis. The findings show that the current top three digital skills in demand are “information and data literacy”, “problem-solving”, and “digital content creation”. Whereas the top digital skills for future demand are “problem-solving”, “safety”, and “communication and collaboration”. In addition, the most significant (digital) skill gap is found in “communication and collaboration skills” followed by “problem-solving” and “safety” skills.\n\nConclusions These findings provide insights into the digital skills demanded by employers in IR 4.0, allowing the practitioners, education service providers and policymakers to do better planning on human capital management and training development. By focusing on identifying the current and future demand for digital skills while exploring the digital skill gaps among the graduates, this study provides insight into the employability skills required by the graduate before entering the job market.", "keywords": [ "Digital transformation", "Digital society", "Digital economy", "Digital skills", "IR 4.0", "Digital skill gaps", "Graduate employability." ], "content": "Introduction\n\nThe world has entered the new millennium of the Fourth Industrial Revolution (IR 4.0). New technologies and digitalisation significantly change nearly every aspect of our socioeconomic activities (Khan et al., 2021; Tee et al., 2021). Traditional businesses are adopting new technologies to navigate a more extensive and challenging transformation of their operating processes; in the meantime, governments have made efforts to support the adoption of IR 4.0. The digital transformation affects the company’s operating structure and competitiveness and the need for human capital (Rahmat et al., 2021; Tee et al., 2022). As the traditional model embraces new technologies and transforms into an intelligent environment, jobs will become more complex (Caruso, 2018; Tsiligiris and Bowyer, 2021) while a significant workforce deficiency and shift in skill demand have been observed in the workplace [Economic Planning Unit (EPU), 2021; Rahmat et al., 2022]. Automation and digitalisation in the workplace are reshaping the employment landscape and bringing new challenges to human resources management, particularly in aligning the employees’ digital skills and competencies with the technological revolution [Lee, 2019; World Economic Forum (WEF) 2016 and 2020]. Indeed, changes in the job requirements due to digital transformation and automation are the primary causes of job loss (Kimball, 2021).\n\nIn the transition to IR 4.0, the employees’ roles changed because of the changes to the work’s content, processes, and environment (Lim et al., 2021), which caused a shift in the skills demanded for employment. Beyond technical skills, digital skills in information management, communication, content creation, safety and problem-solving in the digital environment are in high demand (Vuorikari et al., 2016). As highlighted by Mercer (2019), recruiting or equipping employees with those digital skills is vital for supporting innovation and technology adoption for economic progress. Specifically, today’s work, employability, education, and social activities are being transformed by digitalisation.\n\nConsidering the skills demand arising from the dynamic transformations in the nature of work, employees, educational institutions, and employers encounter challenges in accurately predicting the requisite skill sets for employment and adequately preparing for the demands of the job market. Nevertheless, past studies [Balcar et al., 2018; Institute of Student Employers (ISE), 2018; Vuorikari et al., 2016] revealed that graduates today lack the fundamental “digital skills” needed in the workplace. The gaps in digital skills among graduates pose a growing concern to educators, industry and the government, particularly the emergence of IR 4.0, which continues to disrupt business operations and occupations at a pace that outpaces employees’ ability to adapt. This circumstance may lead to unemployment or underemployment among graduates globally (Deloitte, 2015). As highlighted by the World Economic Forum (2020), these digital skill gaps are expected to widen as employers increasingly prioritize digital competencies across various professions in the coming five years (2025).\n\nReviewing the statement above, it is evident that adopting IR 4.0 has substantially impacted the industry concerning the demand for skills, skills shortages, and unemployment. It is apparent that the future workforce needs to be technologically savvy; fresh graduates need to have a solid understanding of digital tools and technologies and job knowledge to add value to their work (Khuraisah et al., 2020). In a similar vein, the digital economy has been recognized as a key economic growth area (KEGA) in accomplishing Wawasan Kemakmuran Bersama 2030 (WKB 2030) and the Twelfth Malaysia Plan (RMKe-12), to transform Malaysia into a nation that achieves sustainable development with inclusive growth. The Malaysian government has implemented various measures to cultivate prospective digital talents and upskill or reskill the existing workforce to enhance the nation’s readiness to embrace the digital economy (Economic Planning Unit, 2021).\n\nGiven the prevailing employment landscape, characterised by a demand for multiple skills (Tee and Chan, 2016), one may contemplate whether graduates possess a comprehensive range of requisite abilities, specifically digital proficiencies aligned with the nation’s transition towards a digital economy. Indeed, it is always preferable for young graduates to acquire multiple skill sets, including technical and non-technical digital skills, to enhance their employment prospects (Nair et al., 2019; Rahmat et al., 2022). Nevertheless, information on the actual skill mix and employers’ perspectives on the employability of graduates in IR 4.0 still needs to be explored. This study aims to fill the gaps by (1) discovering the digital skills demanded by employers currently and in the future to justify the change of skills demanded in the workplace due to IR4.0. Thereafter, (2) comparing the entry-level graduates’ level of competencies in digital skills against the important of digital skills to identify the existence of digital skill gaps among entry-level graduates that impact their employability. Most importantly, the views and experiences of employers hiring entry-level graduates will be gathered.\n\n\nLiterature review\n\nThis study aimed to explore the perspective of employers concerning the demand for entry-level graduates’ digital skills. This study was grounded by the Resource-based view (Barney, 1991) in relation to the recruitment of future graduates and sustaining their employability.\n\nUnemployment and underemployment are pervasive challenges all nations face in light of the ongoing digital transformation [International Labour Organisation (ILO), 2020]. Similarly, the issue of graduate unemployment in Malaysia has garnered attention in recent years, attributed to the large number of graduates being produced by various higher education institutions in Malaysia, including public and private colleges and universities, polytechnics, and vocational colleges (Silva et al., 2019; Tee et al., 2022). The graduate unemployment rate in Malaysia was reported to increase to 4.1%, equivalent to 197,400 individuals in the same year (Department of Statistics Malaysia, DoSM, 2020).\n\nGraduate employability pertains to individuals who have completed higher education and navigated their post-graduation life and employment (Bennett, 2018; Tee et al., 2019). Universities have been portrayed in this context as producing graduates with the skills employers need. However, previous studies (Bennett, 2018; Clarke, 2018; Tsiligiris and Bowyer, 2021) found that, in addition to graduate skills and attributes, graduate employability depends on many other factors that are external to the educational process, such as changes in the skill demand as a result of the digital transformation. Also, most studies on employability skills were done before the dawn of the digital age. In contrast, the technical and non-technical skills that employers sought after would have changed over time due to the advancement of knowledge, technology, and globalisation. Therefore, it is imperative to investigate employers’ current and future skills demands and evaluate the present workforce’s (digital) skills and competencies to determine the presence of skills gaps or deficiencies. The findings of this study provide insight into the digital skills needed for graduates to succeed in their current and future jobs while lowering the youth unemployment rate.\n\nDigital skills refer to the competencies required to effectively use information and communication technologies (ICT) in various aspects of life (Gałan, 2022). These skills are essential in the 21st century and enable individuals to navigate and utilize digital tools and technologies for information management, communication, collaboration, critical thinking, creativity, and problem-solving (Saputra et al., 2021). Karacay (2017) found that employees must have information and communications technology (ICT) skills that facilitate collaboration and communication in the digital environment to perform tasks effectively in an I.R. 4.0-based system. Similarly, Van Laar (2020) identified the digital skills in the 21st century, inclusive of technical, informational, communicative, and collaborative competencies in a digital environment. Lee (2019) discovered that the graduates’ ability to use digital media to create creative content, information processing, and social networks is essential and frequently questioned during the job interview. However, Capone (2019) found that employers expect the graduates to have basic knowledge and understanding of operating digital technology to complete routine tasks instead of extensive statistical and programming knowledge. Van Laar (2020) further emphasises the importance of these digital skills as the prerequisites for individuals to thrive in today’s workforce.\n\nThe literature has consistently emphasized the critical need for digital skills across various domains in IR 4.0. Indeed, graduates must be equipped with these skills to effectively navigate the challenges and opportunities in the workplace presented in the digital era (Bastian et al., 2021; Joseph and Khan, 2020). Underpinned by the European Commission’s DigComp 2.0 framework (Vuorikari et al., 2016), this study conceptualizes the digital skills in the IR4.0 landscape consist of five categories: information and data literacy, communication and collaboration, digital content creation, safety, and problem-solving (Table 1). Specifically, this study aims to identify and rank the set of digital skills currently demanded by employers and likely to be in demand in future (next five years) to answer the following research question:\n\nRQ1: “Which areas of digital skills demanded by the Malaysian employers currently and in the future?”\n\nThe IR 4.0 has brought about significant changes in the job market, requiring individuals to possess a wide range of skills, making it challenging for fresh graduates to keep up and compete with more experienced candidates (Rahmat et al., 2021). Past studies have identified skill gaps in graduate employability within the framework of IR 4.0 and recognized that non-technical digital skills are regarded as significant qualities for enhancing employability in conjunction with technical skills (Karacay, 2017; Khuraisah et al., 2020). Indeed, cultivating digital skills is considered essential in higher education, given that they hold equal significance to technical skills (Aidah et al., 2019; Rahmat et al., 2022; Tee et al., 2019). Moreover, a disparity exists between the academic setting and the industry’s demands concerning graduate employability, underscoring the necessity to explore the skill gaps to tackle this concern (Khuraisah et al., 2020; Unni, 2016).\n\nThe Australian Institute of Management (AIM, 2009) defines skill gap as the skill disparity between the skills required by the employers and the employees’ competencies in performing tasks. It reflects the employees need for more skills to meet job requirements (Hogarth and Wilson, 2003; Rathelot and Van Rens, 2017) since the presence of skill gaps is the main contributing factor towards unemployment, thereby having significant financial implications for a nation’s economic development (Rathelot and Van Rens, 2017; Suleman and Laranjeiro, 2018; WEF, 2016). Employers’ viewpoints should be taken into account in order to address the skills gaps (Balcar et al., 2018; Tomlinson, 2017; Truong et al., 2018), and most of the past studies employed the same approach to assess the magnitude of the skills gap by comparing employers’ rating score of the important of different skills (i.e., soft skills, technical skills, and digital skills) with the level of satisfaction on the employees’ performance (Abbasi et al., 2018). Through the skill gaps analysis, companies can assess the candidate’s competencies during the recruitment process by matching the skills possessed by candidates with the tasks required, thereby reflecting the employability skills of the individuals.\n\nThis study employs a methodology similar to the previous researchers (Abbasi et al., 2018; Kenayathulla et al., 2019), wherein employers’ expectations of the skills in demand were compared with the employee’s level of competence in similar skills. This study’s findings can ascertain potential gaps between the skills demanded and the skills possessed by the graduates in justifying their employability. Accordingly, this study aims to answer the following questions:\n\nRQ2: “What are the level of digital competencies of entry-level graduate employees in Malaysia?”\n\nRQ3: “What are the areas of digital skills gap among the entry-level graduate employees in Malaysia?”\n\n\nMethods\n\nThis study examines the employers’ demand for digital skills against the skill competencies of the entry-level graduate workforce with less than two years of working experience. Areas of digital skill gaps were identified by comparing the employers’ perceptions of the essential digital skills against the digital competencies of the employees (i.e., graduates) in performing their tasks.\n\nThis study was approved by the Ethics Committee of Asia Pacific University of Technology and Innovation, Kuala Lumpur, Malaysia (APUFE/02/2023) in July 12, 2023. All of the informants gave written and oral informed consent to participate in the study. Under the Personal Data Protection Act (PDPA) 2010, the researchers assure that all information collected is kept confidential and merely for the academic purposes.\n\nThe population in this study is the companies registered with the Malaysian Productivity Corporation (MPC) office. MPC is a statutory body govern by the Malaysian Ministry of Investment, Trade and Industry (MITI), aims to drive national productivity at all levels. The list of companies registered with MPC was obtained from MPC. The companies in Klang Valley (i.e., Selangor and Kuala Lumpur), Johor and Penang were selected for this study since these states had the most firms located and registered with MPC. Eight hundred ninety-five online questionnaires were distributed, and 393 responses were collected using a simple random sampling technique (i.e., 44% response rate). After the data screening process, 376 responses, including 215 from Klang Valley, 58 from Johor and 103 from Penang, were used for further analysis. In addition, the sectors in which companies operate are mainly the service sector (43%), manufacturing (32%), retail (18%) and other sectors (7%).\n\nThis study aims to identify the digital skills demanded by employers at present and in the future while investigating the presence of the digital skills gaps among Malaysian entry-level graduate employees by comparing the employers’ expectations against the skill competencies of the graduate employees in performing their work. The measuring items of the digital skills were adapted from the European Commission’s Digital Competence 2.0 (Vuorikari et al., 2016). Nineteen (19) items were adapted to measure the five (5) categories of digital skills (i.e., information and data literacy, communication and collaboration, digital content creation, safety, and problem-solving). One (1) question asks the employers to indicate the importance of the three common employability skills (i.e., technical skills, soft skills and digital skills). Another (1) question to measure graduate employability is asking employers to indicate the importance of digital skills when hiring fresh graduates. All items were measured using a 5-point Likert scale: “1= not at all important to 5= very important”.\n\nA descriptive analysis was conducted using IBM SPSS v26 (https://www.ibm.com/spss), to interpret the respondents’ (i.e., the employers) demographic profile and the phenomenon under study. The data was assessed based on the mean scores of the employers’ rating on the importance of digital skills required for the graduate employees to perform their tasks at present and in the future. The digital skill category with the highest mean score ranked one (1), was deemed the most important.\n\nA compare mean analysis using IBM SPSS v26, was conducted to identify the differences in mean scores between skills demanded at present with the level of competence to signify the magnitudes of said skill gaps. A higher mean gap value signifies a significant digital skill gap, and a negative value indicates that graduate employees lack the competencies to meet the employer’s expectations and vice versa. Lastly, a paired sample t-test was conducted to justify the existence of digital skills gaps among the entry-level graduate employees.\n\n\nResults\n\nThe data collected was analysed using descriptive analysis (i.e., means and standard deviation) and inferential statistics via comparison of means using a t-test. In addressing the level of preference for technical skills, soft skills and digital skills among employers, digital skills were regarded as very important and extremely important by 99.5% of the respondents (n=374), followed by soft skills (95.5%, n=359) and technical skills (78.5%, n=295). This result indicates that digital skills are highly demanded by employers in today's workplace, particularly by entry-level graduates.\n\nThe respondents (i.e., employers) were asked to rate the digital skills demanded at present and in the future using a 5-point Likert scale - “1= not at all important to 5= extremely important”. The results in Table 2 summarise the current and future demand for the five categories of digital skills. All these digital skills have mean scores greater than 3.60 (out of 5), denoting that the employers viewed all these skills as “fairly important” and nearing “very important” in the current state. “Information and data literacy” (μ= 4.048), “digital content creation” (μ=4.015) and “problem-solving skills” (μ=3.999) are the three most demanded digital skills by employers at present. Specifically, the mean score for the measuring item “integrating and re-elaborating digital content” has the highest mean (μ=4.213) and the item “engaging in citizenship through digital technologies” has the lowest mean score (μ=3.626).\n\n* Note: “1= very important to 5= very unimportant”.\n\nOn the other hand, all the digital skills are viewed as “very important” and nearing “extremely important” in the future (mean score above 4.0). The three areas of digital skills that are highly demanded in the future are “problem-solving skills” (μ=4.553), “safety” (μ=4.518), and “communication and collaboration” (μ=4.431) (Table 2). Notably, the results show the difference in the demand for digital skills at present and in the future. Both “safety” (μ=3.771) and “communication and collaboration” (μ=3.640), perceived as “fairly important” at present, were rated nearing “extremely important” in the future. It is observed that the demand for “information and data literacy” and “digital content creation” have been normalised, moving them from first and second in current demand to fourth and fifth in future demand.\n\nFurther study on the rising demand for digital skills in the future, the three categories of digital skills that show a significant increase in mean scores of above 0.50 when comparing the current and future demand are: “communication and collaboration”, “safety” and “problem-solving skills” (change in mean scores: 0.791, 0.747 and 0.554 respectively). Specifically, the mean scores for the measuring item “identifying digital competence gaps” has the highest mean (μ=4.566) and the item “browsing, searching and filtering information and digital content” has the lowest mean score (μ=4.045). The results imply that the digital skills demanded have changed over time due to the advancement of knowledge and technology in IR 4.0.\n\nThe entry-level graduate employee’s level of competencies is rated on a 5-point scale – “1=very poor to 5=very good”. The results shown in Table 3 revealed that the existing graduate employees scored “average” to nearing “poor” competence in most of the digital skills (mean score of 2.681 to 3.411, respectively). These employees are poor in “communication and collaboration\" skills (μ=2.713), “safety” skills (μ=3.000), and “problem-solving” (μ=3.135).\n\n* Note: “1= lowest to 5= highest”\n\nA paired sample t-test was conducted to identify digital skills gaps by comparing the differences in mean scores between the skills demanded (level of importance) against the level of competencies. The difference in mean score (i.e., skill gaps) indicates if graduates possess digital skills that meet employers’ expectations. A negative value indicates that the employees lack the competencies to meet the employer's expectations and vice versa.\n\nAs shown in Table 4, the p-value (2-tailed) is less than 0.05, concluding that there is a significant difference in the skill demand scores and competencies scores for pairs 1-5 (i.e., the five categories of digital skills). All negative values indicate the presence of skill gaps among the existing entry-level graduates in all identified digital skills in this study. Specifically, the highest gap exists in “communication and collaboration” (μ=-0.927), followed by “problem-solving” (μ=-0.864), “safety” (μ=-0.771), “digital content creation” and “information and data literacy” (μ=- 0.740 and μ=-0.654 respectively).\n\n\nDiscussion\n\nThe results in this study show that the majority of the employers (99.5%) preferred their entry-level graduate employees to possess digital skills compared to technical skills (78.5%) and soft skills (95.5%). Similarly, most employers (μ=4.5 out of 5) consider digital skills “extremely important” in hiring entry-level graduates. These findings are consistent with past studies that emphasise the high demand for digital skills for graduate employability in Malaysia (Khan et al., 2021; Khuraisah et al., 2020; Rahmat et al., 2022). Although hard skills (i.e., technical skills) are in demand during recruitment, digital skills are highly valued by employers, especially in coping with the technological advancement in IR 4.0 (Chen et al., 2018; Jewell et al., 2020; Malik and Venkatraman, 2017; Siddoo et al., 2019).\n\nThe results indicate that, at present, these digital skills are fairly important and (or) important to the employers. Among the five categories of digital skills, “information and data literacy”, “digital content creation”, and “problem-solving skills” are in high demand by employers at present. Considering the increasing adoption of new technology and information communication technology (ICT) in the workplace, the demand for information and digital literacy, as well as technology knowledge, is high at present (Khuraisah et al., 2020; Valdés et al., 2018). Thus, entry-level graduates are expected to be capable of “analysing and interpreting data and information” as well as “organising and retrieving data and information” in the digital environment, whereas “browsing and searching information” is considered a less important digital skill. This finding is supported by past studies (Jewell et al., 2020; Saunders, 2018), which found that browsing, searching and locating data are considered lower-order skills generally performed by clerical staff instead of graduate employees.\n\nBesides, digital content creation is also in high demand at present due to the rise of new information visualisation tools and the rapid growth of social media (Vuorikari et al., 2016). Consistently, past studies also highlighted the importance of digital content creation for knowledge workers to support their everyday digital practices in presenting, sharing, and reusing information. (Brown et al., 2016; Venkitachalam and Bosua, 2019). Another vital skill highly demanded in this digitisation era is problem-solving skills. While employers do not expect fresh graduates to possess broad expertise upon entering the job market, they expect the employees to be able to solve technical problems when operating devices in digital environments (Spector and Kinshuk, 2011). Jewell et al. (2020) and Aidah et al. (2019) suggest that graduates who can think critically and creatively while using digital tools to solve problems within digital contexts will create a competitive advantage over others.\n\nAs technology evolves, the emergence of new technologies introduces additional layers of complexity along with ongoing changes to the demand for digital skills in the future. The findings show a significant increase in the demand for digital skills in the future, in which all categories of digital skills are viewed as nearing “extremely important” (μ=4.5 out of 5) in the future. Consistently, the digital skills demanded by employers have changed along with the emergence of new technologies. “Problem-solving skills”, “safety”, and “communication and collaboration” are rated as the top three digital skills demanded in the future. The demand for “information and data literacy” and “digital content creation” have been normalised. These findings are consistent with past studies (Jewell et al., 2020; Khuraisah et al., 2020; Suarta and Suwintana, 2021), which addressed the importance of digital problem-solving skills as an instrumental in harnessing the potential of digital innovations while mitigating their risks. Also, the constant emergence of new issues associated with new information and communication technologies elevates the significance of problem-solving as a differentiator in the workforce.\n\nAlong with problem-solving skills, competence in protecting the company’s devices, personal data and privacy (i.e., “safety”) was perceived as an extremely important digital skill in the future. According to Rahmat et al. (2022), companies in digital transformation seem to utilise many digital tools and platforms to integrate internal systems with customer interfaces in their business operation. These companies are exposed to higher risks in data protection and violation of personal privacy. Hence, most employers demand future graduates to have basic “safety” skills to create a safe digital environment in the workplace (Frania, 2014; Tomczyk, 2019). Another vital skill highly demanded in the future is “communications and collaborations”. The Employers expect future graduates to have functional digital literacy and the ability to use core computer applications in data processing and information sharing through digital technologies. Entry-level graduates in this era must and should be able to communicate effectively in all digital forms (Chen et al., 2018; Othman et al., 2018). Indeed, virtual communication and collaboration are two vital skills needed in the future workforce (Ellahi et al., 2019; Picatoste et al., 2018; Siddoo et al., 2019).\n\nThe results indicate that the existing graduate workforce needs more competence in digital skills to meet their employers’ expectations. Gaps were found in all categories of digital skills. Notably, the finding shows that “information and data literacy” (i.e., digital literacy) was ranked relatively low in the skills gap compared to other digital skills. This statement is due to the fact that new generations are inherently tech-savvy, and these younger generations (graduates) tend to quickly adapt to new digital tools and platforms (Helsper and Eynon, 2010; Kennedy et al., 2008). The entry-level graduates’ ability to use digital tools (i.e., browsing and searching information) is increasingly seen as a foundational skill, similar to reading and writing, resulting in a small gap in “information and data literacy” compared to other digital skills.\n\nOn the other hand, the highest digital skill gaps were found in “communication and collaboration” and “problem-solving”. Notably, both are highly demanded skills in future employment. This finding has some consonance with the skills gaps identified in past studies. According to Nardo et al. (2020) and Rahmat et al. (2021), employees are expected to have (non-technical) knowledge and skills to use digital tools and technologies, interact with modern interfaces, and be aware of digital security in the IR 4.0 environment, to complement the lack of technical skills. However, most employers are unsatisfied with existing graduates’ non-technical skills, including communication and problem-solving skills, where the graduates need to adapt to the real working environment (Suleman and Laranjeiro, 2018). In a similar vein, a study on Malaysian graduate work-readiness by Verma et al. (2018) discovered that the university curriculum at present is unable to foster the skills needed in the workplace, which has a notable impact on students’ capacity to communicate effectively and a lack in critical thinking and problem-solving skills.\n\nThis study obtained feedback from employers on areas of digital skills that graduates need to enhance their employability in the new age. It is of practical relevance as the world is moving into the new age of IR 4.0 while there are changes in technology and skills demand. Following the government's aspiration to transform Malaysia into a digitally enabled and technology-driven nation in a digital economy, the findings of this study help various stakeholders (i.e., higher education providers and the authorities) develop a successful plan by highlighting the digital skills required for better employment opportunities. Employers and human resource professionals can use this information to inform their recruitment and talent development plans, specifically to create training and development program to close the identified skill gaps. A holistic approach to skill development beyond technical proficiency is also required, given the future emphasis on problem-solving, safety, and communication skills in a digital context.\n\nMoreover, the shift in the demand for digital skills that has been observed offers direction for curricular development in higher education, including modules that emphasize problem-solving, safety, and communication to equip graduates better to meet industry standards. Collaboration between academic institutions and industry can also help align curriculum with practical business demands. Lastly, the empirical findings in this study can also be used as a reference for the policymakers in Ministry of Education (MOE), Ministry of Human Resources (MOHR), Human Resources Development Foundation (HRDF) and training providers to develop policies and strategies for study/training curricula and methodology to ensure the related skills are imparted.\n\nTheoretically, this study extended from the employers’ perspective, as the “demand” in selecting candidates based on the required skills concerning recruiting future graduates and sustaining their employability. Underpinned by the Resource-based view, the findings of this study elucidate the graduate employment landscape by identifying the digital skills graduates must possess and whether these digital skills can be considered as a firm's resource, which may influence employers' hiring decisions in the 4IR environment.\n\nThis study has limitations that should be considered while interpreting the findings, notwithstanding the contributions and implications. The study focused on specific regions (states) within Malaysia, hence the results might not be easily applicable to other nations with diverse technology and economic environments. A more thorough understanding of the demand for digital skills can result from replicating the study in different contexts.\n\nThe data gathered was based on self-reported assessments of the employers. Due to social desirability or incorrect question interpretation, bias could be present. Using additional techniques, such as conducting interviews or carrying out direct observation, could provide a more comprehensive understanding of the skills and competences. Instead of using an objective evaluation, the study’s method for measuring skills depended on self-evaluation. To verify the self-reported data, future studies can include performance reviews or assessments from independent parties. Future research could examine the demand for digital skills within different sectors to provide tailored insights, given the distinct demands across various sectors. Moreover, this study offers an overview of abilities and skill demand at a specific period. A longitudinal study could monitor shifts in competence and demand over time, giving researchers a more dynamic knowledge of digital skill trends.\n\nThis study was primarily based on the premise that enhancing digital skills able to increase the entry-level graduates’ employability. However, personal qualities of the graduates seem to play crucial roles in their employment ability because higher quality person (i.e., a person with better soft skills) can contribute more to his or her employment ability. Moreover, recent studies have shown personal qualities as an important concern during employment (Al Asefer and Zainal Abidin, 2021; Tsiligiris and Bowyer, 2021). This study focused on the demand for digital skills, digital skills gaps and employability without contemplating the roles of personal qualities. We see this as a significant limitation of this study and suggest future studies to explore this aspect.\n\n\nConclusion\n\nIn light of the growing significance of digital skills in today’s society, this study offers an essential viewpoint concerning the demand for digital skills and the digital skill gaps in IR 4.0. The model developed in this study aims to specify metrics for evaluating digital skills that improve employability in Malaysia. Beyond the current study, future research will examine additional metrics for digital skills that affect graduate employability in Malaysia.\n\nThis study was approved by the Ethics Committee of Asia Pacific University of Technology and Innovation, Kuala Lumpur, Malaysia (APUFE/02/2023) in July 13, 2023. All of the informants gave written and oral informed consent to participate in the study. Under the Personal Data Protection Act (PDPA) 2010, the researchers assure that all information collected is kept confidential and merely for the academic purposes.", "appendix": "Data availability\n\nFigshare: Digital Skills_ Questionnaire & Dataset. figshare. Dataset. https://doi.org/10.6084/m9.figshare.25540798.v2 (Tee, 2024).\n\nThis project contains the following underlying data:\n\n• Data set: Full Data TPK_DS_092023.xlxs.\n\n• Letter for Participation & Questionnaire_TPK_DS.pdf.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” Attribution 4.0 International (CC BY 4.0)\n\n\nAcknowledgments\n\nWe acknowledge the support from the Asia Pacific University (APU) for awarding the Research Development Internal Grant (RDIG/08/2022) in sponsoring for the publication of this article.\n\n\nReferences\n\nAbbasi FK, Ali A, Bibi N: Analysis of skill gap for business graduates: A managerial perspective from the banking industry. Educ. Train. 2018; 60(4): 354–367. Publisher Full Text\n\nAidah AK, Kamariah AB, Parilah MS: Strategic university practices in student information literacy development.2019; 4(18): 9–15.\n\nAl Asefer MI, Zainal Abidin NS: Soft skills and graduates’ employability in the 21st century from employers’ perspectives: a review of literature. International Journal of Infrastructure Research and Management. 2021; 9(2): 44–59.\n\nAustralian Institute of Management (AIM): Australia's workforce skills gap.2009. (accessed 19 June 2023). Reference Source\n\nBalcar J, Šimek M, Filipová L: Soft skills of Czech graduates. Review of Economic Perspectives. 2018; 18(1): 45–60. Publisher Full Text\n\nBarney JB: Firm resources and sustained competitive advantage. J. Manag. 1991; 17(1): 99–120. Publisher Full Text\n\nBastian OA, Rahmat HK, Basri ASH, et al.: Urgensi literasi digital dalam menangkal radikalisme pada generasi millenial di era Revolusi Industri 4.0. Jurnal Dinamika Sosial Budaya. 2021; 23(1): 126–133.\n\nBennett D: Graduate employability and higher education: past, present and future. HERDSA Review of Higher Education. 2018; 5: 31–61.\n\nBrown C, Czerniewicz L, Noakes T: Online content creation: Looking at students’ social media practices through a connected learning lens. Learn. Media Technol. 2016; 41(1): 140–159. Publisher Full Text\n\nCapone M: Data skills and the fourth industrial revolution.2019. (accessed 08 August 2023). Reference Source\n\nCaruso L: Digital innovation and the fourth industrial revolution: epochal social changes? A.I. and Society. 2018; 33(3): 379–392. Publisher Full Text\n\nClarke M: Rethinking graduate employability: the role of capital, individual attributes and context. High. Educ. 2018; 43(9): 1–15.\n\nChen PSL, Cahoon S, Pateman H, et al.: Employability skills of maritime business graduates: industry perspectives. WMU J. Marit. Aff. 2018; 17: 267–292. Publisher Full Text\n\nDeloitte: Industry 4.0 Challenges and Solutions for The Digital Transformation and Use of Exponential Technologies. UK: Deloitte AG; 2015.\n\nDoSM: Unemployment rate.2020. (accessed 10 June 2023). Reference Source\n\nEconomic Planning Unit: Malaysia Digital Economy Blueprint. Putrajaya: Perpustakaan Negara Malaysia; 2021.\n\nEllahi RM, Ali Khan MU, Shah A: Redesigning curriculum in line with Industry 4.0. Procedia Computer Science. 2019; 151: 699–708. Publisher Full Text\n\nFrania M: New educational trends connected with the development of media and innovative technologies – A few reflections on the future perspectives on learning and teaching. Journal of Educational and Social Research. 2014; 4(4): 231–237. Publisher Full Text\n\nGałan B: The role of digital competencies in the glottodidactic process from the perspective of the representatives of the digital native community. e-mentor. 2022; 93(1): 64–76. Publisher Full Text\n\nHelsper EJ, Eynon R: Digital natives: where is the evidence?. Br. Educ. Res. J. 2010; 36(3): 503–520. Publisher Full Text\n\nHogarth T, Wilson R: Skill shortages, vacancies, and local unemployment: a synthesis of the exploring local areas, skills and unemployment analysis.2003. (accessed 19 June 2023). Reference Source\n\nInstitute of Student Employers (ISE): The global skills gap in the 21st century.2018. (accessed 15 June 2023). Reference Source\n\nInternational Labour Organisation (ILO): The socioeconomic impacts of COVID-19 in Malaysia: Policy review and guidance for protecting the most vulnerable and supporting enterprises.2020. (accessed 15 June 2023). Reference Source\n\nJewell P, Reading J, Clarke M, et al.: Information skills for business acumen and employability: A competitive advantage for graduates in Western Sydney. J. Educ. Bus. 2020; 95(2): 88–105. Publisher Full Text\n\nJoseph V, Khan N: Digital literacy tools to enhance English reading and writing skills: a detailed literature. Global Language Review. 2020; 3: 21–33. Publisher Full Text\n\nKaracay G: Talent development for Industry 4.0: managing digital transformation Springer Series in Advanced Manufacturing. Cham: Springer; 2017.\n\nKenayathulla HB, Ahmad NA, Idris AR: Gaps between competence and importance of employability skills: evidence from Malaysia. Higher Education Evaluation and Development. 2019; 13(2): 97–112. Publisher Full Text\n\nKennedy GE, Judd TS, Churchward A, et al.: First-year students' experiences with technology: are they really digital natives?. Australas. J. Educ. Technol. 2008; 24(1): 108–122. Publisher Full Text\n\nKhan N, Khan S, Tan BC, et al.: Driving digital competency model towards IR 4.0 in Malaysia. J. Phys. Conf. Ser. 2021; 1793.\n\nKhuraisah MN, Khalid F, Husnin H: Preparing graduates with digital literacy skills toward fulfilling employability need in 4IR era: a review. Int. J. Adv. Comput. Sci. Appl. 2020; 11(6): 307–316.\n\nKimball D: How digital transformation impacts the future of career transitions.2021. Reference Source\n\nLee MF: Digital skills measurement: a study on the Malaysian youth. 2018 IEEE Conference on e-Learning, eManagement and e-Services. 2019; pp. 52–55.\n\nLim TL, Omar R, Ho TCF, et al.: “The roles of work–family conflict and family–work conflict linking job satisfaction and turnover intention of academic staff”, Australian. J. Career Dev. 2021; 30(3): 177–188.\n\nMalik G, Venkatraman A: The great divide: skill gap between the employer’s expectations and skills possessed by employees. Ind. Commer. Train. 2017; 49(4): 175–182. Publisher Full Text\n\nMercer: Global talent trends 2019.2019. (accessed 20 July 2023). Reference Source\n\nNair S, Kaushik A, Dhoot H: Conceptual framework of a skill-based interactive employee engaging system: in the context of upskilling the present I.T. organisation. Applied Computing and Informatics. 2019; 19(1/2): 82–107.\n\nNardo M, Forino D, Murino T: The evolution of man–machine interaction: the role of the human in Industry 4.0 paradigm. Production & Manufacturing Research. 2020; 8(1): 20–34. Publisher Full Text\n\nOthman Z, Shan SW, Yusoff I, et al.: Classification techniques for predicting graduate employability. International Journal on Advanced Science Engineering and Information Technology. 2018; 8(4–2): 1712–1720. Publisher Full Text\n\nPicatoste J, Pérez-Ortiz L, Ruesga-Benito SM: A new educational pattern in response to new technologies and sustainable development. Enlightening ICT skills for youth employability in the European Union. Telematics Inform. 2018; 35(4): 1031–1038. Publisher Full Text\n\nRahmat AM, Mohd Adnan AH, Mohtar NM: Hybrid capabilities and Industry 4.0 job demands in recruiting Malaysian graduates. The International Journal of Academic Research in Business and Social Sciences. 2021; 11(1): 789–799. Publisher Full Text\n\nRahmat AM, Mohd IH, Omar MK, et al.: Integrating socio-digital skills in the industry 4.0 era for graduates' employability: an employers’ perspective. Journal of Positive School Psychology. 2022; 6(3): 8493–8507.\n\nRathelot R, Van Rens T: Rethinking the skills gap: a better understanding of skills mismatch is essential to finding effective policy options. IZA World of Labour. 2017; 391: 1–11.\n\nSaputra N, Nugroho R, Aisyah H, et al.: Digital skill during Covid-19: Effects of digital leadership and digital collaboration. Journal of Applied Management. 2021; 19(2): 272–281. Publisher Full Text\n\nSaunders L: Information literacy in practice: content and delivery of library instruction tutorials. J. Acad. Librariansh. 2018; 44(2: 269–278. Publisher Full Text\n\nSiddoo V, Sawattawee J, Janchai W, et al.: An exploratory study of digital workforce competency in Thailand. Heliyon. 2019; 5(5): e01723–e01728. Publisher Full Text\n\nSilva VL, Kovaleski JL, Pagani RN: Technology transfer and human capital in the Industrial 4.0 scenario: a theoretical study. Future Studies Research Journal: Trends and Strategies. 2019; 11(1): 102–122. Publisher Full Text\n\nSpector JM, Kinshuk: Learning to solve problems in the digital age: introduction.Ifenthaler D, Spector J, Isaias P, et al., editors. Multiple Perspectives on Problem-solving and Learning in The Digital Age. New York: Springer; 2011.\n\nSuarta IM, Suwintana IK: The new framework of employability skills for digital business. J. Phys. Conf. Ser. 2021; 1833: 012034. Publisher Full Text\n\nSuleman F, Laranjeiro AMC: The employability skills of graduates and employers’ options in Portugal. Educ. Train. 2018; 60(9): 1097–1111. Publisher Full Text\n\nTee PK: Digital Skills_ Questionnaire & Dataset. Dataset. Figshare. 2024. Publisher Full Text\n\nTee PK, Chan YF: Exploring factors towards career success in Malaysia. Int. Bus. Manag. 2016; 10(17): 3936–3943.\n\nTee PK, Cham TH, Low MP, et al.: The role of organisational career management: comparing the academic staff's perception of internal and external employability in determining academic success. Malaysian Online Journal of Educational Management. 2021; 9(3): 41–58.\n\nTee PK, Cham TH, Low MP, et al.: The role of perceived employability in the relationship between protean career attitude and career success. Aust. J. Career Dev. 2022; 31(1): 66–76. Publisher Full Text\n\nTee PK, Eaw HC, Oh SP, et al.: The employability of Chinese graduates in Malaysia upon returning to China employment market. International Journal of Recent Technology & Engineering. 2019; 8(2S): 358–365.\n\nTomczyk L: Skills in the area of digital safety as a key component of digital literacy among teachers. Educ. Inf. Technol. 2019; 25: 471–486. Publisher Full Text\n\nTomlinson M: Forms of graduate capital and their relationship to graduate employability. Educ. Train. 2017; 59(4): 338–352. Publisher Full Text\n\nTruong TTH, Laura RS, Shaw K: The importance of developing soft skill sets for the employability of business graduates in Vietnam: a field study on selected business employers. Journal of Education and Culture Studies. 2018; 2(1): 32–45. Publisher Full Text\n\nTsiligiris V, Bowyer D: Exploring the impact of 4IR on skills and personal qualities for future accountants: a proposed conceptual framework for university accounting education. Acc. Educ. 2021; 30(6): 621–649. Publisher Full Text\n\nUnni J: Skill gaps and employability: higher education in India. Journal of Development Policy and Practice. 2016; 1(1): 18–34. Publisher Full Text\n\nVan Laar E, Van Deursen AJ, Van Dijk JA, et al.: Determinants of 21st-century skills and 21st-century digital skills for workers: a systematic literature review. SAGE Open. 2020; 10(1). Publisher Full Text\n\nValdés RMT, Soriano AS, Álvarez CL: Resignification of educational e-innovation to enhance opportunities for graduate employability in the context of new university degrees. Journal of New Approaches in Educational Research. 2018; 7(1): 70–78. Publisher Full Text\n\nVenkitachalam K, Bosua R: Perspectives on effective digital content management in organisations. Knowl. Process. Manag. 2019; 26(3): 202–209. Publisher Full Text\n\nVerma P, Nankervis A, Priyono S, et al.: Graduate work-readiness challenges in the Asia-Pacific region and the role of HRM. Equality, Diversity and Inclusion. 2018; 37(2): 121–137. Publisher Full Text\n\nVuorikari R, Punie Y, Carretero GS, et al.: DigComp 2.0: The Digital Competence Framework for Citizens. Luxembourg Publication Office of the European Union. EUR 27948; 2016.\n\nWorld Economic Forum (WEF): The future of jobs employment, skills and workforce strategy for the fourth industrial revolution.2016. (accessed 20 June 2023). Reference Source\n\nWorld Economic Forum (WEF): The future of jobs report 2020.2020. (accessed 20 June 2023). Reference Source" }	[ { "id": "274442", "date": "25 May 2024", "name": "Melinde Coetzee", "expertise": [], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is of value and high relevance to the field of employability, especially gathering views from employers hiring entry level graduates. The problem statement is well-justified. The study aims are clear. Contextualization of study: The authors focused primarily on 4IR as context. The recommendation is to critically review and elaborate briefly on the relevance of the study to 5IR technology as well. Apart from 4IR informing the change in skill demand, the authors should critically review the 5IR’s (the future) impact on skills demands Check for grammatical errors- e.g. sentence in paragraph before literature review Thereafter, (2) comparing the entry-level graduates’ level of competencies in digital skills against the important of digital skills to…… - should read importance Literature review- the authors should briefly justify why and how the study is grounded by the Resource-based view Although the paper reflects relatively recent sources from the research literature (2020-2022), one would like to see more recent research literature added (2023/2024) to strengthen the contemporary relevance of the work. Table 1 used a 2016 source of digital competence as framework- what are current digital competence frameworks for 5IR? Is the 2016 competence framework still of relevance? The authors need to justify their assumptions of digital competencies needed by integrating more recent research literature corroborating the 2016 framework and measure. Overall, the paper is well-written and arguments flow logically The research methodology is suitable for the research aims The discussion is enriching and convincing.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "288764", "date": "10 Sep 2024", "name": "Noor Aslinda Abu Seman", "expertise": [ "Reviewer Expertise Management", "Marketing", "Green Supply Chain Management", "SMEs" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, this study is well-executed and provides significant insights into the digital skills demanded by employers in Malaysia, along with highlighting the skill gaps among graduates. The methodology is robust, and the findings are presented clearly. However, there are areas where improvements can be made:\nGraduate Employability Section\nCurrent Text: \"The graduate unemployment rate in Malaysia was reported to increase to 4.1%, equivalent to 197,400 individuals in the same year.\" Improvement: Please specify the year to which this data refers. For example, \"The graduate unemployment rate in Malaysia was reported to increase to 4.1%, equivalent to 197,400 individuals in 20xx.\" This adds clarity and context for the reader.\n\nTable Placement\nCurrent Placement: Table 1 is not optimally placed in the manuscript. Improvement: Table 1 should be placed immediately after the Research Question 1 (RQ1) statement. This will help in better aligning the table with the relevant section of the text, making it easier for readers to follow and understand the presented data.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "303733", "date": "18 Sep 2024", "name": "Md Jahangir Alam", "expertise": [ "Reviewer Expertise The authors need to develop the conceptual framework of this research The result and findings do not align and I recommend reviewing further article." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis research has a very high significance. However, I recommend the authors review the following articles:. As the conceptual and theoretical frameworks are missing, I recommend developing a conceptual framework for this study. To align the result with the discussion, there is still room for improvement. The auditors started with RQ2 and RQ3, but I did not find RQ1.\n\nDigitalization of higher education to achieve sustainability: Investigating students’ attitudes toward digitalization in Bangladesh Skills development for graduate employability in Bangladesh: Japanese language in TVET program e-Learning as a Doubled-Edge Sword for Academic Achievements of University Students in Developing Countries: Insights from Bangladesh Importance of Skills Development for Ensuring Graduates Employability: The Case of Bangladesh Skills development for sustainable career planning in Bangladesh: the case of gender equality in education Future-readiness and employable ICT skills of university graduates in Bangladesh: an analysis during the post-covid era Japanese investment for skills development program in attaining sustainable employability: The case of Bangladesh Sustainable employment for vocational education and training graduates: the case of future skills matching in Bangladesh\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "314046", "date": "20 Sep 2024", "name": "Samia Mokhtar Shahpo", "expertise": [ "Reviewer Expertise EducationLearnersPsychology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe subject of skills necessary to employ graduates is one of the topics that receive attention from the relevant authorities. The researchers formulated a title expressing the content of the research and provided a complete and interesting abstract. The research problem is specific and clear, and the questions are compatible with the objectives of the study. The methodology used is appropriate, and the statistical methods used are appropriate for the study design. Reviewing and discussing the results were logical and supported by evidence. However, the terms in the study were not defined in a specific, measurable procedural form. Benefits from previous studies have not been presented in the present study. For results, I recommend adding open-ended questions to the questionnaire or using interviews with employers and not just using the closed questionnaire.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-389
https://f1000research.com/articles/13-388/v1	25 Apr 24	{ "type": "Case Report", "title": "Case Report: Marfan’s Syndrome with Neurofibromatosis Type-2", "authors": [ "Jayant Vagha", "Naman Mishra", "Aishwarya A. Pashine", "Waqar M. Naqvi", "Ashish R. Varma", "Jayant Vagha", "Naman Mishra", "Aishwarya A. Pashine", "Ashish R. Varma" ], "abstract": "Background Marfan’s syndrome (MFS) and neurofibromatosis type-2 (NF-2) are rare autosomal dominant diseases caused due to mutations in chromosome number 15 and 22, respectively. The chance of both the diseases occurring in the same patient is extremely rare.\n\nCase presentation In this report a rare case of a 16-year-old boy having a coexistence of both MFS and NF-2 is reported. The clinical findings consisted of musculoskeletal abnormalities consisting of laxity of joints, positive Steinberg thumb sign test, positive Walker-Murdoch wrist test, dolichostenomelia, and arachnodactyly. Anthropometric abnormalities reported an increase in lower segment height than the upper segment. Diagnostic assessment revealed pectus carinatum, multiple meningioma, and heterogeneous lesions in bilateral cerebellopontine angle that were ruled out as bilateral schwannoma confirming the diagnosis of MFS and NF-2. However, both must be regarded as novel mutations, and as the position of the two genes is unrelated, it is most probable that two different mutations have occurred. β-blocker was recommended as a prophylactic measure to minimize aortic root stiffness and control aortic root dilatation. Furthermore, surgery and radiation therapy were planned for the management of NF-2; however, the patient expressed skepticism regarding the course of treatment and follow-ups; as a result, this data was reported at the time of discharge with non-specified duration of follow-ups.\n\nConclusions This case report demonstrates a rare case of MFS which is caused due to mutation in chromosome number 15 along with NF-2 which is caused due to mutation in chromosome number 22. Since the positions of the two genes are unrelated, it is concluded that two distinct mutations have occurred. As a result, this report highlights a rare coexistence of both mutations, which will benefit the medical profession in enhancing future studies.", "keywords": [ "Marfan’s Syndrome", "Neurofibromatosis Type-2", "Autosomal Dominant", "Connective Tissue Disease", "Chromosomal Mutations" ], "content": "Introduction\n\nMarfan syndrome (MFS) is an autosomal dominant hereditary connective tissue disease (CTD) with significant presentations in the skeletal, ophthalmic, and cardiovascular systems that are age-related and is caused due to mutation in the protein gene Fibrillin-1 (FBN1) and affects about 1 in 5,000 people worldwide.1–3 De novo variants can be present in up to 25% of patients with MFS,4 which means that the affected person has a new mutation. It has been shown that MFS is caused by FBN1 missense variations, insertions, deletions, and mutations linked to loss of expression from one allele,1,5 which is released and integrated into the extracellular matrix (ECM). Microfibrils, which are also known as FBN1, play a crucial role in ECM structures and are found in tissues or in close proximity to elastin fibres.1\n\nAortic root aneurysms that are asymptomatic, aortic dissections, ocular lens dislocations, and musculoskeletal anomalies with bone overgrowth are the most notable characteristics of MFS. It is not always necessary to perform genetic testing to validate the existence of FBN1 for diagnosis of MFS but can aid in differentiating MFS from other inherited disease syndromes that can demonstrate skeletal characteristics identical to MFS.6,7 Acute aortic dissections, which can be fatal, can develop from untreated aortic root aneurysms. Medical treatment is necessary for MFS to reduce the risk of dissection and slow aneurysm progression. The formation of an aneurysm must be routinely monitored with imaging methods such as echocardiography, Computed Tomography (CT), or Magnetic Resonance Imaging (MRI) in order to determine when precautionary repair surgery should be performed to prevent an acute aortic dissection.1\n\nThe other autosomal dominant disease seen in this case report is Neurofibromatosis type 2 (NF-2), which is marked by schwannomas, meningiomas, and ependymomas.8 The majority of adult patients with NF-2 have bilateral vestibular schwannomas, which are indicative of NF-2. They typically appear as an augmenting mass that extends from the internal acoustic canal into the cerebellopontine cistern.8,9 These tumours, however, may not always be present or may be too small to be seen on a routine CT or MRI scan. When this occurs, the development of non-tumoral calcifications, either with or without tumoral calcifications, indicate that NF-2 is a probable diagnosis.8 There may also be other cancers of the neurological system, such as tumours of the intrinsic spinal cord, spinal nerve root schwannomas and intracranial and spinal meningiomas.9 The coexistence of these two diseases is rare and therefore, this report highlights a rare case of a young boy having MFS along with NF-2.\n\n\nCase report\n\nThe case report was amended according to the CARE guidelines.\n\nA 16-year-old South Asian boy presented at the Acharya Vinoba Bhave Rural Hospital, Sawangi, India, with the chief complaints of swelling at different sites that was progressing in size all over the body, hearing loss and diminution of vision lasting 3 years along with behavioural disturbances. Additionally, his birth was from non-consanguineous marriage. He had a history of road traffic accident six years before that led to subarachnoid and subdural haemorrhages that were managed conservatively at that time.\n\nPhysical examination revealed thin built with the swelling at different sites. The musculoskeletal and anthropometric findings were evaluated based on Revised Ghent Criteria for MFS.1 Anthropometric measurements indicated height of 162 cm and weight of 36 kg, head circumference was found to be 55 cm and arm span was 170 cm. Additionally, upper and lower segment heights were measured separately, which were 65 cm and 97cm, respectively. The thoracic expansion from axillary perimetry was 80.5 cm and xyphoid perimetry was 78.77 cm. Musculoskeletal abnormalities included laxity of joints, a positive Walker-Murdoch wrist test, in which the patient was asked to encircle the wrist with the contralateral hand during which the thumb and the little finger superimposed while encircling the wrist, along with positive Steinberg thumb sign test in which the patient adducted the thumb and flexed the fingers showing distal phalanx of the thumb exceeding the palmar area,as illustrated in Figure 1. Dolichostenomelia and arachnodactyly were observed. A dense cataract with subluxation of lens, previous detachment of retina, minimal light perception, and iridodonesis were detected during ophthalmology examination in the left eye whereas in the right eye only myopia-related iridodonesis was visible. The results of the laboratory investigations were within normal limits.\n\nThe diagnostic assessment involved X-ray in lateral and posterior-anterior position that was performed for spine, chest, and sternum that revealed pectus carinatum (PC). The degree of scoliosis that was analysed by the Cobb’s angle was 20.76 cm describing moderate scoliosis. The MRI scan revealed multiple meningioma, heterogeneous lesions in bilateral cerebellopontine angle, which were ruled out as bilateral schwannoma of size 3.4×2.8×1.2 cm on the right side and 5.2×5.0×3.8 cm on the left side,as shown in Figure 2A, however bilateral vestibular schwannoma and mass effect caused in the form of compression of cerebellum is shown in Figure 2B. Echocardiogram showed minimal mitral regurgitation. The multiple swellings were diagnosed as NF-2. Based on the above findings he was diagnosed with MFS along with NF-2 for which he was referred for neurosurgeon’s opinion.\n\nB: Coronal T1 contrast image in which both yellow arrows pointing towards bilateral vestibular schwannoma and orange arrow indicating mass effect caused in the form of compression of cerebellum.\n\nMFS is similar to Loeys-Dietz syndrome (LDS) in clinical features involving aortic aneurysm/dissection and with Shprintzen-Goldberg syndrome (SGS) in having pectus abnormalities, scoliosis, and arachnodactyly. The features that differentiate MFS from LDS include cleft palate, diffuse aortic and arterial aneurysms, thin skin, easy bruising, craniosynostosis, and club foot whereas, features that differentiate MFS from SGS include craniosynostosis, and intellectual disability.10 The other disease NF-2 is differentially diagnosed from NF-1 that consists of intellectual disability, Lisch nodules, and Café au lait macules. Additionally, NF-1 is caused due to mutation in chromosome number 17 and NF-2 is caused due to mutation in chromosome 22.11\n\nAs a part of the prophylactic measure β-blocker was prescribed to control aortic root dilatation and reduce aortic root stiffness. Additionally, for the management of NF-2 surgery was planned along with occasional radiation therapy but the patient was skeptical about the treatment and follow-ups, hence this data was reported at the time of discharge with non-specified duration of follow-ups.\n\nThe diagnostic assessment of X-ray in lateral and posterior-anterior position for spine, chest, and sternum could be assessed for determining the resolving deformities of chest and spine along with the MRI scan in the follow-ups. Hence, the patient was skeptical for the treatment and follow-ups, hence this data was reported at the time of discharge with non-specified duration of follow-ups. Hence, the case report demonstrates the coexistence of two novel mutations leading to MFS and NF-2 in the patient.\n\n\nDiscussion\n\nThe most prevalent inherited CTD, which is MFS, has a wide range of clinical symptoms.12 MFS is strongly linked to mutations in the FBN1 gene.12 The pathophysiological effects of the elastic fibres’ deterioration in MFS seem to account for the majority of its symptoms. The most significant effect of elastin degeneration is stiffness and impaired aortic distensibility in response to elevated pulse pressure.13 Another theory has recently surfaced in an effort to explain the pathophysiology of MFS, which states that the cytokine Transforming Growth Factor β (TGFβ), which controls cell morphogenesis, is thought to contribute to the MFS phenotype. Abnormal fibrillin prevents the latent TGFβ precursor from being sequestered, which causes excessive TGFβ activation, thus eliciting the MFS-specific symptoms as a result.1,12,14\n\nThe prognosis for these patients is driven by the cardiovascular abnormalities. Therefore, regular cardiovascular monitoring is necessary to increase these patients’ chances of survival. If untreated, people with MFS have a 32-year median life expectancy.3 The elastic and collagen fibres that give ligaments their flexibility and resistance are connected to the connective tissue, and therefore any alterations in the musculoskeletal system occur if the connective tissue is impaired. Hence, this case report illustrated anthropometric and musculoskeletal changes that occur in patients with MFS.15 According to histopathological analysis, patients with MFS who underwent muscular biopsy showed fragmentation of fibrillin, which would result in musculoskeletal symptoms.15,16\n\nOne of the most frequent MFS symptoms involving changes to the chest wall is the pectus, which is defined by an imbalance in the development of the costochondral cartilages and the cartilaginous plates of the sternum. An earlier study found a high prevalence of PC in this population, which may conclude that PC could occur throughout the growth phase and deteriorate, especially in people with a genetic susceptibility. According to PC’s severity and its relationship to other thoracic abnormalities including kyphosis and scoliosis, respiratory issues related to PC may occur. Because of this, it’s essential to recognize musculoskeletal changes early in order to avoid complications.15\n\nA genetic disease known as NF-2 is marked by malignancies such as meningiomas, schwannomas, and ependymomas.8 NF-1 and NF-2 are two independent types of diseases of neurofibromatosis with different diagnostic and clinical findings that result from discrete chromosomes. Inactivation of a tumour suppressor gene that occurs due to mutation on chromosome 17 causes NF-1. However, mutation in the gene on chromosome 22 that encodes a tumour-suppressor protein “Merlin” causes NF-2. The diagnosis of NF-2 is strongly influenced by radiographic examination. The diagnosis is relatively simple when bilateral vestibular schwannomas with the usual appearance of progression into the cerebellopontine cisterns from the internal acoustic canals are observed. However, schwannomas of other nerves, meningiomas, ependymomas, and ocular abnormalities can emerge in some people, particularly children and young adults. Therefore, screening for NF-2 should begin when a young patient presents with one or more schwannomas, as well as numerous extra-axial brain or spine tumours. Small intracanalicular tumours may get easily ignored on MRI in such instances. For this reason, small schwannomas of the vestibular or other cranial nerves should be looked for using axial and coronal thin slice contrast enhanced T1-weighted sequences.8 In our case, in axial T1 contrast image there is evidence of enhancing bilateral cerebellopontine angle mass lesion along with internal auditory canal with extra axial enhancing mass and dural tail, as shown in Figure 2A,whereas coronal T1 contrast image is pointing towards bilateral vestibular schwannoma and mass effect caused in the form of compression of cerebellum, as shown in Figure 2B, that confirmed NF-2.\n\nThe coexistence of these two diseases suggests either a chance occurrence or that the two diseases are etiologically or genetically related. The chances of both the diseases occurring in the same patient is one in 60 million.17 Mutation in the gene FBN1 on chromosome 15q21 causes MFS, whereas mutation in the gene on chromosome 22 causes NF-2. As a result, both conditions must be considered as different mutations, since the position of the two genes are unrelated, it is most probable that two independent mutations have taken place. Additionally, the diagnosis was reliant on clinical standards as the genetic analysis was not performed for the reason that the patient denied for the test. This was considered as a big limitation of reporting this case.\n\n\nConclusions\n\nThis report highlights a rare case of a young boy having coexistence of Marfan’s syndrome along with Neurofibromatosis Type-2 and concludes that when compared to acquired CTD, MFS is rare and inheritable. Since genetic testing is non-specific, the diagnosis is reliant on clinical standards. Despite the morbidity and mortality linked to MFS, lives of many patients can be enhanced or lengthened through appropriate surgical and medical interventions along with future advancements in research. By contrast, NF-2 is a genetic neurocutaneous disease that causes anomalies in the skin and serves as a potential for a variety of brain and spinal cord tumours. MFS is caused due to mutation in chromosome 15, whereas, NF-2 is caused due to mutation in chromosome number 22, since the position of the two genes are unrelated, it concludes that two distinct mutations have taken place hence, this report highlights a rare coexistence of both the mutations, which will prove beneficial for medical profession in enhancing future studies.\n\nThree years back, I felt my abilities to hear and see objects clearly were gradually diminishing but I ignored this feeling it might be my misunderstanding. But then 15 days back, I noticed swelling all over my body, which was accompanied with pain. I visited my nearby hospital wherein, I went through tests and got to know that I am having a rare genetic disorder and a close medical attention is required for my well-being. I am in hospital under observation since then. I and my parents had been informed about the rare nature of my disease and importance of its publication. I am not eligible for signing the informed consent, hence, my parental informed consent was signed for publishing my case.\n\n\nConsent\n\nWritten informed consent for publication of clinical details and images was obtained from the parents of the patient.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nMilewicz DM, Braverman AC, Backer JD, et al.: Marfan Syndrome. Nat. Rev. Dis. Prim. 2021; 7: 64. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKeane MG, Pyeritz RE: Medical Management of Marfan Syndrome. Circulation. 2008; 117(21): 2802–2813. Publisher Full Text\n\nCheema T, Balek M, Smith P, et al.: A Case Report of Marfan Syndrome Presenting With Atypical Chest Pain: A 28-Year-Old Male With Non-ST-Elevation Myocardial Infarction (NSTEMI). Cureus. 2022; 14(2): e22040. eCollection 2022 Feb. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChiu HH, Wu MH, Chen HC, et al.: Epidemiological profile of Marfan syndrome in a general population: a national database study. Mayo Clin. Proc. 2014; 89(1): 34–42. PubMed Abstract \| Publisher Full Text\n\nArnaud P, Milleron O, Hanna N, et al.: Clinical relevance of genotype–phenotype correlations beyond vascular events in a cohort study of 1500 Marfan syndrome patients with FBN1 pathogenic variants. Genet. Med. 2021; 23(7): 1296–304. Epub 2021 Mar 17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLoeys BL, Dietz HC, Braverman AC, et al.: The revised Ghent nosology for the Marfan syndrome. J. Med. Genet. 2010; 47(7): 476–485. Publisher Full Text\n\nFaivre L, Collod-Beroud G, Adès L, et al.: The new Ghent criteria for Marfan syndrome: what do they change? Clin. Genet. 2012; 81(5): 433–442. Epub 2011 Jun 2. PubMed Abstract \| Publisher Full Text\n\nOzgür A, Karaman Y, Apaydin FD, et al.: An Uncommon Case of Neurofibromatosis Type 2: A Tribute to the Intracranial Calcifications. J Clin Imaging Sci. 2013; 3: 21. Print 2013. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAboukais R, Bonne NX, Baroncini M, et al.: Management of multiple tumors in neurofibromatosis type 2 patients. Neurochirurgie. 2018; 64(5): 364–369. Epub 2015 Jun 10. Publisher Full Text\n\nAzrad-Daniel S, Cupa-Galvan C, Farca-Soffer S, et al.: Unusual presentation of Loeys-Dietz syndrome: A case report of clinical findings and treatment challenges. World J. Clin. Cases. 2022; 10(33): 12247–12256. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTamura R: Current Understanding of Neurofibromatosis Type 1, 2, and Schwannomatosis. Int. J. Mol. Sci. 2021 Jun; 22(11): 5850. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Mulla MF: Marfan Syndrome: A Case Study.2013; 01: 01.\n\nDean JCS: Management of Marfan syndrome. Heart. 2002 Jul; 88(1): 97–103. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLacro RV, Dietz HC, Wruck LM, et al.: Rationale and design of a randomized clinical trial of beta-blocker therapy (atenolol) versus angiotensin II receptor blocker therapy (losartan) in individuals with Marfan syndrome. Am. Heart J. 2007 Oct; 154(4): 624–631. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCipriano GFB, Brech GC, Peres PAT, et al.: Anthropometric and musculoskeletal assessment of patients with Marfan syndrome. Rev. Bras. Fisioter. 2011; 15(4): 291–296. PubMed Abstract \| Publisher Full Text\n\nBehan WMH, Longman C, Petty RKH, et al.: Muscle fibrillin deficiency in Marfan’s syndrome myopathy. J. Neurol. Neurosurg. Psychiatry. 2003; 74(5): 633–638. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHartlapp I, Bühring U, Dichgans J, et al.: A patient with Marfan’s syndrome and neurofibromatosis type 1 with polyneuropathy. Eur. J. Neurol. 2004 Sep; 11(9): 641–644. PubMed Abstract \| Publisher Full Text" }	[ { "id": "303150", "date": "27 Jul 2024", "name": "Jaroslava Halper", "expertise": [ "Reviewer Expertise Connective tissue disorders", "growth factors" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case report describes an interesting coincidence of two diseases caused by mutations in two different genes. Though this is an interesting and really unusual case of coincidental occurrence of two rare diseases, I am not sure how much the report is novel regarding genetic analysis (not done), no mention of family history (it was not attempted) and whether the double disease could affect treatment and/or prognosis (and unfortunate for the patient). The diseases are so uncommon that one cannot suggest be on the lookout. In other words, it does not bring much new information. They described meningiomas, schwannomas as malignancies in the fourth paragraph of the Discussion. There are quite a few types, some grammatical errors which need to be corrected.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] } ]	1	https://f1000research.com/articles/13-388
https://f1000research.com/articles/13-387/v1	25 Apr 24	{ "type": "Study Protocol", "title": "A cross-sectional study of neutrophil to lymphocyte ratio as a prognostic marker in acute organophosphorus poisoning in a tertiary care hospital in Central India", "authors": [ "Utkarsh Pradeep", "Dr Satish Mahajan", "Dr Satish Mahajan" ], "abstract": "Background Acute organophosphorus poisoning remains a significant public health concern, with variable clinical outcomes. Prognostic markers are crucial for patient management and risk stratification. This study aims to investigate the Neutrophil Lymphocyte Ratio (NLR) as a potential prognostic marker and its associations with severity and clinical outcomes in acute organophosphorus poisoning.\n\nMethods This cross-sectional observational study will be conducted over two years, involving patients presenting with acute organophosphorus poisoning in the Medicine Ward and Intensive Care Unit of DMIHER Wardha. Informed consent will be obtained, and detailed clinical assessments, laboratory investigations, and NLR calculations will be performed. The Nambaet, Peradeniya, and Bardin classification scales will be used to measure severity. Statistical methods will be applied to explore the relationships between NLR, clinical parameters, and clinical outcomes, including descriptive statistics, bivariate analysis, correlation analysis, multivariate regression, and ROC analysis.\n\nExpected Results The study is anticipated to elucidate the role of NLR as a prognostic marker in acute organophosphorus poisoning. Initial assessments and correlations between NLR and clinical parameters will be presented. The predictive capability of NLR for clinical outcomes, including the need for ventilatory support and length of hospital stay, will be explored. Agreement and discrepancies between the classification scales will be evaluated.", "keywords": [ "Organophosphorus Poisoning", "Neutrophil to Lymphocyte Ratio", "Prognostic Marker", "Severity Classification", "Clinical Outcomes", "Risk Stratification" ], "content": "Introduction\n\nOrganophosphorus compounds are widely used in agriculture, industry, and households, playing a pivotal role in pest control and producing various essential products. However, their ubiquitous presence poses a considerable risk to human health, primarily due to unintentional exposures and deliberate self-harm incidents.1 Acute organophosphorus poisoning, resulting from the inhibition of acetylcholinesterase and the accumulation of acetylcholine, leads to a broad spectrum of clinical manifestations, ranging from mild symptoms to life-threatening toxicity. Effective management of acute organophosphorus poisoning demands early identification of severity and prognostication, as it significantly influences treatment decisions and clinical outcomes.2\n\nIdentifying reliable prognostic markers has been an ongoing pursuit in toxicology, aiming to enhance risk stratification and guide therapeutic strategies.3 The Neutrophil to Lymphocyte Ratio (NLR), an inflammatory marker, has gained recognition for its potential utility in various medical conditions. Its role as a prognostic marker in acute organophosphorus poisoning has piqued interest due to its simplicity and availability as part of routine blood tests.4\n\nThis cross-sectional study investigates the NLR as a potential prognostic marker in acute organophosphorus poisoning. By assessing its associations with the severity of poisoning and clinical outcomes, we aim to contribute to a deeper understanding of NLR’s role in patient management. Our study will utilise established severity classification scales, including the Nambaet, Peradeniya, and Bardin classifications, to comprehensively evaluate the severity of poisoning and to compare their agreement and discrepancies.\n\nIn the era of evidence-based medicine, the quest for novel prognostic markers that can facilitate informed clinical decisions is of paramount importance. This study endeavours to shed light on the utility of the NLR as a potential prognostic marker in acute organophosphorus poisoning, aiming to improve patient outcomes and refine therapeutic approaches in this critical area of toxicology.\n\nThis study aims to investigate the potential utility of the Neutrophil Lymphocyte Ratio as a prognostic marker in patients with acute organophosphorus poisoning.\n\n\n\n1. To determine the Neutrophil Lymphocyte Ratio in patients with acute organophosphorus poisoning.\n\n2. To evaluate the relationship between the Neutrophil Lymphocyte Ratio and the severity of organophosphorus poisoning as classified by the Nambaet classification, Peradeniya organophosphorus poisoning scale, and Bardin classification.\n\n3. To assess whether an elevated neutrophil-to-lymphocyte ratio is associated with the need for ventilatory support in these patients.\n\n4. To investigate whether the Neutrophil to Lymphocyte Ratio is correlated with the dose of atropine administered to patients with acute organophosphorus poisoning.\n\n5. To examine if the Neutrophil to Lymphocyte Ratio can predict the length of hospital stay in patients with acute organophosphorus poisoning.\n\n\nMethod\n\nThis study employs a cross-sectional, observational design to investigate the Neutrophil Lymphocyte Ratio as a potential prognostic marker in patients with acute organophosphorus poisoning. Data will be collected at a single time point setup for the 2023-2024 period.\n\nThe study population consists of patients who have presented with acute organophosphorus poisoning. These patients will be recruited from the Medicine Ward and Medicine Intensive Care Unit of DMIHER Wardha.\n\nThe study will be conducted in the Acharya Vinoba Bhave Rural Hospital Department of Medicine.\n\n\n\n1. Patients with a confirmed history of oral ingestion of organophosphorus compounds.\n\n2. Patients who present at the casualty department or are admitted to the Medicine Ward or Medicine Intensive Care Unit of DMIHER Wardha within 24 hours of organophosphorus compound ingestion.\n\n3. Patients who provide informed consent to participate in the study.\n\n4. Patients of all age groups, regardless of gender.\n\n\n\n1. Patients who decline to provide informed consent.\n\n2. Patients exposed to poisons or compounds other than organophosphorus.\n\n3. Patients with severe chronic comorbidities, including liver cirrhosis, symptomatic heart failure (New York Heart Association class III or IV), end-stage chronic kidney disease (on regular hemodialysis), and chronic obstructive pulmonary disease (COPD).\n\n4. Patients diagnosed with malignancies.\n\n\n\n1. Selection bias: There is a risk that patients who agree to participate in the study may only be representative of some patients with acute organophosphorus poisoning. To mitigate this bias, researchers should use a random or consecutive sampling approach when recruiting participants to ensure that the sample is as representative as possible.\n\n2. Information bias: This can occur if there are inaccuracies or inconsistencies in data collection or measurements. To minimise this bias, researchers should employ standardised data collection tools and procedures, ensure that data collectors are trained, and perform regular quality checks on the collected data.\n\n3. Observer bias: In the context of this study, observer bias could occur when healthcare providers assess and classify patients differently based on their judgments. To address this, researchers should provide clear guidelines and criteria for assessing organophosphorus poisoning severity, ensuring the assessment is consistent among different observers.\n\n\n\n1. Patient identification: Patients admitted to the Medicine Ward or Medicine Intensive Care Unit of DMIHER Wardha with a history of acute organophosphorus poisoning will be identified for enrollment.\n\n2. Informed consent: The first step in enrollment is obtaining informed consent. Patients or their legally authorised representatives will be approached, and the study will be explained in detail, including its purpose, procedures, risks, and benefits. Consent forms in the appropriate language will be provided to the patients or representatives. If the patient is not in a state to provide informed consent, it will be obtained from their relatives.\n\n3. Screening for inclusion and exclusion criteria: After obtaining informed consent, patients will be screened to ensure they meet the inclusion and exclusion criteria defined in the study protocol. Patients who meet these criteria will proceed to the next steps.\n\n4. Baseline data collection: Upon enrollment, baseline data will be collected, which includes demographic information, clinical history, and relevant medical information.\n\n5. Clinical assessments: Patients will undergo clinical assessments, including vital signs and a physical examination. These assessments will provide the necessary data for the classification scales (Nambaet classification, Peradeniya classification, and Bardin classification).\n\n6. Blood sample collection: Blood samples will be collected during the study procedures. These samples will be used to determine the Neutrophil Lymphocyte Ratio, which is one of the main parameters of interest in the study.\n\n7. Grading of severity: The severity of organophosphorus poisoning will be graded using the three classification scales. Clinical parameters and laboratory results will be considered in these assessments.\n\n8. Data recording: All collected data, including clinical assessments, blood test results, and classification scale scores, will be carefully recorded in designated proforma or electronic data management systems.\n\n9. Follow-up: Depending on the study objectives, patients may be followed up during their hospital stay to assess outcomes such as the need for ventilatory support, dose of atropine, and hospital stay duration.\n\n10. Data analysis: After data collection is complete, the collected data will be analysed to address the study’s objectives and assess the Neutrophil Lymphocyte Ratio as a prognostic marker in acute organophosphorus poisoning.\n\n\n\n1. Informed consent: Following a detailed explanation of the study to prospective participants, informed consent will be meticulously acquired from those individuals who meet the study’s inclusion criteria.\n\n2. Clinical assessment in intensive care: Within the confines of the Medicine Intensive Care Unit and ward, subjects will meticulously evaluate their vital signs. This will entail the thorough monitoring of critical physiological parameters.\n\n3. Laboratory blood investigations: Blood tests in the centralised clinical laboratory will be conducted, including a complete blood count (CBC) and potentially other relevant assays. These laboratory results will be instrumental in assessing the participants’ health status.\n\n4. Data recording: All pertinent values and findings derived from these assessments will be meticulously recorded in dedicated proforma, maintaining a precise record of the patient’s clinical data.\n\n5. Clinical history collection: A comprehensive clinical history, particularly related to the organophosphorus poisoning episode, will be systematically gathered from the participants. This will be performed per the pre-established inclusion and exclusion criteria.\n\n6. Patient guidance: Participants will be comprehensively briefed on the importance of ongoing vital sign monitoring and further scheduled blood investigations. Clear instructions will be provided to ensure their understanding and compliance with these critical aspects of care.\n\n7. Blood sample collection: In line with the study’s requirements, blood samples will be skillfully obtained from the study subjects, adhering to the established medical protocols and with due regard for patient comfort.\n\n8. Severity grading: The severity of organophosphorus poisoning will be meticulously graded by employing three distinct classification systems, namely the Nambaet classification, the Peradeniya classification, and the Bardin classification. These classifications provide a multidimensional assessment of the patient’s clinical condition.\n\n9. Nambaet classification: This evaluation method will involve a thorough assessment of various clinical parameters and the measurement of acetylcholinesterase levels to determine the severity of organophosphorus poisoning according to the Nambaet classification.5\n\n10. Peradeniya classification: The Peradeniya classification will be assigned based on the assessment of various clinical parameters, and specific scores will be allocated for each parameter, allowing for a more comprehensive understanding of the patient’s condition.6\n\n11. Bardin classification: The Bardin classification employs a criterion-based system, where the presence of two or more specific criteria will lead to assigning a specific grade. Patients who do not meet at least two criteria will be placed in the preceding category. This approach provides a nuanced assessment of severity based on clinical criteria.7\n\n12. Initial assessment: Upon admission, all three classification scales will be meticulously applied to the study participants, allowing for an early and comprehensive evaluation of their condition and providing a valuable baseline for further analysis. This initial assessment is a critical reference point for the study’s objectives.\n\nSample size: Minimum sample size required\n\nFormula\n\nP = Proportion of death for organ phosphorous poisoning having Neutrophil lymphocyte ratio >12 = 10.2% (As per reference article4)\n\n\n\nThe study will employ diverse statistical techniques to analyse the data comprehensively. Initially, descriptive statistics will be harnessed to provide a clear snapshot of the study population, offering insights into baseline characteristics. This will encompass measures such as means, standard deviations, medians, interquartile ranges for continuous variables, and frequencies and percentages for categorical variables. Bivariate analysis will be pivotal in exploring relationships between different variables. For instance, the Neutrophil to Lymphocyte Ratio will be scrutinised across severity categories using appropriate statistical tests like t-tests, ANOVA, or non-parametric tests tailored to the data distribution. Correlation analysis, featuring statistical measures like Pearson’s correlation coefficient or Spearman’s rank correlation, will unveil the intricate relationships between continuous variables, including the Neutrophil Lymphocyte Ratio and other pertinent clinical parameters.\n\nIn cases where independence and associations are sought, multivariate regression models will come into play. Multiple linear regression will uncover factors associated with the Neutrophil Lymphocyte Ratio. In contrast, logistic regression will predict outcomes such as the need for ventilatory support or the severity of organophosphorus poisoning. Given the utilisation of multiple classification scales (Nambaet, Peradeniya, Bardin), statistical tests like kappa statistics or concordance analyses will be instrumental in evaluating the agreement or disparities between these scales when assessing the severity of poisoning.\n\nSubgroup analyses will investigate variations in associations between variables, such as the Neutrophil Lymphocyte Ratio and outcomes, within diverse study population subgroups, such as age, gender, or comorbid conditions. Furthermore, the diagnostic accuracy of the Neutrophil Lymphocyte Ratio will be quantified using Receiver Operating Characteristic (ROC) analysis, with the Area Under the ROC Curve (AUC) offering a measure of its prognostic potential. If relevant, survival analysis techniques, including Kaplan-Meier curves and Cox regression, will be employed to examine the link between the Neutrophil Lymphocyte Ratio and time-to-event outcomes like the length of hospital stay.\n\nSensitivity analyses will be conducted to ensure the robustness of results and assess the influence of potential confounders or bias. All statistical analyses will be executed with appropriate statistical software, such as SPSS version 23, under the guidance of qualified statisticians and proficient researchers well-versed in statistical methods. Significance levels will be diligently observed, with standard thresholds like p < 0.05 utilised to assess statistical significance.\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol (Reference number: DMIHER (DU)/IEC/2022/941. Date:11-04-2023) CTRI registration- REF/2023/07/070131. Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has yet to start after the publication of the protocol; we will start recruitment in the study.\n\n\nDiscussion\n\nAcute organophosphorus poisoning is a significant public health issue in many parts of the world, presenting clinicians with a diverse range of clinical manifestations and challenges in management. This study protocol outlines a comprehensive investigation into the potential use of the Neutrophil to Lymphocyte Ratio (NLR) as a prognostic marker in acute organophosphorus poisoning, aiming to shed light on its associations with disease severity and clinical outcomes.\n\nThe rationale for this study is grounded in the need for reliable prognostic markers to guide clinical decision-making in cases of acute organophosphorus poisoning. A review of existing literature reveals that despite advances in the management of poisoning cases, identifying markers that can help predict patient outcomes remains a critical research frontier.8 The systemic inflammation response, as represented by the NLR, has been studied extensively in various medical conditions, including poisoning scenarios.9,10 By delving into the relationship between NLR and organophosphorus poisoning, this study aligns itself with the broader research exploring the predictive potential of NLR in clinical settings.\n\nOur study’s methodological rigor, including a cross-sectional design and a sizable sample size, will bolster the reliability of the findings. Consistent with prior studies,11 we anticipate that NLR will be associated with the severity of poisoning, reflected in the clinical parameters and the classification scales used in this study. In line with international guidelines,12,13 this approach ensures that the grading of poisoning severity is both comprehensive and comparable, providing a foundation for assessing the utility of NLR as an additional prognostic tool.\n\nThis study’s findings will contribute to a growing body of research on NLR in clinical prognostication, with relevance extending beyond organophosphorus poisoning. NLR has been previously identified as a prognostic marker in a range of medical conditions, such as acute kidney injury,14 cardiovascular diseases,15 and sepsis,16 underscoring its versatility in clinical prediction. By exploring its applicability in the context of poisoning, this study adds a valuable dimension to the ongoing discourse on NLR as a universal prognostic marker.\n\nFurthermore, this protocol aligns with the call for further research into acute poisoning scenarios, particularly those involving organophosphorus compounds.17 Acute poisoning can lead to rapid clinical deterioration, making early prognostication crucial for timely and effective interventions.18 As such, the results of this study could hold substantial implications for clinicians, public health practitioners, and policymakers, with the potential to influence clinical guidelines for organophosphorus poisoning management.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nChataut J, Adhikari RK, Sinha NP, et al.: Pattern of organophosphorous poisoning: a retrospective community based study. Kathmandu Univ Med J KUMJ. 2011; 9: 31–34. PubMed Abstract \| Publisher Full Text\n\nBlain PG: Organophosphorus poisoning (acute). BMJ Clin Evid. 2011; 2011: 2102.\n\nSingh S, Kaushik AC, Gupta H, et al.: Identification of prognostic markers and potential therapeutic targets using gene expression profiling and simulation studies in pancreatic cancer. Curr Comput Aided Drug Des. 14 September 2023; 20: 955–973. PubMed Abstract \| Publisher Full Text\n\nMu Y, Hu B, Gao N, et al.: Prognostic value of the neutrophil-to-lymphocyte ratio in acute organophosphorus pesticide poisoning. Open Life Sci. 2021; 16: 703–710. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeter JV, Sudarsan TI, Moran JL: Clinical features of organophosphate poisoning: A review of different classification systems and approaches. Indian J Crit Care Med Peer-Rev Off Publ Indian Soc Crit Care Med. 2014; 18: 735–745. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMalaviya NB, Parikh R, Pancholi K, et al.: Assessment of the Peradeniya Organophosphorus Poisoning Scale as a Severity and Prognostic Marker in Patients With Acute Organophosphorus Poisoning Presenting to an Emergency Medicine Department. Cureus. 2023; 15: e40277. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBardin PG, Van Eeden SF: Organophosphate poisoning: grading the severity and comparing treatment between atropine and glycopyrrolate. Crit Care Med. 1990; 18: 956–960. Publisher Full Text\n\nEddleston M, Buckley NA, Eyer P, et al.: Management of acute organophosphorus pesticide poisoning. Lancet. 2008; 371: 597–607. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBi J-B, Zhang J, Ren Y-F, et al.: Neutrophil-to-lymphocyte ratio predicts acute kidney injury occurrence after gastrointestinal and hepatobiliary surgery. World J Gastrointest Surg. 2020; 12: 326–335. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWilliams DJ, Hall M, Auger KA, et al.: Association of White Blood Cell Count and C-Reactive Protein with Outcomes in Children Hospitalized for Community-acquired Pneumonia. Pediatr Infect Dis J. 2015; 34: 792–793. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBalta S, Ozturk C: The platelet-lymphocyte ratio: A simple, inexpensive and rapid prognostic marker for cardiovascular events. Platelets. 2015; 26: 680–681. PubMed Abstract \| Publisher Full Text\n\nSperduto PW, Kased N, Roberge D, et al.: Summary Report on the Graded Prognostic Assessment: An Accurate and Facile Diagnosis-Specific Tool to Estimate Survival for Patients With Brain Metastases. J Clin Oncol. 2012; 30: 419–425. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMalaviya NB, Parikh R, Pancholi K, et al.: Assessment of the Peradeniya Organophosphorus Poisoning Scale as a Severity and Prognostic Marker in Patients With Acute Organophosphorus Poisoning Presenting to an Emergency Medicine Department. Cureus. 2023; 15: e40277. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJahan I, Ahmed R, Ahmed J, et al.: Neutrophil-lymphocyte ratio in Guillain-Barré syndrome: A prognostic biomarker of severe disease and mechanical ventilation in Bangladesh. J Peripher Nerv Syst JPNS. 2023; 28: 47–57. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDiniz LR, de Lima SG , de Amorim Garcia JM , et al.: Neutrophil to Lymphocyte Ratio as a Prognostic Predictor in Older People With Acute Coronary Syndrome. Angiology. 2019; 70: 264–271. PubMed Abstract \| Publisher Full Text\n\nJeon TJ, Park JY: Clinical significance of the neutrophil-lymphocyte ratio as an early predictive marker for adverse outcomes in patients with acute pancreatitis. World J Gastroenterol. 2017; 23: 3883–3889. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPreventing suicide: a resource for pesticide registrars and regulators. Accessed: October 23, 2023. Reference Source\n\nGunnell D, Eddleston M, Phillips MR, et al.: The global distribution of fatal pesticide self-poisoning: Systematic review. BMC Public Health. 2007; 7: 357. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "277315", "date": "07 Jun 2024", "name": "Epari Venkatarao", "expertise": [ "Reviewer Expertise Epidemiological studies", "Validation studies." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a protocol for publication before the research is being conducted. It talks about finding the ability of NLR as a prognostic indicator in organophosphorus poisoning. NLR as a prognostic indicator has been studied extensively in recent times in various other clinical conditions including cancer. Hence, the ROL should look into this including the methodology followed to find its prostic value, which will add further knowledge to the existing body of knowledge. The outcome variables of the study should be well defined before conducting the research. This will help in the designing the study and calculation of an appropriate sample size. The sample size should be calculated using AUC in ROC analysis from published literature.\nThe outcome measures defined by the study's objectives will determine the role of appropriate statistical methods. The authors have not been able to spell out the outcome measures properly. Hence, the specificity of the use of statistical methods seems vague. This can lead to confusion at a later stage after data collection. Dummy tables and dummy analysis before the execution of the study will be useful.\nThe Review of Literature (ROL) lacks a finding of NLR as an inflammatory marker. There is literature available on NLR as a prognostic marker in cancer. The authors have proposed data collection at a single time point, which will have a bias in the analysis as factors like time-to-intervention, dose-response, quality of care, etc., can not be accounted for in the analysis.\n\nFinally, the sample size calculation is inappropriate as the study is NOT trying to find the prevalence of death among organophosphorus poisoning cases with NLR >12, rather with appropriate ROL, sample size calculation method has to be revisited.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "305572", "date": "22 Aug 2024", "name": "Deepak Kumar", "expertise": [ "Reviewer Expertise Point of care", "Poisoning", "Biotechnology", "Analytical Biochemistry" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Editor\nI have gone through the manuscript (study protocol) titled “A cross-sectional study of neutrophil to lymphocyte ratio as a prognostic marker in acute organophosphorus poisoning in a tertiary care hospital in Central India”.\nFollowing are my comments for consideration (Major Revision)\nSeveral studies are already available which showed the role of neutrophil-to-lymphocyte ratio (NLR) as a prognostic marker in acute organophosphorus poisoning with detailed method/protocol (https://www.sciencedirect.com/science/article/abs/pii/S0736467914005034 file:///C:/Users/Dr%20Deepak%20Kumar/Downloads/5-OA-Basanta+Gauli.pdf, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8284330/ ).\nPlease elaborate.\n\nUnder study status it is mentioned as\n“The study has yet to start after the publication of the protocol; we will start recruitment in the study.”\n\nHowever, under study design it is mentioned as\n\n“Data will be collected at a single time point setup for the 2023-2024 period.” Considering the fact that it is mid-August 2024, when will the authors start the work and complete it within 2023-2024 period. So kindly revise the relevant content in the manuscript and its ethical approval accordingly.\n\nInclude the statement that the work will be carried out following the tenets of the Helsinki Declaration.\n\nHow the diagnosis of organophosphorus pesticide exposure will be carried out? Or in other words which method was used to find out the confirmed cases of OP poisoning? How the authors confirm the inclusion and exclusion criteria. Which parameter will be considered for this?\n\nEstimation of AChE activity is of the method for understanding OP poisoning. However, both organophosphorus (OP) and organocarbamates (OC) inhibit AChE activity (https://pubmed.ncbi.nlm.nih.gov/37805177/ ). Then how do the authors distinguish OP cases from OC. Please address this issue. This should be properly mentioned in the protocol. Under objectives, it is mentioned as under\n“To investigate whether the Neutrophil to Lymphocyte Ratio is correlated with the dose of atropine administered to patients with acute organophosphorus poisoning.”\nIn cases where organophosphate poisoning is on the differential but not confirmed, a trial of atropine is generally administered (https://www.ncbi.nlm.nih.gov/books/NBK470430/#:~:text=If%20organophosphate%20poisoning%20is%20on,suspicion%20of%20AChE%20inhibitor%20poisoning. ). Then how do the investigators access the control NLR value (i.e., value before administration of atropine). Please discuss.\n\nMention which clinical/biochemical parameters will be considered for assessment.\n\nKindly include the following in the exclusion criteria:\nThe patients who are on steroids, pregnant patients, and patients with blood disorders (https://www.jcmc.com.np/jcmc/index.php/jcmc/article/download/1311/836 ).\n\nThanks\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-387
https://f1000research.com/articles/13-381/v1	25 Apr 24	{ "type": "Research Article", "title": "Comparison of Antifungal Activity of Thymus Vulgaris Essential Oil and Triple Antibiotic Paste Against Candida Albicans Isolated from Root Canal (In Vitro Study)", "authors": [ "Hadeel Sadoon Abd", "Aseel Haidar M.J. Al. Haidar", "Aseel Haidar M.J. Al. Haidar" ], "abstract": "Background The main objective of chemomechanical endodontic therapy is to reduce or eliminate microorganisms from the root canal system, and intracanal medications are used to accelerate the disinfection process.\n\nThe aim of this study this study was to assess the antifungal activity of thymus vulgaris essential oil against C. albicans compared to that of triple antibiotic paste.\n\nMaterials and methods\nC. albicans was isolated from patients who required endodontic treatment. Using the agar well diffusion method, the efficacy of Thymus vulgaris essential oil against C. albicans was determined at 25 mg/ml, 10 mg/ml, 8 mg/ml, 6 mg/ml, 4 mg/ml, and 2 mg/ml and compared to the triple antibiotic paste. The minimum inhibitory and fungicidal concentrations against Candida albicans were determined using the microbroth dilution method. The constituents were identified using a gas chromatography–mass spectrometer.\n\nResults Thymus vulgaris essential oil demonstrated antifungal activity against C. albicans, which appeared to increase as the extract concentration increased, and the difference between all concentrations and triple antibiotic paste was significant (p ≤ 0.01). The MIC and MFC for Thymus vulgaris essential oil were 0.015 mg/ml and 0.031 mg/ml, respectively. 53 compounds were identified by (GC-MS) analysis, which represented more than 95% of the oil composition. The main component was thymol (35.48%).\n\nConclusion Thymus vulgaris essential oil is effective against C. albicans, suggesting that it has the potential to be applied as an intracanal medication.", "keywords": [ "Candida albicans", "Essential oil", "Regenerative endodontic", "Thymus Vulgaris", "Triple antibiotic paste" ], "content": "Introduction\n\nRevascularization, a new treatment method for managing an immature permanent tooth, was made available in endodontics.1 The American Association of Endodontists approved the term “regenerative endodontics” in 2007.2 Regenerative endodontic therapy (RET) aims to rebuild the pulp-dentine complex of immature necrotic permanent teeth that had been damaged by trauma, infection, or developmental abnormalities.3 A total of 65% of bacteria, 30% of fungi, and 5% of other organisms form heterogeneous microflora. Remarkably, these microbes can survive challenging root canal environments.4 Candida albicans is the most commonly identified root canal fungus and significantly contributes to the failure of root canal therapy.5 An important step in (RET) is the use of intracanal medications to clean the necrotic root canal. The most common intracanal medication used in endodontic regeneration is the triple antibiotic paste (TAP), which includes a combination of metronidazole, ciprofloxacin, and minocycline. It has been employed in more than half of published instances of endodontic regeneration.6 It has been reported that 40% of the teeth treated with TAP have discolored crowns.7 This large percentage indicated a significant clinical problem.8 Jain et al. (2014) reported that herbal remedies could be viable alternatives to traditional pharmaceuticals.9 Thymus vulgaris oil is composed of a blend of monoterpenes, which possess a variety of beneficial properties including antioxidative, antimicrobial, antispasmodic, and antibacterial effects.10 The purpose of this study was to assess the effectiveness of Thymus Vulgaris essential oil (TVEO) in comparison with TAP as a root canal medicament against C. albicans.\n\n\nMethods\n\nThe Research Ethics Committee of the College of Dentistry, University of Baghdad approved this study (Reference number/839) at date 30/8/2023.\n\nThe raw material used during the experiment was acquired from a local market in Baghdad, Iraq, and was classified at the herbarium of the Department of Biology/College of Science/University of Baghdad, it consists from the aerial parts of Thyme Vulgaris. After washing and cleaning, the samples were dried. Drying was performed in a well-ventilated area at room temperature, without exposure to light. After drying, the leaves were collected and chopped in a household blender. The obtained powder was stored in an airtight container until extraction.4\n\nDried thyme leaves (50 g) were hydrodistilled in a Clevenger-type apparatus for 3-4 h. The oils were maintained at 4 °C in sealed vials after drying over anhydrous sodium sulfate.11\n\nTen patients (their age ranged 25-45 years) who had pulpal necrosis, periapical lesions and needed endodontic treatment, were included in this study after signing an informed consent. All the selected teeth had one root. The teeth were symptomatic, and radiographic examination performed in the diagnostic department of a specialized dental clinic (Maysan) verified the diagnosis.\n\nThe selected teeth were isolated using a rubber dam. The working area was cleaned with 10% povidone-iodine solution. All coronal restorations and carious lesions were removed using a sterile carbide fissure bur, followed by field disinfection. Subsequently, an access opening to the root canal was created with a sterile diamond fissure bur, taking care not to go too deep inside the pulp chamber to preserve the microbiota. For the initial instrumentation, new and sterile K files of (15, 20) size were used, and a size #20 rotary file was used with no irrigants. Subsequently, normal saline was used to fill the canal, and the final file was agitated vertically to generate a microbiological suspension. After leaving the paper points inside the canal for one minute, they were transferred to the Brain Heart Infusion Broth to the laboratory for isolation and identification.12\n\n\n\n1- Gram’s stain: According to Gram’s method of Naser and his colleagues 2023.13\n\n2- colony morphology: Colonies of C. albicans were examined according to their morphological characteristics on Sabouraud dextrose agar plates as described by Webb et al. (1998).14\n\n3- Germ tube formation: Human serum (0.5 ml of human serum was suspended in tubes containing a small inoculum from an isolated colony. The inoculated tubes were incubated for three hours at 37 °C. Subsequently, on a clean slide, a drop of the suspension was spread to search for germ tubes using a low-power light microscope.15\n\nThyme Vulgaris essential oil’s chemical compounds analysis was analyzed using a gas chromatograph mass spectrometer (model 5973N, Agilent USA) equipped with a capillary column type HP-5ms (30 m length, 0.25 μm thickness, 0.25 mm diameter) and helium, which was the carrier gas at a flow rate of 1 ml/min. The injector was operated at 280 °C. The oven temperature was programmed as follows: the starting temperature was 60 °C and held for 2 min. The temperature was increased at a rate of 10 °C/min to 300 °C and held for 5 min.16 This procedure was performed by the Ministry of Science and Technology, Department of Water and Environment/Environment Research Centre.\n\nDimethyl sulfoxide (DMSO) (LOBA Chemie, India) was used to dilute (TVEO) to various concentrations (25, 10, 8, 6, 4, and 2 mg/ml). The procedure involved the addition of 10% DMSO to the oil.\n\nThe Sabouraud dextrose agar (SDA) (OXOID, India) plates were inoculated with Candida albicans suspension that was produced as 0.5 McFarland using sterilized cotton swap. Six mm-diameter wells were created on the plate, and 100 μl of TVEO at the previously determined concentrations were placed in each well. Metronidazole (Gulphar, U.A.E.), ciprofloxacine (Pharma International, Jordan), and minocycline (Vulga XR, Jordan) each of these powders was made separately by grinding it into a fine powder by using a clean mortar and pestle. To achieve the desired 1:1:1 proportion, the three antibiotic powders were individually weighed using a digital scale, and then, to make a paste, one gram of powder was combined with one milliliter of sterile water.14 10% DMSO and TAP, on the other hand, served as the negative and positive controls, respectively. The plates were then kept in an incubator for approximately 24 h at 37°C, after which a ruler was used to measure in millimeters the fungal growth inhibition zones around the wells (involving six mm of each well).17\n\nMinimum inhibitory concentration was measured by broth microdilution. μL each of the ten wells, numbered W1 to W10, received 100 μL of SDA broth in a 96-well microtiter plate (NUNC™ Brand products), 100 μL of TVEO at an 8 mg/ml concentration was added to W1, and W1 through W10 received a two-fold serial dilution. W11, which was the positive control, contained the inoculated media. In contrast, W12 contained uninoculated medium and acted as a negative control. 0.5 McFarland, a fungal suspension (20 μl), was used to inoculate all wells and incubated overnight at 37 °C. Following incubation, 30 μl of resazurin was added to each well (30 μl/well) and incubated for 2–4 h18 for the observation of color changes. After completion of incubation, rows with no color change (blue resazurin color remained unchanged) were scored as MFC, whereas the last blue well in the row was recorded as the MIC and the next pink well was recorded as the sub-MIC. The MFC was detected by sub-culturing 100 μl from the MIC well and the well before it on SDA plates. Results were obtained after 24 h of incubation at 37°C. After culturing, the concentration was considered to be MFC if it was equal to or higher than the MIC and there was no fungal growth on SDA.19\n\nSPSS (Statistical Package for social Science) (version -22, Chicago, Illionis, USA) was used. Minimum, maximum, standard error, mean, and standard deviation, as well as the Levene test, Shapiro-Wilk test, and Tukey HSD with one-way analysis of variance (ANOVA) were used for data description, analysis, and presentation.\n\nLevel of significance when p value is less than 0.05.\n\n\nResults\n\nThe essential oil yield was 1%. Freshly isolated essential oil is a golden liquid with a hot-burning taste. The thyme essential oil was analyzed using GC-MS, and 53 components were identified, representing 95.95% of the total detected constituents. The major constituents of the oil are thymol (35.48%), o-cymene (13.82%), γ-terpinene (13.55%), carvacrol (4.04), α-terpinene (3.11%), caryophyllene (2.99%), linalool (2.57%),3-Thujene (2%). Other ingredients were present in less than 2% of the samples (Table 1).\n\nUnder a microscope, the tested isolate showed gram-positive, oval-shaped, or budding yeast cells. Candida colonies on the SDA appeared smooth, creamy, white, and had a yeasty smell. The results of the germ tube test were positive, suggestive of C. albicans.\n\nTVEO was effective against C. albicans at all concentrations and regions around the wells with no fungal growth, termed growth inhibition zones. The lack of an inhibitory zone suggests that the fungi were resistant to the drug under evaluation. Triple antibiotic paste, in contrast to DMSO, demonstrated antifungal activity against Candida albicans and created an inhibitory zone.\n\nAs TVEO concentration increased, the diameter of the growth-inhibitory zone also increased. The results of the ANOVA test showed that there was a highly significant difference between the concentrations of TVEO and TAP (p ≤ 0.01) (Table 2, Figure 1, and Figure 2).\n\nA - 25 mg/ml, B - 10 mg/ml, C - 8 mg/ml, D - 6 mg/ml, E - 4 mg/ml, F - 2 mg/ml, T - triple antibiotic paste (positive control), N - dimethyl sulfoxide (negative control).\n\nSince there was a significant difference between the extract concentrations and the control, each pair of TVEO concentrations was statistically compared using Tukey’s HSD test, and the results revealed a significant difference between them (p ≤ 0.05), while between 2 mg/ml and 4 mg/ml, 6 mg/ml and 8 mg/ml, and 8 mg/ml and 10 mg/ml was not significant (p > 0.05) (Table 3).\n\nMIC of TVEO was 0.015 mg/ml and MFC was 0.031 mg/ml.\n\n\nDiscussion\n\nDifferent chemotypes can be identified in plants, and consequently, in the essential oils of T. vulgaris. Chemical composition analysis confirmed that the essential oil belongs to the thymol chemotype. These results were similar to those obtained by Al-Asmari et al.20 and Micucci et al.,21 who studied the oil composition of thyme of the same species sample, in which thymol was the main component.\n\nMany studies have documented the use of plant extracts in dentistry owing to their antimicrobial properties. The successful treatment of several oral diseases has been reported. Moreover, Herbs are better choices for disinfecting root canals because of their anti-inflammatory, antioxidant, sedative, and antibacterial properties.4\n\nThis study demonstrated the activity of TVEO against C. albicans in comparison with TAP, which had greater inhibition zones than TAP, and this activity increased as the concentration increased.\n\nThis result may be due to the EOs having an antifungal component such as phenol (especially thymol, which is the main component of the essential oil used), alcohols, aldehydes, ketones, ethers, and hydrocarbons, which have the potential to disrupt plasma membrane integrity and produce reversible changes in cellular management that would influence the chemical structure of the cells and their activity.22\n\nOur outcome is consistent with a previous study that found a direct relationship between concentration and antimicrobial activity.19 Mith et al. (2014) used the agar diffusion method to examine the antimicrobial effects of TVEO on several microorganisms and found that TVEO has antimicrobial properties that result in greater suppression of bacterial growth as TVEO concentration increases.23 This result shows considerable promise for using TVEO as a replacement for TAP.\n\n\nConclusion\n\nCompared with the synthetic antimicrobials that are currently available and applied for root canal therapy, TVEO showed noteworthy antifungal activity and could potentially be a potent herbal substitute.\n\n\nEthics and consent\n\nThe Research Ethics Committee of the College of Dentistry, University of Baghdad approved this study (Reference number/839) at date 30/8/2023.\n\nPatients were included in this study after signing an informed consent.", "appendix": "Data availability\n\nZenodo: Raw data for [Comparison of Antifungal Activity of Thymus Vulgaris Essential Oil and Triple Antibiotic Paste Against Candida Albicans Isolated from Root Canal (in vitro study)] Doi: https://zenodo.org/records/10917793. 24\n\nThis project contains the following underlying data: Raw Data (F1000).xlsx (data available in excel format)\n\n[Data available in word format: Under data.docx, Doi: https://doi.org/10.5281/zenodo.10723658 ]\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nThe authors would like to express their sincere gratitude to the bacteriologist Abbas Juma Sultan for his ongoing monitoring and precise observations during the study period.\n\n\nReferences\n\nIwaya S, Ikawa M, Kubota M: Revascularization of an immature permanent tooth with apical periodontitis and sinus tract. Dent. Traumatol. 2001; 17: 185–187. PubMed Abstract \| Publisher Full Text\n\nMurray PE, Garcia-Godoy F, Hargreaves KM: Regenerative endodontics: a review of current status and a call for action. J. Endod. 2007; 33: 377–390. PubMed Abstract \| Publisher Full Text\n\nKim SG, Malek M, Sigurdsson A, et al.: Regenerative endodontics: a comprehensive review. Int. Endod. J. 2018; 51(12): 1367–1388. Publisher Full Text\n\nAl-Shekhli MW, Al- Dhaher ZA: Evaluation of The Antibacterial Activity of Nasturtium officinale (watercress) Essential Oil with Calcium Hydroxide against Enterococcus faecalis Isolated from Root Canal (In vitro study). J. Res. Med. Dent. Sci. 2021; 33(12): 1–5. Publisher Full Text\n\nAshraf H, Samiee M, Eslami G, et al.: Presence of Candida albicans in root canal system of teeth requiring endodontic retreatment with and without periapical lesions. Iran. Endod. J. 2007; 2(1): 24–28. PubMed Abstract \| Free Full Text\n\nNerness AZ, Ehrlich Y, Spolnik K, et al.: Effect of triple antibiotic paste with or without ethylenediaminetetraacetic acid on surface loss and surface roughness of radicular dentine. Odontology. 2016; 104(2): 170–175. Publisher Full Text\n\nTorabinejad M, Nosrat A, Verma P, et al.: Regenerative Endodontic Treatment or Mineral Trioxide Aggregate Apical Plug in Teeth with Necrotic Pulps and Open Apices: A Systematic Review and Meta-analysis. J. Endod. 2017; 43: 1806–1820. Publisher Full Text\n\nBetancourt P, Bucchi C, Arroyo-Bote S: Determination of crown discoloration and fluorescence induced by different medications used in regenerative endodontic procedures: An ex vivo study. J. Clin. Exp. Dent. 2021; 13(8): e755–e761. PubMed Abstract \| Publisher Full Text\n\nJain N, Rajwar YC, Batra M, et al.: Dentistry: Turning towards Herbal Alternatives: A Review. Sch. J. App. Med. Sci. 2014; 2(1C): 253–257.\n\nHosseinzadeh S, Jafarikukhdan A, Hosseini A, et al.: The Application of Medicinal Plants in Traditional and Modern Medicine: A Review of Thymus vulgaris. Int. J. Clin. Med. 2015; 6: 635–642. Publisher Full Text\n\nAl-Badr RJ, Al-Huwaizi HF: Effect of Tea Tree, Thymus Vulgaris and Nigella Sativa Oils on The Elimination of Enterococcus Faecalis (In Vitro Study). J. Baghdad Coll. Dent. 2017; 29(1): 55–62. Publisher Full Text\n\nKamona ZK, Alzobaay AHH: Effect of Essential Oil Extract from Lemongrass (Cymbopogon Citratus) Leaves On Viability of Some Pathogenic Bacteria and Sensory Properties of Fish Balls. Iraqi J. Agric. Sci. 2021; 52(2): 268–275. Publisher Full Text\n\nNaser HJ, Abdul-Ameer FM: Evaluation of the Effect of Lemongrass Essential Oil on Candida Albicans Adhesion on Heat Cured Acrylic Based Soft Lining Material. J. Med. Chem. Sci. 2023; 6(7): 1685–1695.\n\nWebb BC, Thomas CJ, Willcox MDP, et al.: Candida-associated denture stomatitis. Aetiology and management: A review: Part1. Factors influencing distribution of candida species in the oral cavity. Aust. Dent. J. 1998; 43(1): 45–50. PubMed Abstract \| Publisher Full Text\n\nForbes BA, Sahm DF, Weissfeld AS, et al.: Bailey & Scott’s diagnostic microbiology. 12th ed.Mosby: Elsevier; 2007.\n\nAlhazmi HA, Thangavel N: GC–MS profiling and in silico prediction of MAPK receptor activation by fatty acids of watercress oil for hair growth marketed in Saudi Arabia. J. Saudi Chem. Soc. 2021; 25(2): 101196.\n\nDessai A, Shetty N, Saralaya V, et al.: Carnosic Acid as an intracanal medicament performs better than triple antibiotic paste and calcium hydroxide to eradicate Enterococcus faecalis from root canal: An in vitro confocal laser scanning microscopic study. J. Conserv. Dent. 2022; 25(1): 20–25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElshikh M, Ahmed S, Funston S, et al.: Resazurin-based 96-well plate microdilution method for the determination of minimum inhibitory concentration of biosurfactants. Biotechnol. Lett. 2016; 38(6): 1015–1019. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShallal LF, Ahmed MA: Experimental in vitro Study to Assess the Antibacterial Activity of Thymus vulgaris Oil on Streptococcus Sanguinis. J. Bagh. Coll. Dent. 2022 Dec. 15 [cited 2023 Apr. 29]; 34(4): 17–27. Publisher Full Text\n\nAl-Asmari AK, Athar MT, Al-Faraidy AA, et al.: Chemical Composition of Essential Oil of Thymus vulgaris Collected from Saudi Arabian Market. Asian Pac. J. Trop. Biomed. 2017; 7: 147–150. Publisher Full Text\n\nMicucci M, Protti M, Aldini R, et al.: Thymus vulgaris L. Essential Oil Solid Formulation: Chemical Profile and Spasmolytic and Antimicrobial Effects. Biomol. Ther. 2020; 10: 860. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDambolena JS, L´opez AG, C´anepa MC, et al.: Inhibitory effect of cyclic terpenes (limonene, menthol, menthone and thymol) on Fusarium verticillioides MRC 826 growth and fumonisin B1 biosynthesis. Toxicon. 2008; 51: 37–44. PubMed Abstract \| Publisher Full Text\n\nMith H, Dure R, Delcenserie V, et al.: Antimicrobial activities of commercial essential oils and their components against food-borne pathogens and food spoilage bacteria. Food Sci. Nutr. 2014; 2: 403–416. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbd HS, Assis. Prof. Haidar A , Al Haidar MJ: Data for/Comparison of antifungal activity of Thymus vulgaris essential oil and triple antibiotic paste against Candida albicans isolated from root canal (In Vitro Study). [Data set]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "281311", "date": "10 Jun 2024", "name": "Ahmed Mousa", "expertise": [ "Reviewer Expertise SURGERY" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nABSTRACT Result: The MIC and MFC: abbreviations are not allowed in the abstract section of the manuscript, except after writing the whole word. Please mention the whole words first, followed by their abbreviations. (GC-MS) analysis: what does this means? Please clarify. MAIN MANUSCRIPT Result: As we compared the Antifungal Activity of Thymus Vulgaris Essential Oil and Triple Antibiotic Paste Against Candida Albicans Isolated from Root Canal, we should perform the paired samples t-test for comparison between these 2 variables. Also the Kaplan-Meier survival curve must be employed in the result section of the main manuscript to approve which variable is more convenient than the other.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-381
https://f1000research.com/articles/13-380/v1	24 Apr 24	{ "type": "Genome Note", "title": "Isolation and complete genome sequence of Aeromonas bacteriophage Gekk3-15", "authors": [ "A.K. Golomidova", "E.E. Kulikov", "A.S. Kuznetsov", "P. Yu. Pechenov", "I.S. Belalov", "A.V. Letarov", "E.E. Galyov", "A.K. Golomidova", "E.E. Kulikov", "A.S. Kuznetsov", "P. Yu. Pechenov", "I.S. Belalov", "A.V. Letarov" ], "abstract": "Bacteria of the genus Aeromonas, especially A. hydrophila and A. veronii are recognized as important fish pathogens that cause significant economic losses in aquaculture. Environmentally friendly bacteriophage-based solutions for the treatment of fish and for the reduction of colonization by pathogenic bacteria in production facilities are currently in high demand. The bacteriophage Gekk3-15 was isolated during a search for novel phage strains potentially suitable for Aeromonas biocontrol applications. Genome sequencing revealed that this virus is a relatively small myovirus with a 64847 bp long dsDNA genome, which is consistent with virion electron microscopy data. Bacteriophage Gekk3-15 is distinct in its nucleotide and encoded aa sequences from all other sequenced bacteriophage genomes, and may represent a new viral taxon at the genus or subfamily level.", "keywords": [ "bacteriophage", "Aeromonas veronii", "aquaculture", "phage therapy" ], "content": "Introduction\n\nCurrently, aquaculture is the primary producer of nutritional fish in most developed countries.1 The cultivation of hydrobionts in production ponds is associated with very high densities of animal populations, which far exceed the typical population densities in wild habitats. Such conditions make cultivated fish specifically vulnerable to bacterial infections, of which aeromonoses comprise a significant fraction.2,3 The use of antibiotics to reduce economic losses associated with bacterial infections is restricted or prohibited in many countries; therefore, using phages as a tool for environmentally friendly biocontrol of the iсhtyopathogenic Aeromonas has attracted significant interest in scientific and business communities. Therefore, the search for new bacteriophage strains that are potentially suitable for use as phage therapy agents is important. Here, we present the isolation and sequencing of a novel A. veronii bacteriophage that represents a new group of bacteriophages that infect the genus Aeromonas.\n\n\nMethods\n\nThe bacteriophage Gekk3-15 was isolated as part of a project to establish a panel of bacteriophages to target the collection of A. hydrophila and A. veronii strains that cause infections in aquaculture facilities in Russia. The phage was isolated from a water sample collected from the Norishka Stream in Mikhailovsky Park in Moscow, Russia, on September 14, 2021. The bacteriophage was isolated using the enrichment culture setup as follows: A non-sterilized water sample (0.5 l) was placed in a 2 l sterile plastic bottle and supplemented with 50 ml of sterile 10x LB medium (for 1× medium: 10 g Bacto Tryptone (Amresco, Am-J859-0.25), 5 g yeast extract (Amresco, J850-500G), 10 g NaCl (Amresco, J869-500G), distilled H2O up to 1 l). The culture was supplemented with 0.5 ml of an overnight liquid culture of A. veronii AV-3 strain and incubated at 28 °C in a thermostat without agitation. Following incubation, 1 mL of the enrichment culture was centrifuged at 12 000 rpm in a tabletop microcentrifuge, filter-sterilized using a 0.22 μm syringe membrane filter (Millex-GP, Millipore), and plated onto the lawn of A. veronii strain 4 using the conventional double-layer technique.4\n\nPhage plaques were formed after an overnight incubation at 28°C. The phage was purified using two consecutive single-plaque isolations. To obtain a high-titer lysate, five 90 mm Petri dishes were filled with solid LB medium (15 g of Bacto Agar (BD214030, BD Difco) per 1 l). Without drying the plates, they were overlaid with 5 ml of soft LB agar (6 g Bacto Agar (BD214030, BD Difco) per 1 l) per plate. Soft agar was inoculated with 300 μl of a 4h log-phase liquid culture of the host strain and approximately 1×105 PFU of the phage per plate. The plates were incubated overnight at 28 °C. To extract the phage, the soft agar layer was gently destroyed with a spreader, transferred into 50 ml plastic centrifuge tubes, and layered with 10 ml of LB medium. Chloroform (Fisher Scientific, C298-4)(100 μL) was added to each tube, followed by vigorous vortexing for 1 min, and allowed to stand at room temperature for 2 h. After incubation, the agar fragments and bacterial cells were pelleted by centrifugation at 10 000 g for 5 min, and the supernatant was collected and centrifuged again under the same conditions. The phage was purified using a sucrose gradient as it described elsewhere.5 The purified phage sample was used for DNA extraction and transmission electron microscopy (TEM), as previously described.6\n\nTo extract DNA, the phage stock with a titer of approximately 1011 PFU ml−1 was treated with DNAse (Thermo Scientific, EN0521)(0,01 mg ml−1) for 30 min at room temperature, and the phage particles were then collected by ultracentrifugation in an angle rotor at room temperature (Beckman 45Ti, 1 h, 75000 g). Genomic DNA was extracted from the precipitates with CTAB cetyltrimethylammonium bromide (CTAB) extraction as described previously.7 DNA quality and quantity were assessed using agarose gel electrophoresis and a Qubit dsDNA HS fluorometer assay (Qubit, USA). Phage genomic DNA libraries were prepared and sequenced using an Ion Proton sequencer (Applied Biosystems, Foster City, CA, USA) with the standard chemistry according to the manufacturer’s instructions. The raw reads from the run were combined and filtered using the error correction tool Pollux (https://github.com/emarinier/pollux). Contigs were assembled using Newbler version 3.0 (RRID:SCR_011916) (Roche Diagnostics, USA). A single contig with a phage genome of 64 847 b.p. with an average coverage of 200 bp was obtained.\n\nAnnotation was performed using Prokka (RRID:SCR_014732)8 with subsequent manual curation. Potential open reading frames (ORFs) were detected using GeneMarkS (https://genemark.bme.gatech.edu/genemarks.cgi)(RRID:SCR_011930) and subsequently analyzed using HMMER (RRID:SCR_005305),9 HHPRED (RRID:SCR_010276)10 (MPI Bioinformatics Toolkit), NCBI BLAST (RRID:SCR_004870),11 and tRNAscan-SE (RRID:SCR_008637).12\n\n\nResults\n\nThe bacteriophage Gekk3-15 was found to be a relatively small myovirus with an isometric head (Figure 1). The genome consisted of 64 847 b.p. and encoded 101 ORF, including putative virion structural proteins. A set of proteins for the contractile phage tail was detected, confirming the bacteriophage TEM examination data. The Gekk3-15 genome also contains genes for DNA metabolism enzymes, a cell lysis system, and two potential auxiliary metabolic genes (AMGs), encoding 3-oxoacyl-[acyl-carrier-protein] reductase FabG and glyoxylase/dioxygenase superfamily proteins. No tRNA genes were identified. Phage Gekk3-15 does not contain any markers potentially associated with a lysogenic lifestyle or virulence factors. A BLASTN (RRID:SCR_001598) search against the NCBI nucleotide collection did not produce any relevant hits for related bacteriophage genomes. However, the BLASTX (RRID:SCR_001653) search identified a number of distantly related viruses, among which the closest relative by the large terminase a.a. sequence was the Pseudomonas phage EPa61 (GenBank NC_048744), sharing 57% aa identity with the Gekk3-15 protein. The levels of a. a. identity between the structural proteins of bacteriophages Gekk3-15 and EPa61 varied between 38% and 63%. This degree of similarity indicates that taxonomically, these phages belong to different genera and, probably, different subfamilies within the Caudoviricetes kingdom. Therefore, we conclude that phage Gekk3-15 represents a novel genus and, probably, a novel bacteriophage taxon of a higher rank.\n\n\nEthics and consent\n\nEthical approval and consent were not required.", "appendix": "Data availability\n\nNCBI GenBank: Aeromonas phage Gekk3-15, complete genome. Accession number OR661252; https://www.ncbi.nlm.nih.gov/nuccore/OR661252.1. 13\n\n\nReferences\n\nBondad-Reantaso MG, MacKinnon B, Karunasagar I, et al.: Review of alternatives to antibiotic use in aquaculture. Rev. Aquac. 2023; 15(4): 1421–1451. Publisher Full Text\n\nDien LT, Ngo TPH, Nguyen TV, et al.: Non-antibiotic approaches to combat motile Aeromonas infections in aquaculture: Current state of knowledge and future perspectives. Rev. Aquac. 2022; 15(1): 333–366. Publisher Full Text\n\nRai S, Kaur B, Singh P, et al.: Perspectives on phage therapy for health management in aquaculture. Aquac. Int. 2023; 1–45. Publisher Full Text\n\nLetarov AV, Kulikov EE: Determination of the bacteriophage host range: culture-based approach. Methods Mol. Biol. 2018; 1693: 75–84. PubMed Abstract \| Publisher Full Text\n\nKornienko M, Kuptsov N, Gorodnichev R, et al.: Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails. Sci. Rep. 2020 Oct 29; 10(1): 18612. Epub 2020/10/31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEfimov A, Kulikov E, Golomidova A, et al.: Isolation and sequencing of three RB49-like bacteriophages infecting O antigen-producing E. coli strains. F1000Res. 2021; 10: 1113. Publisher Full Text\n\nKulikov E, Golomidova A, Babenko V, et al.: A simple method for extraction of the horse feces virome DNA, suitable for oxford nanopore sequencing. Microbiology. 2020; 89: 246–249. Publisher Full Text\n\nSeemann T: Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15; 30(14): 2068–2069. Epub 2014/03/20. PubMed Abstract \| Publisher Full Text\n\nEddy SR: Accelerated Profile HMM Searches. PLoS Comput. Biol. 2011 Oct; 7(10): e1002195. Epub 2011/11/01. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSoding J, Biegert A, Lupas AN: The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue): W244–W248. PubMed Abstract \| Free Full Text\n\nAltschul SF, Gish W, Miller W, et al.: Basic local alignment search tool. J. Mol. Biol. 1990 Oct 5; 215(3): 403–410. Epub 1990/10/05. PubMed Abstract \| Publisher Full Text\n\nChan PP, Lin BY, Mak AJ, et al.: tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 2021 Sep 20; 49(16): 9077–9096. Epub 2021/08/22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGolomidov AK, Kulikov EE, Letarov AV: Isolation and complete genome sequences of Aeromonas bacteriophage. [Dataset]. NCBI GenBank. 2023. Reference Source" }	[ { "id": "283363", "date": "10 Jun 2024", "name": "Ruben Avendaño-Herrera", "expertise": [ "Reviewer Expertise Some of my main research topics include pathology in aquaculture", "diseases of aquatic organisms", "biotechnological tools applied to aquaculture", "standardization of procedures to control and validate the appropriate use of antibiotics", "and the development of vaccines against aquatic pathogens." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript is well written and requires the modifications indicated below. On the other hand, the title is too generic, considering that it only has activity against one species of Aeromonas, especially one isolate. The title needs to be more specific. It is suggested to modify it.Â The main issue is that the conclusion is too speculative, and further evidence is needed to confirm whether it corresponds to a new genus. Therefore, this situation should be verified and confirmed, or else it should be concluded that the bacteriophage has activity against an Aeromonas isolate. There are results that are not provided and are indicated at the end of this evaluation.\nAbstract Change to 64,847 bp Amino acids (aa)\nKeywords Italicize Aeromonas veronii\nIntroduction Reference No. 1 could be replaced by the FAO report or another article more relevant to the statement. \"Aeromonoses\" seems to be a term not globally used. Replace it with \"Aeromonas infections\" or \"Aeromonas diseases.\" Bacteriophage isolates Â How many are the isolates from the collection of the two Aeromonas species? LB, the full name of the medium should be provided before the abbreviation. How was it identified that AV-3 corresponds to the species A. veronii? This should be assured, as the taxonomy of this group is not easy and requires molecular analysis. Make this clarification for all Aeromonas used in this study. \"Strain\" or \"isolates,\" I think the latter. Review throughout the article. It is not necessary to give the LB recipe twice; just indicate the agar percentage in the last case. What concentration of DNA was sent for sequencing? This data is very important. Specify what \"bp\" is and correct the abbreviation, removing the periods.\nResults Indicate that it belongs to the family Myoviridae instead of \"myovirus\" in italics. The last lines where the conclusion is drawn, I believe it is too speculative to state that it corresponds to a new genus and further tests are required to confirm it. The article should modify the conclusion and reduce the enthusiasm, unless there are other tests that prove it. I suggest modifying it. If it was tested with a collection of Aeromonas, I would like to know if the activity is broad-spectrum or if it's only an isolate that was analyzed. This situation is very important. Additionally, was any physiological characterization of the virus conducted, considering that the introduction suggests they are an alternative for use in fish aquaculture?\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly", "responses": [] }, { "id": "278893", "date": "17 Jun 2024", "name": "Ben Temperton", "expertise": [ "Reviewer Expertise phage biology", "phage bioinformatics" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nEditorial Note from the F1000Research Editorial Team: This peer-review report was originally published on 17th June 2024, and on 1st July 2024 the report was edited to include an additional paragraph provided by the reviewer relating to Reviewer 1's (Ruben Avendano-Herrera's) report for this article.\nReview for: Isolation and complete genome sequence of Aeromonas bacteriophage Gekk3-15\nThis work details the method of isolation and sequencing of a novel bacteriophage that infects Aeromonas veronii, as well as translations of the genome. This is a useful finding as the isolated phage shares a low degree of similarity to previously sequenced phages, and the most closely related phage infects a host belonging to a different genus.\nMajor comments:\nThe framing of the study may be too broad for the content. The abstract discusses the use of phage in Aeromonas hydrophila, but this is not tested in the main text, and it is unclear if this particular phage would infect this host. We recommend either re-framing the abstract to specify Aeromonas veronii only, as this is the only isolate tested, or to test the phage infectivity on A. hydrophila also. This is especially important if the aim of the phage isolation is to be used in phage therapy.\n\nMinor comments: Page 3, under Methods, 'Phage isolation and cultivation', paragraph 1: \"at 28 deg. Celsius in a thermostat without agitation\". \"at 28 deg. Celsius in a thermostatic incubator without agitation\" would be clearer.\nSame paragraph: please add how many minutes the enrichment culture was centrifuged for. The x g should be listed rather than rpm\nSame paragraph: it is unclear what A. veronii strain was used to isolate this phage, initially it is listed as AV-3 strain, and later as strain 4. Either these are different strains or one was mis-named in the manuscript, but regardless it would be pertinent to introduce any strains used and include information about the origin(s).\nPage 3, under Methods, 'Phage isolation and cultivation', paragraph 2: what method was used for single-plaque isolations? Please provide a reference.\nSame paragraph: should read 'as described elsewhere' not 'as it described'.\nPage 3, under Methods, 'DNA extraction, sequencing, assembly and annotation', paragraph 1: should read '0.01 mg ml-1' not '0,01 mg ml-1'\nPlease use 'L' rather than 'l' for litres as this removes possible confusion between 'l', 'I', and 1.'L' is the approved symbol for litre (https://www.nist.gov/pml/owm/si-units-volume).\nThe authors attempt to classify their phage into an appropriate taxonomy based on amino acid identity of structural proteins. While this is not the gold standard as recommended by the ICTV (nucleotide similarity across the genome as specified by VIRIDIC), it is probably as close as is possible, given the paucity of suitably similar reference genomes. For instance we attempted to identify the closest phage genome in both INPHARED (Cook et al., 20211) and PhageClouds (Rangel-Pineros et al., 20212) (at both 0.15 and 0.2 distance), which yielded no hits. Therefore, the cautious interpretation of the placement by the authors is appropriate and should be revisited when more closely related genomes are deposited.\n\nThe reviewer Ruben Avendano-Herrera is incorrect in requesting that the authors use the term Myoviridae. This term was abandoned by the ICTV in their latest guidance which now requires the use of 'myovirus' to describe morphology, due to a lack of evidence for a shared common ancestor (Turner et al., 2023[ref-3).\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes", "responses": [] }, { "id": "278896", "date": "03 Sep 2024", "name": "Reham M El Tarabili", "expertise": [ "Reviewer Expertise microbiology", "immunology", "mycology", "molecular biology and food safety" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors declared, “Isolation and complete genome sequence of Aeromonas bacteriophage Gekk3-15”. Despite the importance of the study, the article lacks a good presentation. It has many grammar and language mistakes. The order of event writing should be the same either in the abstract, introduction, material, ……….so on. A title should be modified - Please write the scientific names of bacterial pathogens and genes in the correct form (italic form) all over the manuscript and the references section.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-380
https://f1000research.com/articles/12-1310/v1	11 Oct 23	{ "type": "Research Article", "title": "Assessment of the global healthcare industry during COVID-19 pandemic: A content analysis approach", "authors": [ "Malik Ladki", "Latifa Daher", "Robert Abou Chacra", "Elie Kassis", "Chady Ayrout", "Hadi Moubayed", "Amal Abbas", "Nahed Boudani", "Ralph A Doumit", "Sylvana Bitar", "Annie Kizirian", "Rola Hasna", "Darine Barakat", "Wissam H. Faour", "Malik Ladki", "Latifa Daher", "Robert Abou Chacra", "Elie Kassis", "Chady Ayrout", "Hadi Moubayed", "Amal Abbas", "Nahed Boudani", "Ralph A Doumit", "Sylvana Bitar", "Annie Kizirian", "Rola Hasna", "Darine Barakat" ], "abstract": "Background: Content analysis (CA) is an investigative research tool used in healthcare studies to identify imminent challenges while providing lead time for preparedness measures. The objective of this study is to report on the challenges confronting the global healthcare industry. Methods: This study used the conventional CA “bottom-up” approach to a quantitative data. CA is a research technique that uses the qualitative research method and word counts to evaluate communication outcomes. A group of executive master’s in business administration (EMBA) and medical students championed the study. Using 13 periodicals as the data sources, researchers conducted online keyword searches for all articles, titles, and abstracts containing the word “healthcare”. The collected data was gathered from five international, four Middle Eastern, and four Lebanese periodicals from January 1, 2021 to December 31, 2021. Results: CA results indicate remarkable domination of keywords “COVID-19 health impact” as a major worldwide theme. Significant differences were noticeable among subcategories but remained related to COVID-19 in particular, social responsibilities, and research and development. Topics such as comorbid illnesses, social responsibility, healthcare logistics, and the well-being of healthcare service providers were among the least covered topics. Conclusion: Our findings emphasize the importance of global media and their coverage of healthcare issues on the types of healthcare topics (e.g., vaccines, drugs…) covered in the Lebanese periodicals in our study. Thus, global healthcare media are the main source for Lebanese periodicals reporting healthcare issues rather than the Lebanese healthcare authorities. Therefore, there is need for the development of a more efficient technology-driven healthcare management system. At the global level, there is a need to develop a step-by-step action-oriented strategic initiative to respond to emerging pandemics.", "keywords": [ "content analysis", "periodicals", "healthcare", "COVID-19" ], "content": "Introduction\n\nContent analysis (CA) is a multipurpose research technique that deals with the objective, systematic, quantitative, qualitative, and general description of the manifest and latent content of communication.1,2 As a research tool, CA determines the reoccurrence of words, themes, or concepts in qualitative data.3 It is a research technique that uses a set of formalized procedures to classify communication to draw valid inferences. CA provides researchers with the opportunity to unobtrusively study the values, intentions, and ideologies of any group.4–8 Thus, CA enables researchers to quantify and analyze the presence, meanings, and relationships of concepts, words, or themes in various communication mediums.\n\nRegardless of the diversity of CA definitions, many researchers agree on the objectivity, systematic, and generality of any CA analysis.9 Objectivity is maintained when data is collected based on explicitly formulated rules. Researchers tend to use professional judgment in making decisions about their data. Thus, enabling researcher biases or subjectivity to creep into the investigation can skew the results. It is important to minimize biases by establishing and following strict procedures and thus enabling those who duplicate the study to achieve similar results. The systematic requirement is the inclusion and exclusion of content according to a set of applied rules where the investigator biases are eliminated and multiple coders follow established procedures to ensure outcome validity and reliability. Generality entails that the findings must have theoretical relevance and is achieved when some form of harmony or similarity is found when findings are compared.\n\nMost CA investigations center around three distinct approaches: conventional, directed, or summative approaches.4 Regardless of the approach, the outcome of CA is to interpret communication intents or meanings. Coding schemes represent the difference among the approaches, and the conventional technique is the most common coding technique where categories originate from words. Whereas in the directed approach there is a hypothesis and a theory to guide researchers to identify codes. In the summative approach, researchers count and compare words and then interpret the underlying theme.\n\nThe use of CA in health care literature is becoming prevalent.10–14 A surge in the use of qualitative research is being witnessed in many fields including healthcare, medical, and biomedical literature.15,16 Qualitative CA in healthcare research has been applied to draw interpretation from a variety of sources.17–20 The application of CA in healthcare encompasses all disciplines including policies,21 genomic analysis,22 population health,23 biomedical technology,24 medical decision making.25\n\nThe healthcare system throughout various regions confronted major challenges due to coronavirus disease 2019 (COVID-19) pandemic. The purpose of this study is to report on the challenges confronting the global healthcare industry. The study intends to enable health organizations, researchers, professionals, and governments to raise public awareness on the most challenging or critical healthcare issues confronting the industry throughout the various regions of the world.\n\n\nMethods\n\nThe international periodicals were selected among USA based periodicals since the authors concluded that USA media have strong influences worldwide. The listed US periodicals were also chosen since online access to the periodical archives are easily accessible through Lebanese American University (LAU) online library, as well as librarian support about the search tools through these periodicals. The regional periodicals were chosen from two countries that have major influence in the Arabic region: Saudi Arabia and Egypt. As Jordan is a nearby Arabic country to Lebanon and share similar economic situation, thus Jordan times was also preferred and selected. The Lebanese periodicals were chosen to cover the language diversity (Arabic, French and English) that exists in Lebanon and taking into consideration free online access to the periodical archives. The availability of free online access to the periodical archives was also a crucial criterion. In order to minimize bias, students or “coders” were trained in advance on data collection and how to search for data as part of their EMBA course on content analysis. Furthermore, each student was not allowed to interact with the other members in order to prevent judgment bias about the coding process and the collected data. Each student collected data individually and didn’t communicate with any of the students before submitting the data to the corresponding author. Data gathering and analysis was carried out using Excel 2016, and chart lines were made in order to assess the trends of categories among each periodicals on a monthly basis.\n\nThe investigators have gathered data from 13 of the periodicals in various parts of the world from January 1, 2021 to December 31, 2021. This study uses the conventional CA “bottom-up” approach to a qualitative data set.26 This approach enables researchers to collect, sort, and categorize data to identify emerging patterns or to develop theories.27 Briefly, in bottom-approach all the team members involved in data collection will work proactively in each step of the project execution process until the final goal of the project is reached. Therefore, all the team members are involved in decision-making about the process and the strategy to follow as well as the outcomes of the analysis.\n\nThe study was conducted by a collaborative research group of Executive Master in Business Administration (EMBA) and medical students at two universities. Students at the Lebanese American University (Beirut, Lebanon) and the University of Texas Medical Branch (Galveston, Texas) collaborated on this research initiative. The students were divided into three groups: The first group collected data from the following international periodicals: The New York Times, Financial Times, Boston Herald, The Wall Street Journal, and Los Angeles Times. The second group collected data from four of the Middle East’s top English printed periodicals: Saudi Gazette, The Jordan Times, Gulf Daily News, and Daily News Egypt. The third group collected data from four online Lebanese, two Arabic (Al Akhbar, An Nahar), one English (Daily Star) and one French (L’Orient Le Jour) periodicals (Table 1). The underlying data is available through the online repository.37\n\nUsing 13 periodicals as the data source, researchers conducted online keyword searches for all articles, titles, and abstracts containing the word “healthcare”. Researchers manually browsed through each periodical for the period of the study (January 1, 2021 to December 31, 2021) to identify all healthcare related articles. This procedure enabled researchers to compile a comprehensive data set of published communication containing the word “healthcare”. To eliminate the redundancy of collected data, the researchers systematically assigned a specific day as a source of input for each periodical (Table 1).\n\nResearchers have systematically analyzed the content of 13 periodicals once a week for a year. The data set produced the findings of the content from 676 days from within the year 2021. Researchers examined the context in which the occurrences of words, and phrases, related to “healthcare” and recorded then analyzed findings. “Healthcare” was used as major output for all countries due to COVID19 pandemic.\n\nTo ensure the validity and reliability of collected data, all coders were trained and then instructed to follow the following protocol:\n\n(i) Establishing the document inclusion criteria (identifying documents based on the titles & tags of the articles, selecting the ones with topics related to healthcare).\n\n(ii) Gathering documents through online scanning of the periodicals.\n\n(iii) Identifying keywords by manually examining the content of the selected documents.\n\n(iv) Developing coding criteria to ensure validity (being consistent in following coding rules, Table 2).\n\n(v) Eliminating keywords with low-frequency counts (removing irrelevant keywords that are not fully related to healthcare (e.g. salaries, climate changes).\n\n(vi) Classifying the keywords into categories (introducing keywords into a particular category is based on their relevance to that category).\n\n(vii) Drawing conclusions and generalizations (data analysis).\n\nTo come up with an understanding of the investigated research questions, the investigators recorded and analyzed the occurrences of words, phrases, and sentences related to “healthcare”. Based on data interactions, numerous categories were identified and then integrated into a framework comprising a trend line to answer the research questions28 through an in-depth analysis of the most popular periodicals throughout the various regions of the world. By examining word frequency counts and categorizing data, our objectives were to provide a meaningful source of informational input for health organizations, researchers, professionals, and governments, and to raise public awareness on most challenging or critical healthcare issues.\n\nSelected periodicals represent some of the most widely circulated periodical in certain region of the world (Table 2). All periodicals were available through on-line subscriptions at the libraries of participating universities. Data was collected on Excel 2016 and clustered into three groups (International periodicals, Middle Eastern periodicals, and Lebanese periodicals). The proportions of the keywords frequencies were then calculated and used to create the trend lines shown in the figures. Though the 13 periodicals were printed in three different languages (English, French, and Arabic), coders were versatile and fluent in the above foreign languages and were able to read, write, and analyze data.\n\nData was collected from all periodicals once a week throughout the investigation period of 2021. Coders were trained, then assigned to investigate specific periodicals in each cluster. Regular meetings were held to monitor the coders’ compliance with the objectives of the study and the use of agreed upon coding schemes. Results represent data for each region of the world. Further, all regions were compressed together, and the global data set emerged. The result section of the compressed global data obtained after regrouping the keywords in sets resulted in 10 categories which represent the most frequently reported healthcare issues during 2021 and are defined in Table 2.\n\n\nResults\n\nIn keeping with the effect of COVID-19 internationally, our data showed that international periodicals shared similar coverage about the improvements in COVID-19 in health care but further focused on the strategic plan against COVID-19 pandemic in addition to its social and economic impacts. For instance, the category “strategic action plan for COVID” showed the highest frequency percentage of 25.7%, followed by the category “COVID Health impact” with 21.3%, while the percentage of the “Health care future and research and development (R&D)” category was 14.2%. Furthermore, the categories covering social responsibility, healthcare logistics, and the well-being of healthcare service providers in addition to the social, economic, and financial impact of COVID-9 were also covered in all periodicals but at a lower frequency.\n\nFigure 2 shows the impact of COVID-19 on health systems, how it is a major concern and ranked first among all other topics in all chosen Middle Eastern journals including Gulf Daily News, Saudi Gazette, and The Jordan times, except for Daily News Egypt. Accordingly, the category “COVID health impact” showed the highest frequency percentage of 25.7%, followed by the category “Strategic plan for COVID” with a frequency percentage of 25.1%, and the category “COVID affected party” ranked third with a frequency percentage of 16.0%. While Daily News Egypt showed a different pattern where the strategic plan to fight COVID-19 was ranked first, COVID-19 health impact was still considered a topic of high importance and ranked third among other topics. All other topics including social responsibility, healthcare logistics, and the well-being of healthcare service providers in addition to the social, economic, and financial impact during COVID-19 were covered at a lower frequency with the highest being for the category “Healthcare system authority” with 8.6% and the category “Healthcare disease” showed the least frequency percentage of 0.7% in all these periodicals.\n\nFigure 3 shows that the health impact of COVID-19 was a major concern and ranked first among the topic in the national periodicals including L’Orient Le jour, Al-Akhbar, and Daily Star throughout the year 2021. Furthermore, the finding corroborated and was similar to the data found in the international periodicals where the impact on health and strategic action plan for COVID-19 were among the most covered topic in these periodicals. Accordingly, the category “COVID health impact” showed the highest frequency percentage of 33%, followed by the category “Health care future an R&D” with a frequency percentage of 23%. Finally, the category “Strategic plan for COVID” was ranked third with a frequency percentage of 13%. Finally, all other topics including social responsibility, healthcare logistics, and the well-being of healthcare service providers in addition to social, economic, and financial impact of COVID-19 were not sufficiently covered in all these periodicals.\n\n\nDiscussion\n\nHealthcare systems worldwide faced major challenges during COVID-19 pandemic. At the beginning of the pandemic, healthcare systems worldwide were chaotically responding to the outbreak and its consequences.29 While healthcare is mostly focused on providing proper treatment to infected patients, soon after, healthcare managers recognized that existing intervention policies are not serving their purpose.30\n\nOur data showed that international periodicals served as a source of COVID-19 data input for local and regional COVID-19 news. Our data concluded that international periodicals act as “trendsetters” whereas regional and local news were followers. Such finding is highlighted by the fact that coverage of “vaccines” and other keywords that mentioned in local and regional periodicals at the early stages of COVID-19 only started to appear after their appearance/coverage in the international media. Accordingly, we believe that low-income countries will continue to rely on developed countries to prioritize healthcare spending. This was expected by the authors given the scarcity of resources allocated to R&D COVID-19, in addition to the lack of policies and health task forces to face challenges such as COVID-19 pandemic.\n\nThe development of new global and local COVID-19 prevention strategies (curfews, use of masks, limiting social contact, use of sanitizers) enabled the healthcare system to effectively use its scarce resources to serve the largest number of infected patients,31,32 thus preventing the collapse of the healthcare systems. COVID-19 fightback strategies became a popular and a frequently reported healthcare issue, thus shifting attention from other diseases and negatively influencing the communication outflow for chronic illnesses (e.g. diabetes, cancer, kidney diseases).33–35 The latter finding was highlighted with the reduced frequencies of “health diseases” that did not bypass 10% in international newspapers and was almost inexistent in Middle East and national periodicals (Figures 1, 2 and 3).\n\nThe scarcity of resources worldwide subjected countries with strong healthcare systems to experience COVID-19 transfer waves originating from less developed countries. At first, the USA, China, and Europe were interested in fighting COVID-19 within their borders. Due to the massive movement of people, such a strategy was not effective. Therefore, it was of utmost importance to find better and sustainable solutions not only to stop COVID-19 waves but also to establish better health policies worldwide, thus limiting the spread of COVID-19. In addition, many countries worldwide were convinced that the spread of infectious diseases could not be limited by geographical boundaries thus collective international efforts must be initiated in order to face not only COVID-19 but also future challenges.36\n\nInitially, in the beginning of data collection, it was observed by the authors that COVID-19 influence on the healthcare was worldwide and was not country specific. All countries were significantly affected by COVID-19 with various degrees, therefore it was expected that COVID-19 related news on health care were at the forefront. Our data corroborated these findings and further showed that the keyword “healthcare” was the most frequent keyword repeated in the study. A case in point, strategies to fight the pandemic started to surface in the periodicals in response to the collapsing Italian healthcare system in 2020. Accordingly, the category “strategic action plan for COVID-19” was the mostly reported with frequencies bypassing 25% international newspapers, 30% in Middle East newspapers and 35% in Lebanese periodicals. Fear from future collapse of other healthcare systems fueled the news with the importance of taking measures to fight the pandemic without compromising the efficacy of the healthcare system. Accordingly, strategies to reduce disease spread through vaccination as an alternative tool to reduce the pressure on the healthcare system were among the earliest measures adopted by the healthcare authorities.37 While strategies and policies to fight COVID-19 where among the repeated keywords in the study, other important keywords such as “healthcare budget” were not highly reported in the media and showed low frequency of reporting as compared to other keywords. All the chosen periodicals showed similar trend lines (health care, strategies), where the corresponding categories were reported at frequencies ranging 5–15% among all newspapers.\n\nDiscrepancies were found among surveyed periodicals, where the keyword “research and development” was frequently reported in international periodicals while it was mostly missing in local and regional periodicals (Figures 1, 2 and 3). Accordingly, the keyword “vaccines” appeared as one of the most frequent keywords in the study and the earliest in international periodicals (Figure 1). The latter findings reflect the trend of developed countries to use R&D in fighting diseases and providing policies and procedures to develop their healthcare interventions. Accordingly, the keyword “vaccines” was not reported in regional and national periodicals at the beginning of the pandemic. The impact of COVID-19 on the healthcare system and the economies appeared early months of the studied year in the international periodicals where the keyword “healthcare” was reported at a very high frequency of 60% compared to the regional and local periodicals (around 30%).\n\nThe limitation of the study is associated with the human factor as decoding the periodicals manually which may have created discrepancies among the coders. Such coding processes can be influenced by all the well-known human factors including emotions, language barriers, efficiency, and understanding of the objectives. However, reducing the workload on each team member and providing proper training before starting the research process greatly contributed to minimizing such bias. While the content analysis research approach is well-known in the literature, to our knowledge it is the first study that tackles COVID-19. Interestingly, in the era of artificial intelligence and the availability of powerful search engines on the web, the human factor remains essential in deciphering the quality and quantity of information needed to formulate proper policies that are compatible with nowadays challenges. Lastly, we believe that periodicals whether they are published at the local, regional or international level were found to have an important role in guiding and raising awareness about strategic health care issues that could be of great importance globally.\n\n\nConclusions\n\nOur data showed that international periodicals served as sources of COVID-19 data input for local and regional COVID-19 news. Our data concluded that international periodicals act as “trendsetters” whereas regional and local news were followers. This is expected given the scarcity of resources allocated to R&D COVID-19, in addition to the lack of policies and health task forces to face challenges such as COVID-19 pandemic. Therefore, global media can be a crucial source of up-to-date healthcare policies originating for low income countries in order to respond fast and actively to future local and global health care challenges.", "appendix": "Data availability\n\nZenodo: Content Analysis Data set. https://doi.org/10.5281/zenodo.7785825. 38\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nBerelson B: Content analysis in communication research. Free Press; 1952.\n\nHolsti OR: Content Analysis.Lindzey G, Aronson E, editors. Handbook of Social Psychology. Vol. 2. 1968.\n\nMorris RJ: Computerized Content Analysis in Management Research: A Demonstration of Advantages & Limitations. J. Manag. 1994; 20: 903–931. Publisher Full Text\n\nHsieh H-F, Shannon SE: Three Approaches to Qualitative Content Analysis. Qual. Health Res. 2005; 15(9): 1277–1288. Publisher Full Text\n\nKeating NL, Gandhi TK, Orav EJ, et al.: Patient characteristics and experiences associated with trust in specialist physicians. Arch. Intern. Med. 2004; 164(9): 1015–1020. PubMed Abstract \| Publisher Full Text\n\nMason J: Qualitative Researching. Second ed.Sage Publications Ltd.; 2002.\n\nMayring P: Qualitative Content Analysis. Forum Qual. Sozialforsch. 2000; 1: 2.\n\nRidder H-G: Book Review: Qualitative Data Analysis. A Methods Sourcebook. Zeitschrift für Personalforschung/German Journal of Research in Human Resource Management. 2014; 28(4): 485–487. Publisher Full Text\n\nMiles MB, Huberman AM: Qualitative data analysis: An expanded sourcebook. 2nd ed. Vol. xiv. . Thousand Oaks, CA, US: Sage Publications, Inc; 1994; pp. 338.\n\nBoettger R, Palmer L: Quantitative Content Analysis: Its Use in Technical Communication. Professional Communication, IEEE Transactions on. 2011; 53: 346–357. Publisher Full Text\n\nGittelman S, Lange V, Gotway Crawford CA, et al.: A new source of data for public health surveillance: Facebook likes. J. Med. Internet Res. 2015; 17(4): e98. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHiggins JW, Naylor PJ, Berry T, et al.: The health buck stops where? Thematic framing of health discourse to understand the context for CVD prevention. J. Health Commun. 2006; 11(3): 343–358. PubMed Abstract \| Publisher Full Text\n\nHinyard LJ, Kreuter MW: Using narrative communication as a tool for health behavior change: a conceptual, theoretical, and empirical overview. Health Education & Behavior: The Official Publication of the Society for Public Health Education. 2007; 34(5): 777–792. PubMed Abstract \| Publisher Full Text\n\nLima A, De Domenico M, Pejovic V, et al.: Disease Containment Strategies based on Mobility and Information Dissemination. Sci. Rep. 2015; 5: 10650. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Busaidi ZQ: Qualitative research and its uses in health care. Sultan Qaboos Univ. Med. J. 2008; 8(1): 11–19. PubMed Abstract\n\nErlingsson C, Brysiewicz P: A hands-on guide to doing content analysis. Afr. J. Emerg. Med. 2017; 7(3): 93–99. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBerg A, Welander HU: Dementia care nurses’ experiences of systematic clinical group supervision and supervised planned nursing care. J. Nurs. Manag. 2000; 8(6): 357–368. Publisher Full Text\n\nLatter S, Yerrell P, Rycroft-Malone J, et al.: Nursing, medication education and the new policy agenda: the evidence base. Int. J. Nurs. Stud. 2000; 37(6): 469–479. PubMed Abstract \| Publisher Full Text\n\nO’Brien B, Relyea J, Lidstone T: Diary reports of nausea and vomiting during pregnancy. Clin. Nurs. Res. 1997; 6(3): 239–252. PubMed Abstract \| Publisher Full Text\n\nSöderberg S, Lundman B: TRANSITIONS EXPERIENCED BY WOMEN WITH FIBROMYALGIA. Health Care Women Int. 2001; 22(7): 617–631. PubMed Abstract \| Publisher Full Text\n\nLedoux C, Pilot E, Diaz E, et al.: Migrants’ access to healthcare services within the European Union: a content analysis of policy documents in Ireland, Portugal and Spain. Glob. Health. 2018; 14(1): 57. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHalley MC, Young JL, Fernandez L, et al.: Perceived utility and disutility of genomic sequencing for pediatric patients: Perspectives from parents with diverse sociodemographic characteristics. Am. J. Med. Genet. A. 2022; 188(4): 1088–1101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCrouzet L, Scarlett H, Colleville AC, et al.: Impact of the COVID-19 pandemic on vulnerable groups, including homeless persons and migrants, in France: A qualitative study. Prev. Med. Rep. 2022; 26: 101727. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLao SSW, Chair SY: The feasibility of smartphone-based application on cardiac rehabilitation for Chinese patients with percutaneous coronary intervention in Macau: a qualitative evaluation. Int. J. Qual. Stud. Health Well Being. 2022; 17(1): 2023940. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSingh GK, Rego J, Chambers S, et al.: Health Professionals’ Perspectives of the Role of Palliative Care During COVID-19: Content Analysis of Articles and Blogs Posted on Twitter. Am. J. Hosp. Palliat. Care. 2022; 39(4): 487–493. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRichards T, Richards L: Using Computers in Qualitative Research. Chapter 8 in Collecting and Interpreting Qualitative Materials. Denzin NK, Lincoln YS, editors. Thousand Oaks, CA, USA: SAGE Publications; 1998.\n\nWilliamson K, Given L, Scifleet P: Qualitative data analysis.2018; pp. 453–476.\n\nHallgren KA: Computing Inter-Rater Reliability for Observational Data: An Overview and Tutorial. Tutor. Quant. Methods Psychol. 2012; 8(1): 23–34. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReynolds NR, Baker D, D’Aoust R, et al.: COVID-19: Implications for Nursing and Health Care in the United States. J. Nurs. Scholarsh. 2023; 55(1): 187–201. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRenosa MDC, Wachinger J, Barnighausen K, et al.: Misinformation, infighting, backlash, and an ‘endless’ recovery; policymakers recount challenges and mitigating measures after a vaccine scare in the Philippines. Glob. Health Action. 2022; 15(1): 2077536. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEne JC, Ajibo HT: Covid-19 Recovery and Growth: Promoting Technology Innovation in Healthcare Sector on Hygiene and Safe Medication Practices in Low-Resourced Nigerian Societies. Sci. Afr. 2023; 19: e01542. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhunti K, Aroda VR, Aschner P, et al.: The impact of the COVID-19 pandemic on diabetes services: planning for a global recovery. Lancet Diabetes Endocrinol. 2022; 10(12): 890–900. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurayzat SM, Kilani M, Al-Ghawanmeh R, et al.: Evaluation of the Effect Coronavirus Lockdown had on Chronic Disease Management Care in Pediatrics: A Survey of Jordanian Pediatricians. Int. J. Clin. Pract. 2022; 2022: 8710176.\n\nGeetha D, Kronbichler A, Rutter M, et al.: Impact of the COVID-19 pandemic on the kidney community: lessons learned and future directions. Nat. Rev. Nephrol. 2022; 18(11): 724–737. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNasseh J, Podevin C, Ternynck C, et al.: Self-reported Impact of the Early 2020 COVID-19 Crisis on the Healthcare Pathway During and After Lockdown in Patients With Chronic Immune-Mediated Inflammatory Diseases: A Practical Survey. J. Patient Exp. 2022; 9: 237437352211437. Publisher Full Text\n\nDutta A: COVID-19 waves: variant dynamics and control. Sci. Rep. 2022; 12: 9332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAgus DB, Nguyen A, Sall AA, et al.: COVID-19 and other adult vaccines can drive global disease prevention. Lancet (London, England). 2023; 401(10370): 8–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFaour W: Content Analysis Data set. [Data]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "224457", "date": "13 Feb 2024", "name": "Clara Abou Samra", "expertise": [ "Reviewer Expertise health policy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study aims to analyze the impact of the COVID-19 pandemic on the global healthcare industry using Content Analysis (CA) of periodicals from different regions. The researchers collected data throughout 2021, applying a conventional CA approach to identify emerging patterns and trends in healthcare-related content. The study is well presented. However, the literature review lacks depth and in some cases citations. It is suggested to incorporate a more comprehensive literature review with studies on content analysis in health research and the impact of COVID-19 on healthcare systems. While the methodology is well-detailed, more information on the training of coders, addressing potential biases and ensuring consistency in data collection is needed. Providing additional details in these areas would enhance the replicability of the study. It is also suggested to provide details on how others can access the online repository containing source data. This is essential for ensuring transparency and replicability. Although the conclusions align with the results, the study lacks an in-depth discussion of limitations, potential biases, and implications. The claim that international periodicals act as \"trendsetters\" needs more exploration and discussion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11383", "date": "20 Jun 2024", "name": "Wissam Faour", "role": "Author Response", "response": "On behalf of the authors, I would like to thank you and the reviewers for their effort and constructive comments. Please find below our answers to each of the comments raised by the authors. The study aims to analyze the impact of the COVID-19 pandemic on the global healthcare industry using Content Analysis (CA) of periodicals from different regions. The researchers collected data throughout 2021, applying a conventional CA approach to identify emerging patterns and trends in healthcare-related content. The study is well presented. However, the literature review lacks depth and in some cases citations. We thank the reviewer for this comment. Regarding the introduction, it was meant to introduce the methodology and its importance to perform the search related to the topic. We tried to be as much specific as possible to reduce potential redundancy and unnecessary increase in length. In addition, we included 29 references out of 42 in the introduction to make it rich and focus It is suggested to incorporate a more comprehensive literature review with studies on content analysis in health research and the impact of COVID-19 on healthcare systems. We thank the reviewer for this comment, and we add the following references along with the corresponding paragraph in the introduction as requested: 26. Dolatkhah, R., et al., Content analysis of identity challenges in patients with haemophilia: A qualitative study. Nurs Open, 2021. 8(3): p. 1444-1451. 27. Karanikola, M.N.K., Content Analysis in Critical and Emergency Care: A Discussion Paper. sgrwfccn, (1): p. 8-23. 28. Gyberg, A., et al., Struggling for access to appropriate healthcare services: A qualitative content analysis of patient complaints. Journal of Advanced Nursing, 2023. 79(10): p. 3748-3759. 29. Reifegerste, D. and A. Wiedicke, Content Analysis in the Research Field of Health Coverage, in Standardisierte Inhaltsanalyse in der Kommunikationswissenschaft – Standardized Content Analysis in Communication Research: Ein Handbuch - A Handbook, F. Oehmer-Pedrazzi, et al., Editors. 2023, Springer Fachmedien Wiesbaden: Wiesbaden. p. 179-191. While the methodology is well-detailed, more information on the training of coders, addressing potential biases and ensuring consistency in data collection is needed. Providing additional details in these areas would enhance the replicability of the study We thank the reviewer for the comments, as such we added the following section to the methodology to further clarify the used method. Training the coders and search procedure Two weeks prior to the initiation of the coding process, coders went through several intensive training sessions. Over time and with ongoing practice, coders developed the technical skills of matching. The 13 coders were broken down into 3 clusters, cluster 1 (International periodicals) was composed of 5 coders, cluster 2 (ME) and cluster 3 (Lebanese), both clusters were composed of 4 coders each respectively. Coders visited the library where all periodicals for five years period was awaiting for them. Each coder was issued a specific periodical for one year. The coders were first instructed to select all healthcare related articles, then look for keywords related to “healthcare”. Once the keyword was identified it will be counted as one data point. As example, any article in the periodical containing a healthcare related keyword “Vaccine” it is consider as one data point for the vaccine keyword. Similarly keywords such as “Hospital” if it exists in the article it adds one point to the hospital keyword count. The presence of the word is counted once only. To improve data validity and reliability the number of times the keyword is repeated in the article was not counted. Data was collected from all periodicals once a week throughout the investigation period of 2021. Coders were trained, then assigned to investigate specific periodicals in each cluster. Regular meetings were held to monitor the coders’ compliance with the objectives of the study and the use of agreed upon coding schemes. Results represent data for each region of the world. Further, all regions were compressed together, and the global data set emerged. The result section of the compressed global data obtained after regrouping the keywords in sets resulted in 10 categories which represent the most frequently reported healthcare issues during 2021 and are defined in It is also suggested to provide details on how others can access the online repository containing source data. This is essential for ensuring transparency and replicability. The link to the repository is added at the end of the references and numbered 42 Although the conclusions align with the results, the study lacks an in-depth discussion of limitations, potential biases, and implications. The claim that international periodicals act as \"trendsetters\" needs more exploration and discussion. Answer: We than the reviewer for this comment, and the following paragraph of the discussion section is modified to answer the reviewer’s comment: Discrepancies were found among surveyed periodicals, where the keyword “research and development” was frequently reported in international periodicals while it was mostly missing in local and regional periodicals ( Figures 1, 2 and 3). The latter findings reflect the trend of developed countries to use R&D in fighting diseases and providing policies and procedures to develop their healthcare interventions, which is lacking in other studied countries. Also, the keyword “vaccines” appeared as one of the most frequent keywords in the study and the earliest in international periodicals ( Figure 1). Accordingly, the keyword “vaccines” was not reported in regional and national periodicals at the beginning of the pandemic. The impact of COVID-19 on the healthcare system and the economies appeared early months of the studied year in the international periodicals where the keyword “healthcare” was reported at a very high frequency of 60% compared to the regional and local periodicals (around 30%). The above-mentioned data, showed that healthcare news are described first in international periodicals then appear in local and regional periodicals setting a trend of considering international periodicals as a source of data. Furthermore, theses data highlight the fact that local and regional periodicals are quick followers and stay current with the news as soon as it is published in the international periodicals. Accordingly. They use international periodicals as source of information, they identify the piece of information they are interested in and get it translated and immediately (1-2 days max) published in the local or regional media Is the work clearly and accurately presented and does it cite the current literature? Partly Answer: more references were added to the introduction to make it rich Is the study design appropriate and is the work technically sound? Yes Thanks for the comments Are sufficient details of methods and analysis provided to allow replication by others? Partly Answer: we added an entire section describing the methodology as requested If applicable, is the statistical analysis and its interpretation appropriate? Not applicable Are all the source data underlying the results available to ensure full reproducibility? Partly Answer: The data are available in the repository referenced in the paper Are the conclusions drawn adequately supported by the results? Partly Answer: We clarified the points that requires further discussion as requested by the reviewers" } ] } ]	1	https://f1000research.com/articles/12-1310
https://f1000research.com/articles/13-379/v1	24 Apr 24	{ "type": "Case Report", "title": "Case Report: Allogenic Wharton's jelly mesenchymal stem cell and exosome therapy are safe and effective for diabetic kidney failure", "authors": [ "Umm E Habiba", "David Lawrence Greene", "Khalil Ahmad", "Sabiha Shamim", "Nasar Khan", "Amna Umer", "Umm E Habiba", "David Lawrence Greene", "Khalil Ahmad", "Sabiha Shamim", "Amna Umer" ], "abstract": "Diabetes typically leads to repercussions such as chronic kidney disease (CKD), a worldwide health problem. Dialysis is typical for severe renal function loss (eGFR 15), but complications continue to exist. Chronic dialysis shortens life expectancy, and the wait for a transplant can be long, resulting in significant mortality. Human umbilical cord-derived Wharton’s jelly mesenchymal stem cells (hWJ-MSCs) have shown potential in regenerative healthcare for kidney repair, with unique capacities in restoring function and repairing damaged kidneys in animal models of chronic renal failure. The need to advance alternative medicines, such as regenerative medicine, in addressing crucial concerns in CKD care is stressed. We present the first case report in humans of a 70-year-old male with stage V chronic kidney disease caused by type 2 diabetes mellitus who received allogenic hWJ-MSCs and exosomes. The procedure includes the intravenous infusion of 100 million stem cells and 100 billion exosomes, which proved to be safe with no side effects. The renal profile improved significantly between the first and fourth months after infusion, according to assessments comprising lab results and the KDQOL-36TM questionnaire. Human umbilical cord Wharton’s jelly-derived mesenchymal stem cell implantations proved safe and effective in treating CKD.", "keywords": [ "Chronic Kidney Disease", "Stem Cell", "Diabetes", "Exosome", "Wharton’s Jelly" ], "content": "Introduction\n\nDiabetes is a significant public health issue in both developed and developing countries (de Boer et al. 2020; Sun et al. 2022). Type 2 diabetes mellitus (T2DM) accounts for over 90% of the global diabetes burden (Sun et al. 2022; Shaw, Sicree, and Zimmet 2010; Chen, Magliano, and Zimmet 2011). The global diabetes population has more than doubled in the last 20 years, owing to the obesity epidemic, which has resulted in a nearly tripling of obesity since 1975 (Manne-Goehler et al. 2016; Koye et al. 2018; Bentham et al. 2017). Obesity prevalence in children, adolescents, and adults has increased in every country throughout this time period (Bentham et al. 2017). Diabetes has an anticipated global prevalence of 11% among adults aged 20 to 79 in 2021, which is expected to rise to 12% by 2045 (Sun et al. 2022). Diabetes prevalence was similar in men and women in 2021, growing steadily with age, higher in urban (12%) than rural (8%) locations, and higher in high-income (11%) and middle-income (11%) countries compared to low-income countries (6%). Notably, the International Diabetes Federation (IDF) published a report in 2021 indicating that the number of people with diabetes globally and per IDF region in 2045 (20-79 years) will increase by 46% globally, 24% in North America and the Caribbean, 13% in Europe, 27% in the Western Pacific, 50% in South and Central America, 134% in the Middle East and North Africa, and 68% in South-East Asia (Figure A) (International Diabetes Federation 2021).\n\nThis global picture depicts the diabetes occurrence starting from 2021, 2030 and an estimated projection by 2045. The numbers were acquired from International diabetes federation (IDF) atlas handbook and histograms were created in the excel. The project contains the image file and IDF Diabetes Atlas 10th edition 2021.xlsx file.\n\nDiabetes mellitus has been recognized as the major risk factor for CKD in developed nations, as evidenced by epidemiological studies. In the United States, the prevalence of CKD stages 3-4 among diagnosed diabetics was 24.5% from 2011 to 2014, 14.3% among prediabetics, and 4.9% among nondiabetics (Stempniewicz et al. 2021). A meta-analysis of 82 global studies (Hill et al. 2016) found a link between diabetes mellitus and the incidence of CKD. Diabetes mellitus has a well-established effect on renal function as well as the onset and progression of CKD, also known as diabetic kidney disease (DKD) (de Boer et al. 2020). DKD is usually characterized as the presence of chronic kidney disease (CKD) in a diabetic person with continuously (at least 3 months) elevated urinary albumin excretion (albumin-to-creatine ratio [ACR] 30 mg/g) and/or low estimated glomerular filtration rate (eGFR 60 mL/min/1.73 m2). With a lower GFR and rising albuminuria, the risk of unfavorable outcomes, including death and ESKD, rises. Individuals with a GFR less than 30 mL/min/1.73 m2 (i.e., CKD stage 4-5) are especially vulnerable to all types of albuminuria (Levin et al. 2013). Diabetic kidney damage occurs in approximately fifty percent of T2DM patients and one-third of T1DM individuals throughout their lifespan. It is one of the most common, expensive, and time-consuming long-term consequences of diabetes (Sun et al. 2022). Approximately 20% of T2DM patients have an eGFR of 60 mL/min/1.73 m2, and 30-50% have increased UACR. After a median follow-up of 15 years, 28% of participants in the UK Prospective Diabetes Study had an eGFR of 60 mL/min/1.73 m2, and 28% had albuminuria (Retnakaran et al. 2006). If T2DM occurs between the ages of 15 and 24 years, the probability of developing moderate albuminuria is about 100% (Zimmet et al. 2014).\n\nClinical guidelines propose treating numerous risk variables at the same time to enhance kidney outcome in T2DM, which is consistent with the multifaceted etiology of DKD. These therapies include lifestyle interventions such as a balanced diet and physical activity to lose weight, smoking cessation, and pharmaceutical glucose, blood pressure, and lipid management (Eckardt et al. 2018).\n\nAngiotensin-converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs) are particularly suggested for blood pressure control, as these RAAS inhibitors have shown reno-protective characteristics and their capacity to lower blood pressure. Few clinical trials have recently reported the new medication classes which may aid in glucose-lowering such as sodium-glucose cotransporter-2 inhibitors (sGLT2i). These new-generation medicines have been found to enhance the renal functions in patients of T2DM (Muskiet, Wheeler, and Heerspink 2019).\n\nFurthermore, since 1980, the advancements in treatment modalities have been beneficial in reducing the average annual drop in renal function of DKD patients by 65% (Barrera-Chimal et al. 2022).\n\nThe possibility of DKD development and cardiac diseases is very relatable and substantial. In the cases of DKD, steroidal mineralocorticoid receptor antagonists (MRAs), which include spironolactone and eplerenone, have been utilized previously. These MRAs possess anti-inflammatory and anti-fibrotic capabilities and aid in reducing albuminuria. The main highlight of using these MRAs is to moderate the decline in kidney function (Agarwal et al. 2021). However, the possible hormonal side effects and the increased risk of hyperkalemia from using these drugs undermine their use. In recent times, the concept of regenerative therapies has provided a shred of more significant evidence in managing CKD induced by diabetes. By inhibiting various pathogenic processes and promoting pro-regenerative mechanisms, stem or progenitor cell therapies provide a substitute treatment modality for controlling complicated disease processes (Xu, Liu, and Li 2022).\n\nMesenchymal stem cells (MSCs) have shown distinctive promise due to their simple accessibility from adult tissues and varied modes of action, including releasing paracrine anti-inflammatory and cytoprotective contents. Numerous experimental studies have used autologous or allogeneic MSC origins (e.g., placenta, amniotic, umbilical cord, bone marrow, adipose, tooth pulp) to treat DKD. Animal model results demonstrate a potential for systemic MSC infusion to regulate DKD development favorably. However, only a few early-phase clinical trials have started, and efficacy in humans has yet to be established (Sávio-Silva et al. 2020). To some extent, we present the first case study in which umbilical cord Wharton’s jelly derived MSCs and exosomes were administered to a patient with CKD stage V caused by T2DM with a follow-up period of 4 months.\n\n\nCase presentation\n\nWe present a case study of a 71-year-old American white male previously diagnosed with stage V CKD. He had type 2 diabetes mellitus, which had been affecting his kidneys for more than three years, with an estimated glomerular filtration rate (eGFR) of ~ 11, blood urea nitrogen (BUN) of 115 mg/dL, and creatinine (Cr) of 5.1 mg/dL. He was treated with allogenic hWJ-MSCs and exosome administration protocol. This protocol involves the implantation of 100 million hWJ-MSCs and 100 billion exosomes intravenously. A premedication regimen consisting of a Myers cocktail (multivitamins, vitamin C, and B complex) was also administered. The Myers cocktail is administered when the patient arrives at the clinic, and about 45 minutes after the MSCs are administered directly, the IV is pushed together with the exosomes.\n\nThe protocol administration product was purchased from the Biogenesis laboratory located in Ensenada, Baja California. This facility is registered with the Federal Committee for Protection from Sanitary Risks (COFEPRIS). The certificate of analysis (COA) was also obtained before purchasing the product. Before the procedure, the patient was guided about the procedure, and a signed informed consent form was also acquired. The patient’s baseline medical history, physical exam, laboratory tests (renal function tests; RFTs), blood pressure, pulse rate, body temperature, oxygen saturation, and chest auscultation were recorded. The parameters mentioned above, excluding RFTs, were continuously monitored during the infusion, every 15 minutes during the first hour, and hourly during the subsequent three hours after the administration. This approach was utilized to observe any possible treatment-related or unrelated side effects.\n\nThe patient was thoroughly attended for after-infusion adverse events to anticipate the overall safety of the treatment. These reactions include self-limiting fever, rash, chest pain, vomiting, allergic reaction, nausea, difficulty breathing, and hives. All occurrences were captured over an 8-hour observation period. Following this observation, he could leave the Case Report Forms (CRFs) if no adverse occurrences (AE) unfolded. The primary objective of this study was to forecast and assess the safety and efficacy of the product infusion on his renal profile. A questionnaire (Kidney Disease and Quality Of Life; KDQOLTM-36) was used to assess his quality of life with renal disease both before and after stem cell therapy.\n\nTo the best of our knowledge, the patient has self-reported a diagnosis of hypertension. In the context of other medical conditions, the patient has disclosed a history of gout and sleep apnea. Regarding surgical history, the patient reports three prior surgical procedures: (1) Nasal surgery in the mid-90s, (2) cyst removal from the wrist in 2002, and (3) Uvulopalatopharyngoplasty (UPPP) in 2007. In terms of social history, the patient is a non-smoker. However, the patient acknowledges consuming alcohol, approximately one drink per week. There is no reported family history of diabetes mellitus or renal dysfunction.\n\nThe patient was assessed for his renal quality by kidney disease quality of life -36 questionnaire (KDQOL-36TM) and his results were compared with reference to before and after stem cell therapy (1st and 4th month follow-up).\n\nIn this case study, laboratory reports and questionnaire data about kidney disease and quality of life (KDQOL-36TM) were recorded before and after 100 × 106 hWJ-MSCs and 100 billion exosome treatments. Both data sets, quantitative (from laboratory reports) and qualitative (from questionnaire), were analyzed using the Statistical Package for Social Sciences (SPSS Inc., Chicago, IL, USA) version 26. The graphical visualization of the means of before and after MSCs was accomplished using the R package ggplot2 because it is declaratively and efficient in creating data visualization based on The Grammar of Graphics. The two-sample paired t-test was applied to test the significant difference between before and after MSC treatment at a 5% significance level. The frequency (n) and percentage (%) were computed from the qualitative data collected through the questionnaire (KDQOL-36TM) filled by the patient before MSCs, after one month of MSC transplantation, and after four months of MSC treatment. Multiple bar charts were also generated to show the consistent improvement in the patient’s quality of life due to the MSC transplantation.\n\n\nResults\n\nThe patient was advised to keep his routine, which included exercise and food, and to report any unexpected reactions he experiences in the next 90 days. The subject underwent the treatment only once, and thankfully, the surgery was safe and did not result in any adverse effects following stem cell transplantation; as we all know, an allergic reaction is one of the most concerning outcomes of MSC intravenous injection. At a 4-month follow-up, hWJ-MSCs implantations improved kidney functioning significantly. The individual was advised to disclose his clinical biochemical analysis whenever he received it during the next 90 days or so. Fortunately, we were able to contact him. Table 1 summarizes his baseline and outcome data at various time intervals. Table 2 provides a comprehensive overview of descriptive statistics, encompassing sample size (n), mean, standard deviation (SD), standard error of mean (SE), 95% confidence interval for mean, minimum, and maximum observations for essential biomarkers such as eGFR, Calcium, Glucose, BUN, Creatinine, BUN/Creatinine Ratio, Sodium, Potassium, Chloride, CO2, AGap, Phosphorus, and Albumin. The means, accompanied by error bars for all parameters, are graphically depicted in Figure 14 to illustrate the efficacy of hWJ-MSC treatment. Meanwhile, Table 3 outlines the results of paired t-tests, evaluating the significance of differences before and after MSCs treatment at a 5% level of significance.\n\n* CKD Stage 1= (GFR > 90 mL/min), Stage 2 Mild CKD (GFR = 60-89 mL/min), Stage 3A Moderate CKD (GFR = 45-59 mL/min), Stage 3B Moderate CKD (GFR = 30-44 mL/min), Stage 4 Severe CKD (GFR = 15-29 mL/min), Stage 5 End Stage CKD (GFR <15 mL/min).\n\nThe reference ranges displayed may vary due to potential changes in laboratory testing methods.\n\nAnalyzing the results from Tables 2 and 3 reveals the following insights: eGFR, a key indicator of kidney function, exhibited a mean increase from 12.50 mL/min before MSC treatment (Stage V) to 16.4 mL/min after MSCs treatment (p-value = 0.054 > 0.05). This places the mean eGFR within the range for Stage IV (GFR = 15-29 mL/min), transitioning from Stage V (GFR < 15 mL/min), as depicted in Figure 1. Calcium levels, both before (9.4 ± 1.7) and after treatment (8.4 ± 0.2), remained within the normal range, showcased in Figure 2. However, glucose levels experienced a non-significant increase from 121.38 mg/dL to 163.8 mg/dL post-treatment (p-value=0.146 > 0.05), surpassing the normal range of glucose levels (<117 mg/dL), as illustrated in Figure 3.\n\nWhile BUN exhibited a non-significant decrease from 76.40 mg/dL to 57.5 mg/dL post-MSC treatment (p-value=0.141 < 0.05), approaching the normal range of 6-24 mg/dL over the short follow-up period, Figure 4 portrays this trend. Creatinine, demonstrating a significant decrease (p-value=0.080 < 0.05) from 4.7 mg/dL to 3.9 mg/dL post-MSC treatment, remained above the normal range (0.66-1.25 mg/dL for men), depicted in Figure 5. BUN/Creatinine ratios stayed within the normal range of 10:1 to 20:1 for both time points, illustrated in Figure 6.\n\nSodium levels increased significantly post-MSC transplantation (p-value=0.032 < 0.05), maintaining a range within normal levels (136-144 mmol/L), as shown in Figure 7. Potassium levels, while decreasing post-MSC treatment, remained within the normal range of 3.7-5.1 mmol/L, as illustrated in Figure 8. Chloride levels were abnormal both before (109.4 ± 8.3) and after treatment (110 ± 2.9), given the normal range of 97-105 mmol/L, illustrated in Figure 9. CO2 levels, although increasing post-MSC treatment, remained below the normal range of 23-29 mmol/L, as shown in Figure 10. Anion Gap (AGap) levels did not exhibit a significant difference between the two time points, illustrated in Figure 11. Phosphorus levels remained within the normal range (3.0-4.5 mg/dL) for both time points, portrayed in Figure 12. Albumin levels, with a reference range for men (3.5-5.3 mg/dL) and women (3.8-5.2 mg/dL), were (4.2 ± 0.4) before SCT and (4.3 ± 0.1) after MSC treatment, shown in Figure 13.\n\nNo statistics were computed for Osmolality, Hemoglobin A1C%, Iron total, and Saturation due to limited data availability. The statistical results offer crucial insights into the impact of MSC treatment on various biomarkers in CKD patients, revealing significant improvements in eGFR, BUN, and Creatinine levels. However, normalization was constrained by the very short follow-up period. Furthermore, certain parameters, including glucose and CO2, exhibited significant changes post-treatment but remained outside the normal range. Three questionnaires collected at different time points aimed to assess the patient’s kidney disease condition and quality of life after MSC transplantation. Limited data collected using KDQOL-36TM and the statistical analysis results presented in Table 4, along with their graphical representation in Table 5 (Exteded data), provide valuable insights into the impact of MSC transplantation on the quality of life of a patient with CKD at different time points.\n\nBefore MSC treatment, the patient reported poor general health, significant limitations in moderate activities, climbing stairs, and accomplishment of work or other activities, both physically and emotionally. After one month of MSC treatment, a remarkable improvement is observed, with the patient reporting excellent health, no limitations in activities, and a reduction in pain interference with normal work. The positive trend continues after four months, with the patient maintaining improved health perceptions and minimal interference with social activities. Additionally, emotional well-being shows positive changes, including reduced feelings of frustration and burden, and improved energy levels. The patient also reports less interference with various aspects of life, such as work, travel, and personal appearance. These findings collectively suggest that MSC transplantation contributes positively to the patient’s quality of life, addressing both physical and emotional aspects of CKD. The outcomes underscore the potential efficacy of MSCs in improving health-related aspects and enhancing overall well-being in CKD patients.\n\n\nDiscussion\n\nMSCs have a unique ability to self-renew and differentiate. These cells can differentiate into osteoblasts, chondrocytes, adipocytes, myoblasts, and neuronal cells (both in vitro or in vivo), which highlights their broader therapeutic potential and applications. They can be obtained from the origins like bone marrow, umbilical cord, umbilical cord blood, periosteum, muscle, thymus, skin, and adipose. The umbilical cord comprises the development of stem cells, which then migrate during embryo development. Umbilical cord-derived stem cells have been recognized as the most convenient origin due to less-ethical concerns. Wharton’s jelly is a continuous skeleton made up of interwoven collagen and tiny fibers that wrap the umbilical cord and contain many myofibroblast-like mesenchymal cells (Han et al. 2013). Umbilical cord MSCs offer multiple benefits, suggesting they could be a valuable source of allogeneic MSCs for cellular treatment, as evidenced by worldwide trends in MSC clinical studies. hUC-MSCs have numerous advantages over bone marrow MSCs, including a wide diversity of sources, ease of procurement, strong proliferation ability, low immunogenicity, and fewer bioethical problems. As a result, hUC-WJ-MSCs are a suitable alternative for bone marrow MSCs. The optimization of hUC-MSC in vitro isolation and growth and the investigation of their biological features pose essential conditions for their application (Figure 16). Umbilical cords come off after birth, enabling easy access to cells, lowering the possibility of contamination, offering no ethical concerns, and being high in MSCs. Additionally, unlike bone marrow MSCs, hUC-MSCs lack fibroblast characteristics and have zero likelihood of growing solid tumors (Peired, Sisti, and Romagnani 2016).\n\nWe found 473 preclinical research focusing on the therapeutic effects of MSCs in renal disease published between 2004 and 2023. In these investigations, MSC injection can be classified as systemic or local to the kidney (Figure 15). The intravenous approach is the most accessible method of MSC transplantation. This approach resulted in MSC distribution, predominantly in the lungs, spleen, liver, bone marrow, thymus, kidney, skin, and malignancies (Nakamizo et al. 2005).\n\nRecently, MSCs have been investigated in two clinical trials for DKD. The first human clinical study (NCT01843378) was launched in 2016. This prospective, randomized control clinical trial adopted double blinding, dose escalation, and a sequential method to evaluate the safety and efficacy of the administered product, mesenchymal precursor cells (MPCs), in 30 DKD patients. The patients were given their allotted dose of either MPCs or a placebo (Packham et al. 2016).\n\nLikewise, a second clinical trial, The Novel Stromal Cell Therapy for Diabetic Kidney Disease (NEPHSTROM), was completed in 2023. This phase 1b/2a clinical investigation was conducted across three European sites. Details on this trial can be found at (NCT02585622). Table 6 outlines the basic information of these two trials, including the administration product, route of injection, sample size, potential outcomes, etc. (Perico et al. 2023).\n\nAnother clinical trial enrolled seven patients with CKD stage IV and administered autologous MSCs at a dose of 2 × 106 cells/kg. These stem cells were obtained through their bone marrow biopsies. The participants underwent follow-ups for one, three, six, twelve, and eighteen months, adhering to stem cell therapy. The radioactive isotope (a scanning technique) was utilized to measure changes or fluctuations in the glomerular filtration rate (GFR). However, no publications are present till the date (NCT0219532). The brief data is reported in the Table 6. The global prevalence of CKD is increasing, owing primarily to an increase in atherosclerosis and type 2 diabetes. A decrease in kidney regeneration capacity defines CKD. Numerous in vivo investigations in CKD animal models show that cell-based therapies have beneficial therapeutic effects. Notably, MSCs produce a variety of growth factors and cytokines that influence encircling parenchymal cells, resulting in tissue regeneration (Figure 16). MSCs have been shown in preclinical models of CKD to preserve renal structure and function since their administration preserved renal function and decreased renal injury in numerous mouse models of diabetic kidney disease, unilateral nephrectomy, and chronic allograft nephropathy. The ability of MSCs to modulate immune cells via paracrine interactions now explains their therapeutic promise. MSCs have been administered successfully in CKD experimental models, including diabetes, hypertension, and chronic allograft nephropathy in recent years (Sávio-Silva et al. 2020). Similarly, Exosomes are rich in microRNAs (miRNAs), which play critical roles in immunoregulation, cell function regulation, and homing pathways.\n\nA previously conducted study looked into the methods by which hUC-MSC-derived exosomes reduce inflammation and improve damage repair in diabetes-induced CKD development. HUC-MSC-derived exosomes reduce inflammation, decrease the NLRP3 signaling pathway, and improve kidney injury in both in vitro podocyte cells and diabetic rats. Exosomes may offer a promising cell-free therapy method for DKD, according to the study, which identifies miR-22-3p as a critical role in this process (Wang et al. 2023). Therapies or treatments that would help to prevent the progression of diabetic kidney failure to End Stage Renal Failure (ESRF) would be extremely beneficial in both clinical and economic terms. Allogenic MSCs have anti-inflammatory, immunomodulatory, and paracrine attributes, making them a potential candidate therapy for chronic medical conditions (Figure 16).\n\nThis is the first human case study that utilized allogeneic human umbilical cord Wharton’s jelly-derived mesenchymal stem cells and exosomes to treat chronic kidney disease stage V caused by type 2 diabetes with a short follow-up period of 4-months. The case was explored to assess the safety and efficacy of a single infusion of hWJ-MSCs and Exosomes intravenously. The infusion was well tolerated, and the patient reported no adverse events. The theoretical concerns of allogeneic cell therapy include allergy risks from excipients such as fetal calf serum and immunogenic responses to human antigens (donor HLA) were not observed. The absence of acute immunological responses to unmatched allogeneic hWJ -MSCs and exosomes is of particular significance, especially for patients who might consider kidney transplantation in the future. Repeated administration of this protocol may improve eGFR or other renal functionalities. Future studies may evaluate the safety, tolerability, and efficacy of single and repeat dosages of MSCs.\n\nThe patient’s renal health witnessed a remarkable turnaround following stem cell therapy. Despite initial challenges, such as a decline in eGFR, elevated BUN, Creatinine levels, and an unfavorable BUN/Cr ratio, the subsequent improvement highlighted the potential effectiveness of stem cell treatment in addressing and reversing kidney-related issues. This positive response suggests the promising impact of stem cell therapy on renal function, emphasizing its potential as a valuable intervention for individuals facing similar complications. Initial symptoms, such as impaired typing speed and speech difficulties, vanished, indicating a positive response to the stem cell intervention. The overall well-being of the patient seemed promising. Throughout the patient’s health journey, a decline in eGFR prompted the individual to engage in self-medication with torsemide, resulting in dehydration and kidney stress. Subsequent medical advice led to using Lokelma, which positively impacted potassium levels. This incident highlights the risks associated with unsupervised health management, stressing the importance of avoiding self-medication in conventional and regenerative medicine. Despite facing challenges, the patient’s overall quality of life has improved, with a renewed focus on diabetes management and renal health. The adoption of insulin and additional measures helping him in regaining control over blood glucose levels. Thus, we concluded that the potential of allogenic hWJ-MSCs and exosomes could be a possible treatment option for such kind of diseases. Future research should delve into the mechanisms of MSCs in CKD, exploring factors like disease stage, repeat dosages, injection methods, and other variables.\n\nThere are a few limitations to our case study. First, we studied only one patient, and it is a small sample size to predict the statistically significant effects on renal function. Second, the 16-week follow-up period used to analyze the long-term effects of a single infusion is insufficient for evaluating a chronic condition with complicated variability and progression. Lastly, more lab profiles are needed to make a full assessment of the patient’s health status easier. The study also recognizes the patient’s participation in self-medication practices, introducing potential confounding factors that could influence the observed outcomes. Recognizing and overcoming these limitations is critical for a nuanced interpretation of the study’s findings, and it highlights the need for additional research with more extended follow-up periods and a larger dataset.\n\n\nConclusion\n\nThe study evaluated the safety and possible efficacy of a single intravenous dosage of hWJ-derived MSCs and exosomes in a person with Type-2 diabetes-induced chronic kidney disease (CKD), a major global health concern. In the renal profile, the operation was well tolerated and proved to be beneficial. However, the study has a few flaws, the most notable of which is the very short follow-up period. This limitation makes it difficult to thoroughly understand the long-term impact and sustainability of the reported effects.\n\n\nDeclarations\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patient.\n\nUEH wrote the original draft and prepared the tables and figures, DLG conceptualized the study, KA conducted the statistical analysis. SS wrote the references and assisted in proofreading. NK supervised the team and revised the manuscript, and AU proofread the manuscript.", "appendix": "Data availability statement\n\nNo data associated with this article.\n\nFigshare: Case report- Allogenic Wharton’s jelly mesenchymal stem cell and exosome therapy are safe and effective for diabetic kidney failure. https://doi.org/10.6084/m9.figshare.25532989.v1\n\nThe project contains the following underlying data:\n\nTable 5: Graphical Representation of the KDQOL-36 TM questionnaire after MSCs Transplantation. This table presents the statistical analysis of the questionnaire that is commonly used to assess the overall quality of life of renal disease patients. The bar chart depicts the outcome of mesenchymal stem cell transplantation with before, 1st month and at 4th month follow-up.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe authors appreciated Mr. Munim Qazi for providing great help with the figures in this manuscript.\n\n\nReferences\n\nAgarwal R, Kolkhof P, Bakris G, et al.: Steroidal and Non-Steroidal Mineralocorticoid Receptor Antagonists in Cardiorenal Medicine. Eur. Heart J. 2021; 42(2): 152–161. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarrera-Chimal J, Lima-Posada I, Bakris GL, et al.: Mineralocorticoid Receptor Antagonists in Diabetic Kidney Disease - Mechanistic and Therapeutic Effects. Nat. Rev. Nephrol. 2022; 18(1): 56–70. PubMed Abstract \| Publisher Full Text\n\nBentham J, Di Cesare M, Ver Bilano HB, et al.: Worldwide Trends in Body-Mass Index, Underweight, Overweight, and Obesity from 1975 to 2016: A Pooled Analysis of 2416 Population-Based Measurement Studies in 128·9 Million Children, Adolescents, and Adults. Lancet (London, England). 2017; 390(10113): 2627–2642. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nde Boer IH , Caramori ML, Chan JCN, et al.: Executive Summary of the 2020 KDIGO Diabetes Management in CKD Guideline: Evidence-Based Advances in Monitoring and Treatment. Kidney Int. 2020; 98(4): 839–848. PubMed Abstract \| Publisher Full Text\n\nChen L, Magliano DJ, Zimmet PZ: The Worldwide Epidemiology of Type 2 Diabetes Mellitus--Present and Future Perspectives. Nat. Rev. Endocrinol. 2011; 8(4): 228–236. PubMed Abstract \| Publisher Full Text\n\nEckardt KU, Bansal N, Coresh J, et al.: Improving the Prognosis of Patients with Severely Decreased Glomerular Filtration Rate (CKD G4+): Conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference. Kidney Int. 2018; 93(6): 1281–1292. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHan YF, Tao R, Sun TJ, et al.: Optimization of Human Umbilical Cord Mesenchymal Stem Cell Isolation and Culture Methods. Cytotechnology. 2013; 65(5): 819–827. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHill NR, Fatoba ST, Oke JL, et al.: Global Prevalence of Chronic Kidney Disease - A Systematic Review and Meta-Analysis. PloS One. 2016; 11(7): e0158765. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nInternational Diabetes Federation: IDF Diabetes Atlas 2021\|IDF Diabetes Atlas.2021. Reference Source\n\nKoye DN, Magliano DJ, Nelson RG, et al.: The Global Epidemiology of Diabetes and Kidney Disease. Adv. Chronic Kidney Dis. 2018; 25(2): 121–132. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLevin A, Stevens PE, Bilous RW, et al.: Kidney Disease: Improving Global Outcomes (KDIGO) CKD Work Group. KDIGO 2012 Clinical Practice Guideline for the Evaluation and Management of Chronic Kidney Disease. Kidney Int. Suppl. 2013; 3 (1): 1–150. Nature Publishing Group. Publisher Full Text\n\nManne-Goehler J, Atun R, Stokes A, et al.: Diabetes Diagnosis and Care in Sub-Saharan Africa: Pooled Analysis of Individual Data from 12 Countries. Lancet Diabetes Endocrinol. 2016; 4(11): 903–912. PubMed Abstract \| Publisher Full Text\n\nMuskiet MHA, Wheeler DC, Heerspink HJL: New Pharmacological Strategies for Protecting Kidney Function in Type 2 Diabetes. Lancet Diabetes Endocrinol. 2019; 7(5): 397–412. PubMed Abstract \| Publisher Full Text\n\nNakamizo A, Marini F, Amano T, et al.: Human Bone Marrow-Derived Mesenchymal Stem Cells in the Treatment of Gliomas. Cancer Res. 2005; 65(8): 3307–3318. Publisher Full Text\n\nPackham DK, Fraser IR, Kerr PG, et al.: Allogeneic Mesenchymal Precursor Cells (MPC) in Diabetic Nephropathy: A Randomized, Placebo-Controlled, Dose Escalation Study. EBioMedicine. 2016; 12(October): 263–269. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeired AJ, Sisti A, Romagnani P: Mesenchymal Stem Cell-Based Therapy for Kidney Disease: A Review of Clinical Evidence. Stem Cells Int. 2016; 2016: 1–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPerico N, Remuzzi G, Griffin MD, et al.: Safety and Preliminary Efficacy of Mesenchymal Stromal Cell (ORBCEL-M) Therapy in Diabetic Kidney Disease: A Randomized Clinical Trial (NEPHSTROM). J. Am. Soc. Nephrol. 2023; 34 (10): 1733–51. Wolters Kluwer Health. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRetnakaran R, Cull CA, Thorne KI, et al.: Risk Factors for Renal Dysfunction in Type 2 Diabetes: U.K. Prospective Diabetes Study 74. Diabetes. 2006; 55(6): 1832–1839. Publisher Full Text\n\nSávio-Silva C, Beyerstedt S, Soinski-Sousa PE, et al.: Mesenchymal Stem Cell Therapy for Diabetic Kidney Disease: A Review of the Studies Using Syngeneic, Autologous, Allogeneic, and Xenogeneic Cells. Stem Cells Int. 2020; 2020: 1–28. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShaw JE, Sicree RA, Zimmet PZ: Global Estimates of the Prevalence of Diabetes for 2010 and 2030. Diabetes Res. Clin. Pract. 2010; 87(1): 4–14. PubMed Abstract \| Publisher Full Text\n\nStempniewicz N, Vassalotti JA, Cuddeback JK, et al.: Chronic Kidney Disease Testing Among Primary Care Patients With Type 2 Diabetes Across 24 U.S. Health Care Organizations. Diabetes Care. 2021; 44(9): 2000–2009. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSun H, Saeedi P, Karuranga S, et al.: IDF Diabetes Atlas: Global, Regional and Country-Level Diabetes Prevalence Estimates for 2021 and Projections for 2045. Diabetes Res. Clin. Pract. 2022; 183(January): 109119. PubMed Abstract \| Publisher Full Text\n\nWang Y, Liu J, Wang H, et al.: Mesenchymal Stem Cell-Derived Exosomes Ameliorate Diabetic Kidney Disease Through the NLRP3 Signaling Pathway. Stem Cells (Dayton, Ohio). 2023; 41(4): 368–383. PubMed Abstract \| Publisher Full Text\n\nXu N, Liu J, Li X: Therapeutic Role of Mesenchymal Stem Cells (MSCs) in Diabetic Kidney Disease (DKD). Endocr. J. 2022; 69(10): 1159–1172. PubMed Abstract \| Publisher Full Text\n\nZimmet PZ, Magliano DJ, Herman WH, et al.: Diabetes: A 21st Century Challenge. Lancet Diabetes Endocrinol. 2014; 2(1): 56–64. Publisher Full Text" }	[ { "id": "324719", "date": "15 Oct 2024", "name": "Giuseppe Remuzzi", "expertise": [ "Reviewer Expertise Nephrology", "CKD", "AKI", "Diabetes", "Stem cells" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Authors presented the case of a 70-year-old patient with stage 5 chronic kidney disease (CKD) caused by type 2 diabetes mellitus who received a single intravenous infusion of 100 million Wharton’s jelly-derived mesenchymal stromal cells (MSCs) and 100 billion exosomes. They reported that the procedure was safe, with no adverse events being recorded. According to the Authors, kidney function parameters significantly improved over the four month follow-up. The following points are for the Author’s consideration:\nIn the Introduction, rather than drawing a picture of the epidemiology of diabetes mellitus and CKD, the rationale underpinning the decision to simultaneous administer MSCs and exosomes to a patient with stage 5 CKD should be provided. In fact, the combined infusion of the two biological products did not enable to disentangle the specific effects – in terms of safety and efficacy – of either intervention. This issue is of particular relevance for exosomes, for which scarce clinical data are available. The rationale behind the selected doses of MSCs (100 millions) and exosomes (100 billions) should also be outlined. As for the procedures of preparation and administration of MSCs and exosomes, I have the following concerns: i) Information regarding isolation and characterization of Wharton’s jelly-derived MSCs and exosomes should be provided; ii) it should be clarified whether exosomes derived from Wharton’s jelly-derived MSCs or from another source; iii) the clinical center where the patient received MSC and exosome infusion has not been indicated. This is an important issue since the biological products were provided by a Mexican company (Biogenesis laboratory, Baja California, Mexico), whereas the Authors’ affiliations are from the United States and Pakistan. Evidence should be provided that storage and shipment of MSCs and exosomes from the production facility to the clinical site for thaw and administration followed validated procedures, in order to ensure the stability, integrity and overall quality of the biological products. Throughout the manuscript it was argued that four months after MSC and exosome infusion kidney function improved significantly. I have the following concerns regarding the reliability of this conclusion: i) none of the kidney function parameter under investigation (i.e., estimated GFR, serum creatinine, blood urea nitrogen) significantly improved after MSC and exosome infusion, with all P values exceeding the threshold of 0.05. Noteworthy is also that for these parameters, eight measurements before and after treatment with MSCs and exosomes were claimed to be available (Table 2), but it is unclear over which time period prior to administration of the biological products the parameters were collected; ii) GFR was not measured with a gold-standard technique (e.g., clearance of iohexol or iothalamate), but estimated with a formula, which could at least partially account for the variability in GFR values among visits; iii) the fact that following administration of MSCs and exosomes the patient needed treatment with torasemide and sodium zirconium cyclosilicate for the management of edema and hyperkalemia, respectively, argues against the highlighted significant improvement of kidney function; iv) information regarding urinary protein excretion prior to MSC and exosome infusion was not available, an issue that should be acknowledged as a study limitation. Regarding the Case Report Form, the sentence in the Results section whereby the patient “could leave the case report forms if no adverse occurrences unfolded” (Page 4, lines 54-55) is unclear and deserves elucidation. Some information regarding the medications used by the patient was mentioned in passing in the Discussion. A comprehensive presentation patient therapy before and after MSC and exosome infusion should be provided in the Results section. As for the results of the Kidney Disease and Quality of Life™ (KDQOL™-36) questionnaire, a remarkable improvement in quality of life was claimed to have been reported one month after MSC and exosome treatment, with the positive trends having continued after four months (Page 13, lines 9-12). This information appears to be misleading since, according to the results of the actual questionnaire reported in Table 4, most of the quality of life indicators improved one month after MSC treatment, but the same degree of satisfaction was not maintained at four month follow-up. A more balanced presentation of these study findings is warranted. Rather than providing the rationale underlying MSC- and exosome-based therapies in diabetic kidney disease, in the Discussion section the findings of this Case Report should be commented in the context of the available literature on this topic. In the Discussion, it was argued that immunogenic responses to human antigens (donor HLA) were not observed (Page 18, lines 40-41). Nevertheless, based on the information reported throughout the manuscript, it can be inferred that screening for donor-specific anti-HLA antibodies in serum samples of the patient was not performed (neither before nor after MSC and exosome infusion). This issue deserves clarification.\n\nMinor\nThroughout the manuscript, estimated GFR values should be accompanied by the unit of measure. The equation used to estimate GFR should also be outlined. Based on the information reported throughout the manuscript, it can be inferred that the patient was not as yet in chronic dialysis. This issue deserves clarification. The patient received a single intravenous infusion of 100 million Wharton’s jelly-derived MSCs and 100 billion exosomes. Since in the majority of clinical trials MSC doses have been reported as cells per kilogram of recipient weight, to put the results of the present Case Report in the context of the available literature, the patient body weight is worth providing. The patient was 70-year-old based on the information in the Abstract, but 71-year-old according to data in the Results section. Moreover, the follow-up after MSC and exosome treatment was reported to be of 90 days at the beginning of the Results section, but of 4 months throughout the remaining manuscript. These inconsistencies should be explained or corrected. More recent studies on the epidemiology of diabetes mellitus have been published (Lancet 2023; 402:203-234) compared to those cited in the Introduction. Similarly, the 2012 KDIGO Clinical Practice Guidelines for the Evaluation and Management of Chronic Kidney Disease were quoted (Kidney Int Suppl 2013; 3:1-150), but these were updated in 2024 (Kidney Int 2024; 105:S117-S314). Figures from 1 to 13 appear to be redundant, since they provide data that have already been reported in the Tables. Moreover, Figure 7 presents serum sodium, and not serum calcium levels. Please correct. P value of 0.146 referred to the changes in glucose levels after MSC and exosome infusion according to the information provided in the manuscript (Page 8, line 6), but it referred to changes in calcium levels based on data in Table 3. The reliability of the sentence in the Results section whereby blood urea nitrogen decreased from 76.40 mg/dL to 57.7 mg/dL post-MSC treatment, approaching the normal range of 6-24 mg/dL over the short follow-up period (Page 9, lines 1-2), appears questionable, since blood urea nitrogen levels were still far from the normal range after MSC and exosome treatment. The sentence should be revised accordingly. Although accumulating evidence from randomized controlled trials points to the safety of MSC administration (Thompson M, et al., 2020 [Ref 1]), the sentence in the Discussion whereby umbilical cord-derived MSCs “have zero likelihood of growing solid tumors” should be tempered. When describing a clinical study that tested autologous bone marrow-derived MSCs in seven patients with CKD, the authors argued that the results are not as yet published (Page 18, lines 11-15). Instead, the results of this study have been published (Makhlough A, et al., 2018 [Ref 2]); 20:660-669), and the corresponding ClinicalTrials.gov identifier is NCT02195323, rather than NCT0219532 (Page 18, line 15). Similarly, the ClinicalTrials.gov identifier of the study carried out by Packham et al. (EBioMedicine 2016: 12:263-269) is NCT01843387, and not NCT01843378 (Page 18, line 1).\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] }, { "id": "341952", "date": "12 Dec 2024", "name": "Sinan Kandır", "expertise": [ "Reviewer Expertise Veterinary Medicine", "Physiology", "Hematology", "Neuroscience", "Mesenchymal Stem Cells", "Chronic Kidney Disease", "Endoplasmic Reticulum Stress" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWe would like to acknowledge the authors for their efforts in presenting a case report on an innovative therapeutic approach using allogeneic Wharton’s jelly mesenchymal stem cells (hWJ-MSCs) and exosomes to treat diabetic kidney failure. The study addresses a critical clinical challenge and explores a novel regenerative medicine technique, providing preliminary data on its safety and potential efficacy. The detailed description of the patient’s clinical profile and the utilization of diverse assessment tools, including laboratory parameters and quality-of-life questionnaires, are commendable. Despite the study's potential contribution to the field, a detailed review has identified significant methodological, ethical, and transparency-related concerns that require further scrutiny. These concerns collectively highlight potential conflicts with F1000 Research’s ethical principles, which emphasize rigorous methodology, transparency, and the independence of scientific inquiry. 1- Although the manuscript claims no funder involvement in study design, data collection, or publication decisions, the authors’ direct and/or indirect contacts with R3 Medical Research LLC, the funding body, raises significant conflict-of-interest concerns, potentially compromising objectivity and posing a threat to F1000 Research’s ethical standards. 2- The treatment protocol details are not clear sufficiently. 3- The therapy protocol involved intravenous administration of 100 million hWJ-MSCs and 100 billion exosomes. While this approach is innovative, there is limited evidence supporting its standardization and reproducibility. 4- Potential risks, such as immunogenic responses or complications arising from the use of allogenic cells, are not sufficiently addressed, even though no adverse effects were reported in this single case.\nThe manuscript should be rejected due to significant conflict-of-interest concerns and insufficient ethical transparency.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] } ]	1	https://f1000research.com/articles/13-379
https://f1000research.com/articles/13-378/v1	24 Apr 24	{ "type": "Research Article", "title": "Information and Communication Technologies (ICT) and Economic Growth in Latin America: An Empirical Analysis for the 2000-2020 Period", "authors": [ "María Gabriela González Bautista", "Edwin Joel Velasco Pucha", "Eduardo Ramiro Dávalos Mayorga", "Mariana Isabel Puente Riofrío", "María Gabriela González Bautista", "Edwin Joel Velasco Pucha", "Mariana Isabel Puente Riofrío" ], "abstract": "Introduction ICTs (Information and Communication Technologies) play a crucial role in improving efficiency and productivity in various economic sectors. The research focuses on measuring the impact of ICTs on the economic growth of Latin American nations during the period 2000-2020.\n\nMethods A fixed effects, panel data model covering 17 countries in the region has been applied using ordinary least squares methodology. The variables selected for the empirical exercise are: the number of individuals using the Internet, fixed and mobile telephone subscriptions, trade balance, domestic credit, foreign direct investment and gross domestic product per capita.\n\nResults The study’s findings show that ICTs have a positive impact on economic growth. That is, for every percentage point increase in the percentage of the population using the Internet, GDP per capita increases by US$16.82.\n\nConclusion This highlights the unique influence exerted by digital connectivity in shaping the regional economic landscape. At the same time, mobile and fixed telephone subscriptions are not significant variables in the model.", "keywords": [ "Panel data", "fixed effects", "technological infrastructure", "GDP per capita" ], "content": "Introduction\n\nSince the early 1990s, Information and Communication Technologies (ICT) have gradually transformed all aspects of human life, eliminating geographical boundaries, bringing societies and cultures closer together, and influencing economic activities such as Foreign Direct Investment (FDI) and trade (Ahmed & Le, 2021). The importance of ICT infrastructure for the development of emerging economies has been highlighted by several researchers (Niebel, 2018; Bahrini & Qaffas, 2019; Myovella, Karacuka, & Haucap, 2020; Röller & Waverman, 2001). However, it has been argued that the focus on ICT expansion as an engine of growth has overshadowed critical aspects such as human capital, health and civil infrastructure (roads, drinking water, electricity, etc.) (Bollou, 2006; Komninos, 2019).\n\nDespite the debates, advocates of ICT infrastructure expansion argue that it facilitates the movement of capital, coordination of production and transportation, as well as new forms of cross-border investments and expansion of services (Antonelli, 2003). Various scholars have strongly endorsed the necessity and effectiveness of the development and application of technological infrastructures to drive economic and social advancement (Jordá-Borrell, & López-Otero, 2020; German-Soto et al., 2021; Yu, H. 2021; Appiah-Otoo & Song, 2021). In the words of Brynjolfsson & McAfee (2014) and Singh, Luthra, Mangla & Uniyal (2019) explain that investment in technology is essential to improve productivity and economic efficiency. In line, Nicholas Carr (2008) posits that IT adoption is not only an economic necessity, but also a catalyst for collective intelligence enhancement.\n\nFurthermore, it has been argued that the impact of ICT extends beyond the economic realm, with positive effects on social dimensions such as learning (Abdullayev, 2020; Roztocki, Soja, & Weistroffer, 2019; Ahmed, Nathaniel, & Shahbaz, 2021), healthcare (Roztocki, Soja, & Weistroffer, 2019), women’s empowerment, promotion of indigenous knowledge, and good governance (Aduwa-Ogiegbaen & Iyamu, 2005; Von Lubitz & Wickramasinghe, 2006; Gurumurthi et al., 2003; Jain, 2006; Meso et al., 2005).\n\nInstitutions such as the World Bank, the International Telecommunication Union (ITU) and the International Monetary Fund (IMF) put pressure on Latin American economies to invest in the expansion of ICT infrastructure (Jain, 2006). However, the idea that ICT expansion guarantees high rates of economic growth has come under scrutiny (Gutiérrez & Berg, 2000). In that sense, the effectiveness of ICTs in driving economic development may be conditioned by various factors, such as the lack of adequate infrastructure, the digital divide, or inadequate technological implementation policies (Fraga, 2017). Also, resistance to the adoption of new technologies by some economic sectors (Rodrik, 2018).\n\nDeveloping countries may not obtain the same returns on ICT investment as developed countries as they lack the absorptive capacity to implement and take advantage of ICTs, in addition to inadequate technological infrastructure and digital divides that limit equitable access and promote disparity (Mwakaje, 2010). In Latin America, ICT penetration is below developed world figures, and its impact on economic growth depends on crucial elements such as adequate access, diffusion of digital technologies, healthy business dynamism and adequate competition in the digital sector of the economy (Zapata et al., 2020). Although there has been a significant expansion of the Internet in the region, connection speeds remain low compared to the world average, limiting the digital services available (CEPAL, 2020).\n\nIn countries such as Brazil, Mexico, Chile and Argentina, the Internet infrastructure-based economy contributes significantly to GDP, according to Boston Consulting Group [BCG], (2021) and McKinsey (2022). However, the figures vary, and despite the improvement in connection speeds, the region remains below the world average. In this regard, the average investment of Latin American countries is projected to reach 3.3% in 2016 (CEPAL, 2013). Most research has focused on the impact of privatization on network expansion and efficiency (Birdsall & Nellis, 2003) or on institutional problems and socioeconomic barriers to technological adoption and development (García Martínez & Payró, 2022; Parente & Prescott, 1994). It is suggested that factors such as GDP per capita may affect ICT expansion rates (Bollou, 2006), but more research is needed to identify these factors and measure their effect.\n\nProductivity growth, driven by investments in Information and Communication Technologies (ICT), has been recognized as essential for improving living standards, especially in developed countries, where most studies support the positive and economically significant relationship between ICT and productivity (Kretschmer, 2012). However, in Latin America, economic growth has experienced notable limitations, especially during the Covid-19 pandemic, with a stagnant trajectory and low average growth rates (CEPAL, 2021).\n\nIn the contemporary era, the role of Information and Communication Technologies (ICTs) has been the subject of extensive economic scrutiny. Several research studies have explored the relationship between ICT penetration and economic growth in different regions of the world. In this regard, Vu (2011), in his analysis focusing on 102 European countries, highlights how the penetration of Internet, cell phone and personal computer users impacts economic growth. The author reveals that the marginal effect of Internet penetration exceeds that of other devices, although this impact decreases as penetration increases. Using the Generalized Method of Momentum (GMM), Vu highlights that ICT positively influences growth by facilitating knowledge diffusion, improving decision making and reducing production costs.\n\nFor their part, Siddiqui and Singh (2019) delved into the relationship between ICT penetration, trade openness and economic growth in selected countries. They highlighted the significant connection between ICT penetration and growth, especially in emerging and high-income countries. These findings are in agreement with (Majeed and Ayub, 2018; Sinha and Sengupta, 2022) who highlighted positive and significant effects of ICT on economic growth. Likewise, Toader et al. (2018) evidence a positive effect of ICT infrastructure on growth in the European Union, but with varying magnitudes depending on the technology analyzed. In addition, macroeconomic factors such as inflation, unemployment and foreign direct investment also play a crucial role in GDP per capita.\n\nFor their part, Neffati and Besbes (2013), focusing on Arab countries, supported the endogenous growth theory by suggesting that ICT and labor skills are key factors for economic growth. Taken together, these studies reveal the complexity of the interactions between ICT, trade openness, foreign investment and financial development, highlighting their role in the global economic landscape.\n\nIn contrast, Nabi et al. (2022) explored ICT expansion in N11 countries, revealing a long-term negative impact on economic growth. Furthermore, they emphasized that financial development has both short- and long-term adverse effects. These findings are consistent with (Cardona, 2013; Van Reenen et al., 2010; Banco Mundial, 2022) who point out that despite the recognition of the potential of ICTs to reduce poverty, increase productivity and foster economic growth, the empirical evidence in developing countries, such as those in Latin America, has been weak and ambiguous. The differential impact of ICTs in developing countries is articulated with possible limitations in absorptive capacities, such as the lack of human capital and other complementary factors, has been pointed out as a relevant variable (Steinmueller, 2001).\n\nBased on the above, the presence of digital divides associated with unequal access to ICTs according to income, age and geographic location is highlighted, which impacts Internet use and, therefore, the contribution of ICTs to economic growth in the region (CEPAL, 2013). Therefore, this research highlights the complexities and challenges faced by Latin America in the effective adoption of ICTs to boost its economic development.\n\n\nMethods\n\nThis research adopts the hypothetico-deductive method, starting from a problem related to Information and Communication Technologies (ICT) and economic growth in Latin America. It is classified as an explanatory research, since it examines the key events and trends related to ICTs and economic growth in the region during the study period. In addition, it is considered correlational, since it uses an econometric model to explain the relationship between the variables of interest in a specific period.\n\nTo carry out the research, a fixed effects econometric model is implemented using panel data. Among the nested data regression models, the fixed effects approach stands out for making various assumptions about the behavior of the residuals, being the most fundamental and consistent (Martínez, 2016). This model minimizes assumptions about the behavior of the residuals by assuming that the model to be estimated is as follows:\n\nWhere αi=α+vi, then replacing in (1) is:\n\nThat is, it assumes that the error (εit) can be broken down into two parts a fixed part, constant for each individual (vi) and another random one that meets the MCO requirements (uit) (εit=vi+uit), which is equivalent to obtaining a general trend by regression giving each individual a different point of origin (ordinates). This operation can be performed in several ways, one of them is by introducing a dummy for each individual (eliminating one of them for statistical reasons) and estimating by OLS. Consistent (fixed effects) and efficient (random effects) estimates differ significantly. This implies that it is preferable to select the estimator that we consider more consistent, which in this case is the fixed effects estimator. In contrast, if they are orthogonally equal, the most efficient estimator should be chosen, which is the random effects estimator (Martínez, 2016).\n\nFor the application of a nested data model, the Hausman test is used, which compares the estimates between the fixed effects model and the random effects model. If systematic differences are identified (the null hypothesis of equality is rejected, i.e. a high test value and a low p-value, less than 0.05, is obtained) and provided we are reasonably confident of the specification, we can conclude that the correlation between the error and regressors persists. (Cov(X_it, u_i) ≠ 0), being preferable to choose the fixed-effect model (Martínez, 2016).\n\nSince ICT penetration cannot be explained by a single variable and there is no aggregate index available to measure ICT penetration in a country, this research uses three of the most relevant variables to measure ICT penetration. The variables used are: a) Individuals using the Internet (as a percentage of the population), b) Fixed telephone subscriptions (per 100 people) and c) Mobile cellular subscriptions (per 100 people).\n\nOnce the ICT variables have been determined, the panel data analysis is carried out, starting by verifying the stationarity of the series, panel cointegration and, finally, panel regression. To evaluate the research objectives, the equation formulated is as follows:\n\nWhere:\n\nGDP per capita is annual data at constant prices in US dollars.\n\nICT is ICT penetration, measured by the variables: Individuals using the Internet, fixed telephone subscriptions and mobile cellular subscriptions.\n\nBC trade balance of goods and services) in relation to GDP.\n\nFDI is foreign direct investment as a percentage of GDP.\n\nIC is domestic credit provided by financial institutions as a percentage of GDP used as a proxy for financial development.\n\n\nResults\n\nIn the last decade, Information and Communication Technologies (ICTs) have played a crucial role in economic and social transformation worldwide. Latin America, as a developing region, has not been immune to this phenomenon. ICTs, which include the Internet, mobile telephony, and other forms of digital technologies, have significantly altered the way societies communicate, access information, and participate in the global economy (Parra, Agudelo, García, Hernández, Sellens, de Llano Feliú & Chamorro, 2022). The behavior of variables aligned with ICTs in Latin America is shown below.\n\nAs shown in Figure 1, the percentage of people using the Internet in Latin America has grown. Latin America grew from 3.2% in 2000 to 64.8% in 2020. In this regard, Pérez (2022) highlights the importance of policies that promote connectivity in rural areas to maximize the positive impact on economic growth. Table 1 below shows the variables used, the source of information and the expected sign.\n\nSource: Own elaboration based on Banco Mundial (2023b).\n\nFigure 2 shows that during the 2000-2020 period, Chile stands out with 52.43% on average, exceeding Uruguay by 7 percentage points. Argentina is in third place with 43.58% on average. Guatemala, Honduras and Argentina occupy the last places with 17.69%, 16.68% and 13.94% respectively. Internet access has boosted business productivity by enabling instant communication, online collaboration and rapid access to resources and data. This contributes to operational efficiency, decision making and allows companies to innovate and develop new products (Smith and Johnson, 2019; López, 2021; García et al., 2020).\n\nSource: Own elaboration based on data from Banco Mundial (2023b).\n\nAs shown in Figure 3, fixed telephony subscriptions per 100 people on average in Latin America have shown a constant behavior, the maximum level reached occurred in 2008 with 15.0%, and the lowest data is generated in 2020 with 12%. This behavior is associated with the fact that currently fixed telephones are less used so there have been changes in consumer behavior (García, et al., 2017), technological advances (Martínez and López, 2018) cost considerations (Pérez, 2020) and adaptation to demographic and cultural changes (Pérez, 2020).\n\nSource: Own elaboration based on data from Banco Mundial (2023c); Banco Mundial (2023d).\n\nMobile cellular subscriptions per 100 inhabitants on average in Latin America have experienced growth throughout the study period. The highest point was recorded in 2013 with 116.1%, while the lowest point was in 2000 with 9.3%. This significant increase is due to factors such as decreasing costs of mobile devices, increasing mobile network coverage and the availability of affordable data plans have contributed to the growth in mobile adoption in Latin America (Barrantes, Galperin, & Mariscal, 2015; World Bank 2021; IDB [Inter-American Development Bank], 2018).\n\nMobile and fixed telephony has had a positive impact on economic growth in Latin American countries by improving communications infrastructure, fostering financial inclusion (Martínez et al., 2020), stimulating business development, and facilitating access to markets (Guizado Perez, 2019). However, continued efforts are required to address challenges and ensure equitable and sustainable implementation of these technologies (López, 2021).\n\nFigure 4 shows the average GDP per capita during the period 2000-2020, which has maintained a growth until the year 2019 in Latin America, with USD 7684.5 dollars. On the other hand, by 2020 the GDP per capita contracts and reaches USD 6724 dollars, explained by the impact of the COVID 19 pandemic.\n\nSource: Prepared by the authors based on data from Banco Mundial (2023a).\n\nThe average GDP per capita during the period 2000-2020, is led by Uruguay with an average of USD 12959.56 dollars, its immediate follower is Argentina with 12298.67. The countries with the lowest GDP per capita are: Bolivia with 2548.82, Honduras with 2100.52 and Nicaragua with 1750.29, on average.\n\nRegarding the results of the econometric model, the following results are evident.\n\nAfter correcting the seasonality problem in the series, the Hausman test is performed. The Hausman test evaluates whether the individual effects of the behavior of the variables are correlated with the explanatory variables, i.e. it helps to determine the best model, whether fixed or random effects. The following hypotheses are used:\n\nH0 = Random effects model → Prob > 5%.\n\nH1 = Fixed effects model → Prob < 5%.\n\nAs can be verified in Table 2 by means of the Hausman test and given the probability both in the cross section and in the time section, Prob < 5%, therefore a fixed effects model will be applied.\n\nAfter performing the unit root tests and the Hausman test, it was found that the fixed effects model was a better fit. The equation derived from the econometric model is shown below.\n\nDónde: δ1: Fixed effects on individuals λ1: Fixed effects over time\n\nThus, as can be seen in Table 3 and in the equation (5), trade openness measured by the trade balance is significant and negatively affects economic growth in Latin America; for every percentage point by which the trade balance increases (% of GDP), GDP per capita decreases by USD 11.49 dollars.\n\nOn the other hand, financial development as measured by domestic credit granted by banks is significant and negatively affects economic growth in Latin America; for every percentage point by which domestic credit increases (% of GDP), GDP per capita decreases by USD 19.61.\n\nForeign investment as a net capital inflow (% of GDP) is significant and positively affects economic growth in Latin America; for each percentage point as a percentage of GDP by which foreign investment increases, GDP increases by USD 29.94 dollars.\n\nAmong the variables used to measure the penetration of ICTs in economic growth, the only significant variable was the use of the Internet as a percentage of the population, contributing positively to economic growth; for each percentage point increase in the number of people using the Internet, GDP per capita increases by USD 16.82 dollars.\n\n\nDiscussion\n\nWithin the instruments used to measure the penetration of ICTs in economic growth, the only significant variable was Internet use, contributing positively to economic growth with a coefficient value of (16.82). That is, for each percentage point increase in people using the internet as a percentage of the population, GDP per capita increases by USD 16.82 dollars, being one of the most used variables worldwide, while fixed telephone subscriptions and mobile cellular subscriptions are not significant variables since the value of the t-statistic is less than 2. These findings are in line with the research of Hofman et al. (2016) and Cardona (2013) who for the panel data set reveal that Foreign Direct Investment and ICT expansion positively and significantly impact economic growth, and in addition to that, ICT expansion also has a positive effect on FDI inflows. On the other hand these findings contrast with the study of Bollou (2006) in which fixed telephone subscriptions is a significant variable and in the research of Siddiqui and Singh (2019) in which mobile cellular subscriptions is also a significant variable with a coefficient value of (0.279).\n\nIn this sense, the slow progress of ICT’s in Latin America is justified by the insufficient existing technological infrastructure and the lack of knowledge of the institutions and governments of these countries, regarding the importance of these cross-cutting digital technologies (Quiroga-Parra et al., 2017).\n\nRegarding the trade balance, this variable has a negative influence on economic growth with a coefficient of -11.49 being this variable not significant, this finding has been contrary to the results of Toader et al. (2018) that in EU countries their coefficient of (0.14) has been significant. For the Latin American context this behavior is due to the impact on the balance of payments restriction, trade liberalization has not relaxed this restriction, which may limit the economic growth of Latin American countries (Pacheco López, 2009). In addition, the region faces a complex external scenario, marked by low growth in economic activity and world trade, which affects macroeconomic performance (CEPAL, 2023). Dependence on commodity exports has also been a relevant factor in the historical evolution of the region (Ocampo et al., 2017).\n\nRegarding domestic credit, this variable negatively influences economic growth with -19.61096, this finding is in contrast to the results of the EU study by Toader et al. (2018) where the value of the coefficient (0.59) and is a significant variable. Domestic credit in Latin American countries can have a negative impact on economic growth due to debt accumulation, volatility in financial markets, reduced private consumption and limited investment.\n\nForeign investment positively affects economic growth in Latin America with a coefficient of 29.949 due to the improved openness of FDI in these countries. Meanwhile, Stanley, Doucouliagos and Steel (2018) also found a similar result in their study conducted in developed and developing countries. An expansion of ICT’s allows multinational companies to take advantage of cheap labor and capital, easy access to local and international markets, and regular and continuous communication with the respective headquarters. This influences multinational companies to invest in countries that have a good ICT base (Majeed and Ayub, 2018).\n\n\nConclusions\n\nThe literature supports the positive effects of ICT penetration on the economic growth of nations. ICTs are an important driver for providing access to information, which stimulates faster growth due to better investment. ICTs impact economic growth in both direct and indirect ways. They influence economic growth directly because they increase capital endowment and indirectly through total factor productivity.\n\nIn terms of access to and use of ICTs, the countries that use the Internet the most as a percentage of the population are: Chile, Uruguay and Argentina with 52.43% 45.41% and 43.58% respectively. On the other hand, the countries with the lowest rates of Internet access and use are Guatemala, Honduras and Nicaragua with 16.69%, 16.68% and 13.94% respectively.\n\nThe region experienced per capita gross domestic product growth through 2019, reaching an average of USD 7684.5 dollars. However, the disruptive impact of the COVID-19 pandemic in 2020 generated a significant contraction, reducing GDP per capita to USD 6724 dollars. This phenomenon highlights the region’s economic vulnerability to unexpected events and underscores the need for resilience and adaptation strategies. The implementation of policies focused on economic diversification, investment in education and technology, and the promotion of economic stability could be essential to foster sustainable and inclusive growth in the region.\n\nICTs have a positive impact on Latin America; according to this study, for every percentage point increase in the number of people using the Internet as a percentage of the population, GDP per capita increases by US$16.82. In this sense, it highlights the significant influence of Internet use on economic growth in Latin America, showing that widespread access to ICTs, particularly through Internet connectivity, can be a crucial driver of economic development in the region. Although fixed and mobile telephony subscriptions were not significant, the importance of the Internet as a catalyst for growth is in line with the global trend and underscores the importance of policies and strategies that encourage the expansion of digital infrastructure.\n\nThe study also highlights the persistent challenges facing the region in terms of trade balance and domestic credit. The trade balance, although not significant, continues to be a factor to be taken into account due to its impact on the balance of payments constraint. Likewise, the negative influence of domestic credit suggests the need to proactively address volatility in financial markets. Policies that encourage economic diversification, improve technological infrastructure and promote financial stability could be key to overcoming these challenges and fostering sustainable economic growth in Latin America in the digital era.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nAbdullayev AA: System of information and communication technologies in the education. Sci. World Int. Sci. J. 2020; 2: 19–21. Reference Source\n\nAduwa-Ogiegbaen SE, Iyamu EOS: Using information and communication technology in secondary schools in Nigeria: Problems and prospects. J. Educ. Technol. Soc. 2005; 8(1): 104–112. Reference Source\n\nAhmed Z, Le HP: Linkig Information Communication Technology, trade globalization index, and CO2 emissions: Evidence from advanced panel techniques. Environ. Sci. Pollut. Res. 2021; 28(7): 8770–8781. PubMed Abstract \| Publisher Full Text\n\nAhmed Z, Nathaniel SP, Shahbaz M: The criticality of information and communication technology and human capital in environmental sustainability: evidence from Latin American and Caribbean countries. J. Clean. Prod. 2021; 286: 125529. Publisher Full Text\n\nAntonelli C: The digital divide: Understanding the economics of new information and communication technology in the global economy. Inf. Econ. Policy. 2003; 15(2): 173–199. Publisher Full Text\n\nAppiah-Otoo I, Song N: The impact of ICT on economic growth-Comparing rich and poor countries. Telecommun. Policy. 2021; 45(2): 102082. Publisher Full Text\n\nBahrini R, Qaffas AA: Impact of Information and Communication Technology on Economic Growth: Evidence from Developing Countries. Economies. 2019; 7(1): Article 1. Publisher Full Text\n\nBanco Mundial: La inclusión financiera es un elemento facilitador clave para reducir la pobreza y promover la prosperidad.2022. Reference Source\n\nBanco Mundial: PIB percápita (precios constantes).2023a. Reference Source\n\nBanco Mundial: Personas que usan internet (Porcentaje de la población).2023b. Reference Source\n\nBanco Mundial: Suscripciones a telefonía fija (por cada 100 personas).2023c. Reference Source\n\nBanco Mundial: Suscripciones a telefonía celular móvil (por cada 100 personas).2023d. Reference Source\n\nBanco Mundial: Balanza comercial de bienes y servicios (% del PIB).2023e. Reference Source\n\nBanco Mundial: Crédito interno al sector privado otorgado por los bancos (% del PIB).2023f. Reference Source\n\nBanco Mundial: Inversión extranjera directa, entrada neta de capital (% del PIB).2023g. Reference Source\n\nBarrantes R, Galperin H, Mariscal J: Mobile telecommunications in Latin America: An overview of major regional trends. Telecommun. Policy. 2015; 39(4): 365–382.\n\nBirdsall N, Nellis J: Winners and losers: Assessing the distributional impact of privatization. World Dev. 2003; 31(10): 1617–1633. Publisher Full Text\n\nBollou F: ICT Infrastructure Expansion in Sub-Saharan Africa: An Analysis of Six West African Countries from 1995 to 2002. Electron. J. Inf. Syst. Dev. Ctries. 2006; 26(1): 1–16. Publisher Full Text\n\nBoston Consulting Group: Consultoría de Gestión Estratégica\|Grupo de consultas de Boston. BCG Global; 2021. Reference Source\n\nBrynjolfsson E, McAfee A: The second machine age: Work, progress, and prosperity in a time of brilliant technologies. WW Norton & Company; 2014. Reference Source\n\nCardona M: Identificacion de nuevos caminos hacia la innovacion educativa. Revista iberoamericanapara la investigacion y el desarrollo educativo. 2013; 10.\n\nCardona Serrano A, Fandiño Parra YJ, Galindo J: Formación docente: creencias, actitudes y competencias para el uso de TIC. Lenguaje. 2014; 42(1):173–208. Publisher Full Text\n\nCarr N: Is Google making us stupid? Teach. Coll. Rec. 2008; 110(14): 89–94. Reference Source\n\nCEPAL: Las oportunidades de la digitalización en América Latina frente al covid-19.2020. Reference Source\n\nCEPAL: América Latina y el Caribe crecerá 5,9% en 2021, reflejando un arrastre estadístico que se modera a 2,9% en 2022. CEPAL; 2021, agosto 31. Reference Source\n\nCEPAL: Economía digital para el cambio estructural y la igualdad. CEPAL; 2013. Reference Source\n\nCEPAL: Economías de América Latina y el Caribe crecerán 1,2% en 2023 en un contexto de crecientes incertidumbres.2023. Reference Source\n\nFraga A: Digital transformation and economic growth: A global analysis. Telecommun. Policy. 2017; 41(6): 485–500. Reference Source\n\nGarcía A, et al.: Cambios en los Hábitos de Consumo de Comunicación en América Latina. Revista de Comunicación. 2017; 24(3): 45–60.\n\nGarcía M, et al.: Internet and Innovation: A Case Study of Latin American Firms. J. Econ. Dev. 2020; 35(4): 210–225.\n\nGarcía Martínez V, Silva Payró MP: Percepción académica sobre las barreras en la adopción de innovaciones tecnológicas durante la pandemia por la covid-19. Apertura (Guadalajara, Jal.). 2022; 14(1): 96–113.\n\nGerman-Soto V, Soto Rubio M, Gutiérrez Flores L: Innovación y crecimiento económico regional: evidencia para México. Problemas del desarrollo. 2021; 52(205): 145–172. Publisher Full Text\n\nGurumurthi S, Sivasubramaniam A, Kandemir M, et al.: DRPM: Dynamic speed control for power management in server class disks. ACM SIGARCH Comput. Archit. News. 2003; 31(2): 169–181. Publisher Full Text\n\nGuizado Perez JM: Gestión clínica y las Tecnologías de Información y Comunicación (TICs) en profesionales de salud de la Clínica Tezza, Surco. 2019. Publisher Full Text\n\nGutiérrez LH, Berg S: Telecommunications liberalization and regulatory governance: Lessons from Latin America. Telecommun. Policy. 2000; 24(10-11): 865–884. Publisher Full Text\n\nHofman A, Aravena C, Aliaga V: Information and communication technologies and their impact in the economic growth of Latin America, 1990–2013. Telecommun. Policy. 2016; 40(5): 485–501. Publisher Full Text\n\nIDB (Inter-American Development Bank): Digital Transformation in Latin America and the Caribbean: What Are the Benefits for Governments? IDB; 2018. Publisher Full Text\n\nJain AK, Bolle R, Pankanti S: Biometrics: personal identification in networked society. vol. 479. ; 2006. Springer Science & Business Media.\n\nJordá-Borrell R, López-Otero J: Factores de crecimiento económico en los países en desarrollo: el papel de las TICs. Boletín de la Asociación de Geógrafos Españoles. 2020; 86. Publisher Full Text\n\nKretschmer T: Information and communication technologies and productivity growth: A survey of the literature.2012.\n\nKomninos N: Smart Cities and Connected Intelligence: Platforms, ecosystems and network effects. Routledge; 2019.\n\nMartínez G, Garmendia M, Garitaonandia: La infancia y la adolescencia ante las Tecnologías de la Información y la Comunicación (TICs): oportunidades, riesgos y daño. ZER: Revista De Estudios De Comunicación = Komunikazio Ikasketen Aldizkaria. 2020; 25:349–362. Publisher Full Text\n\nMartínez J: ¿Qué factores macroeconómicos influyen en la obtención de medallas olímpicas y paralímpicas?2016. Reference Source\n\nMartínez J, López M: Avances Tecnológicos y Conectividad Móvil en América Latina. J. Mob. Technol. 2018; 15(2): 112–128.\n\nMajeed MT, Ayub T: Information and communication technology (ICT) and economic growth nexus: A comparative global analysis. Pak. J. Commer. Soc. Sci. 2018; 12(2): 443–476.\n\nMcKinsey: Consultoría de gestión global\|McKinsey y compañía.2022. Reference Source\n\nMeso P, Musa P, Mbarika V: Towards a model of consumer use of mobile information and communication technology in LDCs: The case of sub-Saharan Africa. Inf. Syst. J. 2005; 15(2): 119–146. Publisher Full Text\n\nMyovella G, Karacuka M, Haucap J: Digitalization and economic growth: A comparative analysis of Sub-Saharan Africa and OECD economies. Telecommun. Policy. 2020; 44(2): 101856. Publisher Full Text\n\nMwakaje AG: Information and Communication Technology for Rural Farmers Market Access in Tanzania.2010. Reference Source\n\nNabi S, Ahmad M, Ibrahim M, et al.: AdPSO: adaptive PSO-based task scheduling approach for cloud computing. Sensors. 2022; 22(3):920. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNeffati M, Besbes L: Correlation ICT education and economic growth: Case of the Arab economies. Int. J. Econ. Finance Manag. 2013; 2(1):135–142.\n\nNiebel T: ICT and economic growth–Comparing developing, emerging and developed countries. World Dev. 2018; 104: 197–211. Publisher Full Text\n\nLópez A: The Role of Internet Access in Fostering Entrepreneurship: Evidence from a Cross-Country Analysis. Int. J. Bus. Econ. Dev. 2021; 27(3): 112–130.\n\nOcampo J, Pulupa J, Knezevich A: Beneficios y limitaciones del empleo de TIC en la orientación vocacional de estudiantes de educación secundaria de Guayaquil, Ecuador. Maskana. 2017; 8:333–342.\n\nPacheco López P: Efectos de la liberación comercial en el crecimiento económico y la balanza de pagos en América Latina. Investigación económica. 2009; 68(267): 13–49. Recuperado en 27 de noviembre de 2023. Reference Source\n\nParra DJQ, Agudelo CAM, García EAH, et al.: Las nuevas fuentes de productividad: perspectiva en América Latina. Fondo Editorial–Ediciones Universidad Cooperativa de Colombia; 2022. Publisher Full Text\n\nParente SL, Prescott EC: Barriers to technology adoption and development. J. Polit. Econ. 1994; 102(2): 298–321. Publisher Full Text\n\nPérez R: Costos y Accesibilidad en Telefonía Fija: Un Análisis en América Latina. Int. J. Telecommun. 2020; 27(4): 75–90.\n\nPérez R: Addressing the Digital Divide: Policy Implications for Internet Connectivity in Latin America. J. Inf. Technol. Soc. 2022; 15(2): 45–60.\n\nQuiroga-Parra DJ, Torrent-Sellens J, Murcia Zorrilla CP: Uses of ICT in Latin America: A characterization. Ingeniare. Revista chilena de ingeniería. 2017; 25(2): 289–305. Publisher Full Text\n\nRodrik D: New technologies, global value chains, and developing economies. IMF Econ. Rev. 2018; 66(2): 315–359.\n\nRöller L-H, Waverman L: Telecommunications infrastructure and economic development: A simultaneous approach. Am. Econ. Rev. 2001; 91(4): 909–923. Publisher Full Text\n\nRoztocki N, Soja P, Weistroffer HR: The role of information and communication technologies in socioeconomic development: towards a multi-dimensional framework. Inf. Technol. Dev. 2019; 25(2):171–183. Publisher Full Text\n\nSiddiqui AA, Singh P: ICT Penetration and Economic Growth: An Empirical Analysis of Major Trading Nations. Indian Econ. J. 2019; 67(3-4): 312–333. Publisher Full Text\n\nSingh RK, Luthra S, Mangla SK, et al.: Applications of information and communication technology for sustainable growth of SMEs in India food industry. Resour. Conserv. Recycl. 2019; 147: 10–18. Publisher Full Text\n\nSinha M, Sengupta PP: FDI Inflow, ICT Expansion and Economic Growth: An Empirical Study on Asia-Pacific Developing Countries. Glob. Bus. Rev. 2022; 23(3): 804–821. Publisher Full Text\n\nSmith J, Johnson K: The Impact of Internet Adoption on Business Productivity. J. Technol. Econ. Dev. 2019; 18(1): 75–90.\n\nStanley TD, Doucouliagos H, Steel P: Does ICT generate economic growth? A meta-regression analysis. J. Econ. Surv. 2018; 32(3):705–726. Publisher Full Text\n\nSteinmueller WE: ICTs and the possibilities for leapfrogging by developing countries. Int’l Lab. Rev. 2001; 140: 193–210. Publisher Full Text\n\nToader E, Firtescu BN, Roman A, et al.: Impact of Information and Communication Technology Infrastructure on Economic Growth: An Empirical Assessment for the EU Countries. Sustainability. 2018; 10(10): Article 10. Publisher Full Text\n\nVan Reenen J, Bloom N, Draca M, et al.: The Economic Impact of ICT. Centre for Economic Performance, London School of Economics; 2010.\n\nVon Lubitz D, Wickramasinghe N: Healthcare and technology: The doctrine of networkcentric healthcare. Int. J. Electron. Healthc. 2006; 2(4): 322–344. PubMed Abstract \| Publisher Full Text\n\nVu KM: ICT as a source of economic growth in the information age: Empirical evidence from the 1996–2005 period. Telecommun. Policy. 2011; 35(4): 357–372. Publisher Full Text\n\nWorld Bank: Information and Communications for Development 2021: Data-driven digital transformation. World Bank; 2021. Publisher Full Text\n\nYu H: Analysis of the impact of the new infrastructure on economic growth——based on empirical test charging pile of new energy vehicles. IOP Conference Series: Earth and Environmental Science. IOP Publishing; 2021, May; Vol. 769(4): p. 042020.\n\nZapata E, Stirling R, Pasquarelli W, et al.: The GovTech Index 2020 Unlocking the Potential of GovTech Ecosystems in Latin America, Spain and Portugal. CAF, Oxford Insights; 2020. Reference Source" }	[ { "id": "289830", "date": "08 Jul 2024", "name": "Julio Galárraga", "expertise": [ "Reviewer Expertise Human capital", "Education Economics", "Econometrics", "Health Economics." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this paper the authors explore the relationship between Information and Communication Technolgies (ICT) and economic growth. They build a data panel with 17 Latin American countries with information between 2000 and 2020 and use Ordinary Least Squares to estimate the parameters of their model. The authors state that for every percentage point increase in the percentage of the population using the Internet, GDP per capita increases by US$16.82, mentioning that ICTs have a positive impact on economic growth. In my opinion the paper should be rejected by F1000 Research in its current version because it requires very deep changes to achieve a sufficient level for publication. The work done by the authors is moderately good, they explore an interesting topic that is important for Latin America, but it lacks theoretical support (economic theories and an identification strategy) and there are various econometric details that must be explicated for their results to be considered robust. Writing is good and concise, variables used in the paper are accessible in public sources, but they are not enough to build a robust econometric model that can explain economic growth. Results are presented in a confusing way and seem to be bad interpreted. The methodology is moderately explained and requires various clarifications. In my view, if the paper will be publicized needs to be adjusted, with the following changes to be done:\nInclude literature like: (Saba et al,2023)(Ref-1); (Fernadez, Almodóvar et al.,2020); (Niebel et al.,2022) But also include economics literature about an economic growth model that will later be extended to include ICT, this will give a theoretical support to the econometric model stated. The paper is not adequately designed, because the relationship stated lacks a theoretical support, in this sense, it is fundamental that first it starts from an economic growth model and then will include ICT variables according to what theory states, this will also shed light on other fundamental control variables must be included to explain economic growth, like human capital (education and health), among others. The identification strategy must be addressed because the model presented has the problem of simultaneity between ICT and economic growth, as the authors cannot account which one of those two variables moved first. This problem causes the estimators to be biased and the results can be flawed. The use of a fixed effects panel must be justified beyond the Hausman test, the theoretical explanation of the use of this type of estimation is connected to the correct identification of the parameters, their unbiasedness and consistency. Also, to address the bias due to unobserved characteristics of countries captured in the error term that with a panel can be introduced in the form of fixed effects. In modern econometrics the Hausman tests has a lot of critiques about a bad interpretation of what it does and what the null hypothesis states. In the introduction the authors mention that they measure the impact of ICT on economic growth, but in the methodologic section they state that it is a correlational study. This is a serious problem of confusion between correlation and causality. The use of terms in a paper must be precise when an econometric methodology is applied. A table including the transformation done to the variables and the hypothesis tests applied to check the stationarity of the variables with the transformations must be included. It is suggested that an interaction between time and country fixed effects can be included in the estimations to control other individual tendencies. It is important to address if the panel has problems of time autocorrelation in the errors and in the dependent variable: GDP per capita, if it is true, the order of the autocorrelation has to be identified, because by nature the GDP has time autocorrelation. On the interpretation of the estimators and conclusions sections it is not clear if in the regression it is included ICT or its logarithm. Even tough in equation 3 it is specified that the logarithm of ICT will be included, in equations 4 and 5 it seems to be at level and not in logarithm. Also, when the coefficient is interpreted it is read as a semi elasticity, but if equation 3 was estimated it must be read as an elasticity. In other words, if there is an increase in 1% in ICT, it implies an increase of beta% on GDP per capita. Authors can also transform that result to interpret it in dollars, but in the manner it is presented, the estimator is incorrectly interpreted.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "289829", "date": "23 Jul 2024", "name": "Saizal Bin Pinjaman", "expertise": [ "Reviewer Expertise Econometric analyses" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n- Research significance and theoretical review should be included. - The author used dummy variable in the fixed effects model as shown in equation (4) and (5). The issue with this approach is that it requires equal number of dummy variables to represent the cross-sectional information. For that, many researchers recommend other approaches including the within group estimator in the context of Fixed effect model. - The most crucial part is that no diagnostic test was conducted including the heteroskedasticity and cross-sectional dependence. - An argument for explaining the relationship between the variables needs to be elaborated. - Include specific policy recommendations in the Conclusions.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-378
https://f1000research.com/articles/13-376/v1	23 Apr 24	{ "type": "Research Article", "title": "A cross-sectional study: Is there sex differences in food acceptance, serum albumin, and nutritional status among residents of social shelters in Surabaya, Indonesia?", "authors": [ "Trias Mahmudiono", "Mahmudah Mahmudah", "Diah Indriani", "Chrysoprase Thasya Abihail", "Nur Sahila", "Dono Widiatmoko", "Mahmudah Mahmudah", "Diah Indriani", "Chrysoprase Thasya Abihail", "Nur Sahila", "Dono Widiatmoko" ], "abstract": "Background The conceptual framework for Sex Equality and Social Inclusion (GESI) is a concept that gives special attention to women. Often, they don’t get the attention they deserve and are still excluded from society. This study was a quantitative study with a cross-sectional design with a total of 44 elderlies in Griya Werdha, Surabaya. This study aimed to determine the sex differences in food acceptance, serum albumin, and nutritional status in elderlies.\n\nMethods This was a quantitative study with a cross-sectional design that was located in Griya Werdha, Surabaya, East Java, Indonesia. The sample size of this study was 44 elderly. The collected data included personal information collected by using questionnaires, blood pressure examinations, and urine collection - which were then submitted to the Balai Besar Laboratorium Kesehatan Surabaya (Surabaya Central Health Laboratory Institute). Data were analyzed using a chi-square test.\n\nResults The results showed that most of the respondents were women (68.2%), aged 71-80 years old (38.63%), underweight nutritional status (55.6%), positive albumin (59.0%) and having pre-hypertension (36.3%). Based on the relationship test, there was no significant relationship between hypertension (p = 0.307), nutritional status (p = 0.534), and leftover food (p = 0.822; p = 1.000 p = 0.809; p = 1.000; p = 0.549) with the sex of the respondent. However, albumin status was associated and had differences based on the sex of the respondent (p = 0.014).\n\nConclusion In conclusion, according to these data, there were no sex differences in food acceptance, hypertension, and nutritional status among residents of social shelters in Surabaya. On the other side, there were sex differences in albumin status.", "keywords": [ "Gender equality", "Social inclusion", "Food security", "Elderlies", "Health Well-Being" ], "content": "Introduction\n\nThe conceptual framework for Gender Equality and Social Inclusion (Gesi) is a concept that gives special attention to women, including marginalized groups such as the poor, street children, elderly, and so on.1 Elderlies can be defined as someone who has aged 65 years and above.2 In 2022, there were 771 million people aged 65+ years globally, accounting for almost 10% of the world’s population.3 In Indonesia itself, the number of elderly people in 2023 will be 11.75% of the total population and this figure has increased by 1.27% compared to the previous year which was only 10.48% of the total population in Indonesia.4 Apart from that, the number of elderly people in East Java Province in 2022 also shows quite a large number, namely 14 million or 33.99% of the total population in East Java Province.5 As a person, including the elderly, ages, various health problems will arise. According to the World Health Organization (WHO), health problems that usually occur in the elderly are hearing loss, cataracts and refractive errors, back and neck pain and osteoarthritis, chronic obstructive pulmonary disease, diabetes, depression and dementia, and other diseases such as delirium, falls, urinary incontinence, and pressure ulcers.6\n\nShelters are generally a container that usually provides shelter and residence for the elderly.7 However, unfortunately not all shelters provide adequate services and welfare for their residents. In the world, it is estimated that there are 1.6 billion people living in inadequate shelters.8 In addition to elderlies, neglected people are also included in marginal groups who must receive special attention.9 In Surabaya, there are many social shelters, for example Keputih Social Pondok Environment (Liponsos). In Liponsos, it reported that until 2021, there are as many as 900 people.10 Based on the data obtained, the capacity of Liponsos residents in Surabaya was only 600 people.11 This data shows that shelters in Indonesia are also not good enough for their residents.\n\nFood security is a condition of fulfilling food for the state to individuals, which is available from the availability of sufficient food, both in quantity and quality, safe, diverse, nutritious, equitable and affordable and does not conflict with religion, belief, and culture of the community, in order to be healthy, active, and productive in a sustainable manner.12 A study showed that as many as 82.2% of elderlies eat a variety of foods and only 17.8% of elderlies eat a variety of foods.13 This can affect the nutritional condition of elderlies. Based on the research that has been done, it was found that as many as 47.1% of elderlies have very poor nutritional status.14 Besides that, one study that was conducted in Malaysia showed that as many as 38.5% of elderlies in social shelters had body mass index (BMIs) less than 18.5 kg/m2.15 Another study also showed that elderlies in social shelters were likely to be underweight or at risk of being underweight due to an illness that changed the type of food consumed, eating less than two times per day, and mostly eating alone.16\n\nIn addition, sex is an internal factor that can affect nutritional status.17 A study shows that women have a higher risk of experiencing nutritional status disorders such as malnutrition compared to men.18 This is probably because there is still a traditional tradition that requires women to eat after their children and husband have finished eating.19 Sex differences also affect albumin levels where serum albumin levels in women will decrease dramatically at the age of 60 compared to men with the same age.20 In addition, sex differences can also affect the choice of food to be consumed where women tend to choose healthier foods such as fruit, vegetables, nuts, and whole foods. Meanwhile, men tend to choose foods that contain high energy and fat, such as soda, beer and wine.21 The choice of food will affect how acceptance of food from both male and female elderly towards the food that will be served. Therefore, researchers are interested to know and research the sex differences in food acceptance, serum albumin, nutritional status, and hypertension level of residents in social shelters in Surabaya, Indonesia.\n\nThe conceptual framework for Gender Equality and Social Inclusion (Gesi) is a concept that gives special attention to women, including marginal groups such as the poor, street children, elderly, and so on.1 Elderlies can be defined as someone who have aged 65 years and above.2,22 In 2022, there were 771 million people aged 65+ years globally, accounting for almost 10% of the world’s population.23 In Indonesia itself, the number of elderly individuals in 2023 amounted to 11.75% of the total population, marking an increase of 1.27% compared to the previous year, which was only 10.48% of the total population in Indonesia.24 The number of elderly individuals in East Java Province in 2022 also showed a considerable figure, totaling 14 million (33.99%).25 As someone’s age increases, various health issues may arise. According to the World Health Organization (WHO), health problems commonly experienced by the elderly include hearing loss, cataracts and refractive errors, back and neck pain and osteoarthritis, chronic obstructive pulmonary disease, diabetes, depression and dementia, and others disease such as delirium, falls, urinary incontinence, and pressure ulcers.26\n\nShelters generally serve as a refuge and residence for the elderly. However, unfortunately, not all shelters provide adequate services and welfare for their residents. Worldwide, it is estimated that 1.6 billion people live in inadequate shelters (Habitat for Humanity 2022). In addition to elderlies, neglected people are also included in marginal groups who must receive special attention. In Surabaya, there are many social shelters, for example Keputih Social Pondok Environemnt (Liponsos). In that Liponsos, it reported that until 2021, there are as many as 900 people.5 Based on the data obtained, the capacity of Liponsos residents in Surabaya was only 600 people.6 This data showed that shelters in Indonesia are not considered adequate for their residents\n\nFood security is a condition of fulfilling food for the state to individuals, which is available from the availability of sufficient food, both in quantity and quality, safe, diverse, nutritious, equitable and affordable and does not conflict with religion, belief, and culture of the community, in order to be healthy, active, and productive in a sustainable manner.11 A study showed that as many as 82.2% of elderlies eat a variety of foods and only 17.8% of elderlies eat a variety of foods.12 This can affect the nutritional condition of elderlies. Based on the research that has been done, it was found that as many as 47.1% of elderlies have very poor nutritional status.13 Besides that, one study that was conducted in Malaysia showed that as many as 38.5% of elderlies in social shelters had body mass index (BMIs) less than 18.5 kg/m2.14 Another study also showed that elderlies in social shelters were likely to be underweight or at risk of being underweight due to an illness that changed the type of food consumed, eating less than two times per day, and mostly eating alone.15\n\nIn addition, sex is an internal factor that can affect nutritional status.16 A study shows that women have a higher risk of experiencing nutritional status disorders such as malnutrition compared to men.17 This is probably because there is still a traditional tradition that requires women to eat after their children and husband have finished eating.18 Sex differences also affect albumin levels where serum albumin levels in women will decrease dramatically at the age of 60 compared to men with the same age.19 In addition, sex differences can also affect the choice of food to be consumed where women tend to choose healthier foods such as fruit, vegetables, nuts, and whole foods. Meanwhile, men tend to choose foods that contain high energy and fat, such as soda, beer and wine.20 The choice of food will affect how acceptance of food from both male and female elderly towards the food that will be served. Therefore, researchers are interested to know and research the sex differences in food acceptance, serum albumin, nutritional status, and hypertension level of residents in social shelters in Surabaya, Indonesia.\n\n\nMethods\n\nThis was a quantitative study with a cross-sectional design that was located in Griya Werdha, Surabaya, East Java, Indonesia. The sample size of this study was 44 samples of elderlies. Elderly people in Griya Werdha are divided into 3 groups. The first group is the independent group, consisting of elderly individuals who are capable of carrying out daily activities without assistance from a caregiver. The second group is the partial group, comprising elderly individuals who require caregiver assistance in some daily activities. The last group is the total care group, consisting of elderly individuals who are bedridden and need assistance from a caregiver to carry out daily activities. In this study, we involve elderly individuals from the independent group aged 51-90 years who reside in Griya Werdha, Surabaya, East Java, Indonesia, and are willing to be research respondents. The exclusion criteria are respondents who are not willing to participate in the data collection process and do not fill out the questionnaire completely.\n\nIn this study, the researchers examined several variables such as the characteristics of the respondents which included age, sex, and education level using questionnaires. However, the hypertension level was examined by blood examination. The determination of sex in this study was based on statements and direct confessions from respondents. Nutritional status was determined using the body mass index (BMI) obtained from the results of measurements of the respondent’s weight and height. The measurements for the respondent’s weight and height were done by nurses in that shelter. The nutritional status was classified into two categories, underweight and not underweight. The classification that was used was based on body mass index (BMI) classification guidelines from the Indonesian Health Ministry. The underweight group contains those who have BMI <18.5 kg/m2 and the non underweight group contains those who have BMI >18.5 kg/m2. In addition, other variables that were studied by the researchers were the mean of leftover food and the respondent’s albumin levels. Albumin levels were obtained from collecting urine samples from respondents. The collected urine samples were then sent to the Surabaya National Laboratory for a complete urine examination. Meanwhile, the average of leftover food was obtained by filling out a questionnaire related to food consumed in a day. In this study, the chi-square test was used to examine the relationship between leftover food, hypertension, albumin levels, and the nutritional status of the respondents. In this study, all variables that have been tested using the chi-square test will be tested for the relationship using a multinomial logistic regression test. If the p-value is <0.05, then there is a significant relationship between the various variables that were studied.\n\nIn this study, sex differences were taken into consideration due to differences in brain anatomy, physiology, and neurochemistry, especially given the differential prevalence of many psychiatric and developmental disorders in men and women, signs and symptoms of pathophysiology, and response to treatment cannot be ignored.21,27\n\nAll the study participants provided written informed consent and are all being informed about the research. This study was granted ethical approval by the Health Research Ethics Commission, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia on April 8, 2022, with approval number 152/HRECC.FODM/IV/2022.\n\n\nResults\n\nFrom the data collection, most elderly were between the ages of 71-80 years old (38.63%) and mostly women (68.2%). Nineteen elderly people whose last education was elementary school (43.1%). It was found that the elderly with underweight nutritional status were 25 elderly (55.6%) and 19 elderly who were identified as not underweight. In addition, the elderly with normal blood pressure were two people (4.6%), categorized as pre-hypertension in as many as 16 people (36.3%), hypertension level onein as many as eight people (18.2%), hypertension level two in as many as six people (13.6%), and isolated systolic hypertension as many as 12 people (27.3%). In addition, most of the respondents had positive albumin status (59%) and only 41% of respondents had negative albumin status. The characteristics of respondents can be seen further in Table 1.\n\nFrom the results of filling out questionnaires related to the food consumed by respondents, it was found that most of the food components which included staple food (rice), animal side dishes, vegetable side dishes, vegetables, and fruit were quite well received by the respondents. Most of the respondents in this study only consumed staple food (rice) 50% (60%) and only 2.2% of respondents did not consume and only consumed this food 25%. For animal side dishes, most respondents finished all of the food (82.2%) and there was only one respondent (2.2%) who did not consume or still left the food at 75%. Likewise, with vegetable protein dishes, as many as 68.9% of respondents finished all the vegetable side dishes given. Most respondents did not leave food or consume all the vegetables given (57.8%) for the average leftover vegetables. In addition, for the average fruit leftovers, most respondents also did not leave food or consumed all the fruit that was given by Indonesia’s government (80%). The frequency distribution of the average food waste can be seen further in Table 2.\n\nBased on the relationship test, it showed that there was no significant relationship between characteristics of the respondents such as age (p = 0.196), nutritional status (0.495), and hypertension level (p = 0.669) with sex of respondents. However, albumin level has a significant relationship with the sex of respondents (p = 0.014). From that result, it showed that most of those who had positive albumin status were women (31.8%), but these results were not so different from men (27.3%). The relationship between the characteristics of respondents and the sex of respondents can be seen further in Table 3.\n\n* Significant at p < 0.05.\n\nBesides that, the relationship test showed that the average of leftover food (rice) was not significantly related to the sex of the respondents (p = 0.822). This result was the same as the average of leftover food (animal protein) which also has no significant relationship with the sex of the respondents (p = 1.000). Moreover, there was no significant relationship between the average leftover food (vegetable protein) with the sex of the respondents (p = 0.809). In addition, the average of leftover food (vegetables) and the average of leftover food (fruits) were not significantly related to the sex of the respondents (p = 1.000; p = 0.549). The relationship between leftover food with the sex of the respondents can be seen further in Table 4.\n\n* Significant at p < 0.05.\n\n\nDiscussion\n\nThe aim of this study was to gain an understanding of sex differences in age, food acceptance, serum albumin, and nutritional status among residents of social shelters in Surabaya, Indonesia. This study showed that the elderly’s average leftover food per day in Social Shelters reached 21.8%. That average amount of leftover food was higher when compared to the results of a study by Wirasamadi which found that the average food waste in inpatients at Sanglah Hospital Denpasar Bali reached 14.7%.27 That number was also high when compared to the study conducted by Handayani at GRHA Permata Ibu Hospital Depok which has an average of 17.1%.29 The level of food waste in a person can be caused by two factors, namely internal factors which include psychological and physical conditions, eating habits, age, sex, and work, also external factors which include food quality, variety and type of food, timeliness of serving, food temperature served, and the friendliness of the food serving staff.30\n\nThis study found that there was no significant relationship and difference between the age (p = 0.240), and nutritional status (p = 0.495) with the sex of the respondents. There were no differences between the nutritional status and sex of the respondents because there were various factors that more influenced a person’s nutritional status. A study showed that food intake was a dominant variable that would influence the nutritional status of people.31 In addition, both women and men have no differences in food preferences and eating habits, so sex does not significantly affect a person’s nutritional status.32 However, hypertension levels also did not have a significant relationship and difference based on the sex of the respondents (p = 0.671). Hypertension levels can be influenced by many factors such as older age, being overweight or obese, not being physically active, a high salt diet, drinking too much alcohol, and genetics.33 Although, both men and women have a risk to develop hypertension, but men have a higher incidence of hypertension compared to women at the same age until the 6th decade of life.34–36 This can happen because the male androgen hormone plays a role in the blood pressure mechanism that affects high blood pressure.37 In this study, most of the respondents who experienced hypertension were elderly women, so there might not be a relationship because of this.\n\nThis study found no significant differences between the sex of the respondents with their nutritional status. Our findings were contrary to those reported in a study conducted by Zhang that said sex had a significant effect on the association between nutritional statuses.38 Besides that, this results was in line with another study that showed that sex was not significantly related to nutritional status.39 A study showed that for both women and men, no differences in food preferences and eating habits were found so sex does not significantly affect a person’s nutritional status.32\n\nOn the other hand, this study found that there was a significant relationship between sex and the albumin level of the respondents. The other study reported that there were more elderly women whose urine contained albumin than men. It is in line with Akman’s study that shows at admission to the emergency department, the mean serum albumin levels were found to be higher in women than in men.40 The difference in albumin levels between women and men might be explained by menopause and aging, which affect total serum albumin levels.41\n\nIn addition, our findings showed there is no relationship between the sex of the respondents with the leftover food. These results are in line with research conducted by Nisa (2018) which states that there is no relationship between sex and the respondents’ leftover food.42 This might be due to differences in eating habits at home and in nursing homes which affect the acceptability of the respondents. If the eating habits of male and female respondents do not match the food served, it will affect whether or not the food is finished.43\n\nTo our knowledge, this is the first study to assess elderly leftover food in social shelters in Surabaya, Indonesia. There were some limitations, such as bias. Selection bias may arise from the recruitment of respondents by enumerators. Respondent bias can be caused by the demographic of respondents above the age of 40 and the recall process of the respondents. To minimize memory and measurement bias, we used trained enumerators to guide respondents through questionnaires and used detailed questions where appropriate. Moreover, this study was also limited to a different number of male and female elderly. This happens due to the majority of residents in the shelters are women.\n\nAccording to these data, there were no sex differences in food acceptance, serum albumin, and nutritional status among residents of social shelters in Surabaya, Indonesia based on a relationship test. However, it was found that elderlies having a positive albumin level was the most significant variable that relates to their nutritional status. The leftover food in social shelters was still relatively high. While high food waste will affect the nutritional status, better food service delivery and quality diet modifications are demanded to maintain the health of the elderly. It is hoped that this research can create social shelters both in Surabaya and in Indonesia to pay more attention to the health of the elderly, including in terms of serving and type of food to reduce food waste and which will then have an impact on better nutritional status.\n\nAll the study participants provided written informed consent and are all being informed about the research. This study was granted ethical approval by the Health Research Ethics Commission, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia on April 8, 2022, with approval number 152/HRECC.FODM/IV/2022.", "appendix": "Data availability\n\nThe data presented in this study are available on request from the corresponding author. The data are not publicly available due to the privacy of the respondents. The data contains health examination results from respondents who underwent a complete urine examination. Therefore, the data cannot be widely disseminated. The readers can request the data through trias.m@fkm.unair.ac.id.\n\n\nAcknowledgements\n\nWe would like to thank Griya Werdha and all the respondents who were involved in this research, as well as Universitas Airlangga for funding this research.\n\n\nReferences\n\nPrasetyo D, Astini F, Fillaili R, et al.: Analisis Kontekstual/Penelitian Formatif Kesetaraan Gender dan Inklusi Sosial (GESI) untuk Program Water for Women (WfW) Plan Internasional di Indonesia. The SMERU Research Institute; 2019 [dikutip 2 Oktober 2022]. Reference Source\n\nUNICEF: A Study on Street Children in Zimbabwe.2002 [dikutip 5 Mei 2023]. Reference Source\n\nIndonesian Central Bureau of Statistics: Penyandang Masalah Kesejahteraan Sosial Menurut Kabupaten/Kota di Provinsi Jawa Timur.2017 [dikutip 5 Mei 2023]. Reference Source\n\nHerlina A: Kehidupan anak jalanan di Indonesia: faktor penyebab, tatanan hidup dan kerentanan berperilaku menyimpang. Pus Pengkajian, Pengolah Data dan Inf Sekr. 2014; 5: 145–155.\n\nAbdul H: Penghuni Liponsos Keputih Surabaya lebihi daya tampung.2019 [dikutip 5 Mei 2023]. Reference Source\n\nRoy A: Liponsos Keputih Surabaya Overload.2019. Reference Source\n\nWorld Health Organization: Mental health: strengthening our response.2018. Reference Source\n\nDinas Kesehatan Provinsi Kota Surabaya: Anak Jalanan Rentan Mengalami Gangguan Psikologis.2012. Reference Source\n\nCDC: Populations and Vulnerabilities.2022 [dikutip 5 Mei 2023]. Reference Source\n\nPietrangelo A: Is High Blood Pressure in Older Age Inevitable?2020 [dikutip 5 Mei 2023]. Reference Source\n\nKetahanan K: Undang-undang Republik Indonesia Nomor 18 Tahun 2012 tentang Pangan.2016.\n\nYang FF, Dengan Keragaman B, Pada P, et al.: FAKTOR-FAKTOR YANG BERHUBUNGAN DENGAN KERAGAMAN PANGAN PADA ANAK JALANAN DI KOTA SEMARANG. J. Nutr. Coll. 26 November 2019 [dikutip 5 Mei 2023]; 8(4): 254–263. Publisher Full Text Reference Source\n\nLailani N: Hubungan Pola Konsumsi Makanan dengan Status Gizi pada Anak Jalanan di Rumah Singgah KOPA Kecamatan Medan Maimun. Universitas Sumatera Utara; 2019 [dikutip 5 Mei 2023]. Reference Source\n\nSuzana S, Earland J, Suriah AR, et al.: Social and health factors influencing poor nutritional status among rural elderly Malays - PubMed. J. Nutr. Health Aging. 2002 [dikutip 5 Mei 2023]; 6(6): 363–369. PubMed Abstract\n\nVisvanathan R, Zaiton A, Sherina MS, et al.: The nutritional status of 1081 elderly people residing in publicly funded shelter homes in Peninsular Malaysia. Eur. J. Clin. Nutr. 3 November 2004 [dikutip 5 Mei 2023]; 59(3): 318–324. Publisher Full Text Reference Source\n\nCastel H, Harman-Boehm I, Shahar D: Gender Differences in Factors Associated with Nutritional Status of Older Medical Patients.1 April 2013 [dikutip 13 Juni 2023]; 25(2): 128–134. Publisher Full Text\n\nShuremu M, Belachew T, Hassen K, et al.: Nutritional status and its associated factors among elderly people in Ilu Aba Bor Zone, Southwest Ethiopia: a community-based cross-sectional study. BMJ Open. 1 Januari 2023 [dikutip 13 Juni 2023]; 13(1): e067787. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nJoymati O, Ningombam M, Rajkumari B, et al.: Assessment of nutritional status among elderly population in a rural area in Manipur: community-based cross-sectional study. Int. J. Community Med. Public Heal. 22 Juni 2018 [dikutip 13 Juni 2023]; 5(7): 3125–3129. Publisher Full Text Reference Source\n\nWeaving G, Batstone GF, Jones RG: Age and sex variation in serum albumin concentration: an observational study. Ann. Clin. Biochem. 1 Januari 2016 [dikutip 13 Juni 2023]; 53(1): 106–111. PubMed Abstract \| Publisher Full Text\n\nMasella R, Malorni W: Gender-related differences in dietary habits. Clin. Manag. Issues. 10 Juli 2017; 11(2). Publisher Full Text\n\nIvan S, Daniela O, Jaroslava BD: Sex differences matter: Males and females are equal but not the same. Physiol. Behav. 1 Februari 2023; 259: 114038.\n\nSingh S, Bajorek B: Defining ‘elderly’ in clinical practice guidelines for pharmacotherapy. Pharm. Pract (Granada). 2014 Oct 1 [cited 2024 Feb 28]; 12(4): 489. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlvarez P: Charted: The World’s Aging Population from 1950-2100. Visual Capitalist. 2023 [cited 2024 Feb 28]. Reference Source\n\nBadan Pusat Statistik: Statistik Penduduk Lanjut Usia. Direktorat Statistik Kesejahteraan Rakyat, editor. Jakarrta: Badan Pusat Statistik; 2023. 287 p. Reference Source\n\nBPS Jawa Timur: 2024. Provinsi Jawa Timur dalam Angka. Surabaya: BPS Jawa Timur; 699. Reference Source\n\nWorld Health Organization: Ageing and health.2022 [cited 2024 Feb 28]. Reference Source\n\nWirasamadi NLP, Adhi KT, Weta IW: Analisis Sisa Makanan Pasien Rawat Inap di RSUP Sanglah Denpasar Provinsi Bali. Public Heal. Prev. Med. Arch. 2015; 3(1): 72–77. Publisher Full Text\n\nKementerian Kesehatan Republik Indonesia: Klasifikasi Hipertensi.2018. Reference Source\n\nHandayani A, Srimiati M: HUBUNGAN FAKTOR MAKANAN DAN LINGKUNGAN DENGAN SISA MAKANAN LUNAK PASIEN DEWASA KELAS 2 DAN 3 RUANG RAWAT INAP RUMAH SAKIT GRHA PERMATA IBU KOTA DEPOK. J. Andaliman J. Gizi Pangan, Klin dan Masy. 2021 [dikutip 5 Mei 2023]; 1(1): 22–29. Reference Source\n\nDewi LS: FAKTOR-FAKTOR YANG BERHUBUNGAN DENGAN SISA MAKANAN PADA PASIEN RAWAT INAP DI RUMAH SAKIT DJATIROTO LUMAJANG.2015 [dikutip 5 Mei 2023]. Reference Source\n\nMegersa B, Haile A, Kitron U: Effects of dietary and health factors on nutritional status of children in pastoral settings in Borana, southern Ethiopia, August–October 2015. Arch. Public Health. 1 Desember 2021 [dikutip 5 Mei 2023]; 79(1): 111–169. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDahal M, Basnet A, Khanal S, et al.: Gender Difference in Food Choice and Eating Practice and Their Association with Health among Students of Kathmandu. Nepal. J Obes. 2022; 2022: 1–10. Publisher Full Text\n\nWHO: Hypertension. World Health Organization; 2023 [dikutip 13 Juni 2023]. Reference Source\n\nGillis EE, Sullivan JC: Sex Differences in Hypertension. Hypertension. 1 Desember 2016 [dikutip 13 Juni 2023]; 68(6): 1322–1327. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaranon R, Reckelhoff JF: Sex and Gender Differences in Control of Blood Pressure. Clin. Sci. (Lond.). Oktober 2013 [dikutip 13 Juni 2023]; 125(7): 311–318. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConnelly PJ, Currie G, Delles C: Sex Differences in the Prevalence, Outcomes and Management of Hypertension. Curr. Hypertens. Rep. 1 Juni 2022 [dikutip 13 Juni 2023]; 24(6): 185–192. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReckelhoff JF: Gender Differences in the Regulation of Blood Pressure. Hypertension. 2001 [dikutip 13 Juni 2023]; 37(5): 1199–1208. Publisher Full Text\n\nZhang J, Xu L, Li J, et al.: Gender differences in the association between body mass index and health-related quality of life among adults:a cross-sectional study in Shandong, China. BMC Public Health. 31 Juli 2019 [dikutip 5 Mei 2023]; 19(1): 1–9. Publisher Full Text\n\nSubekti F: Analisis Karakteristik Usia Lanjut Berhubungan dengan Status Gizi di Posyandu Lansia Dusun Wonogiri Jatirejo Lendah Kulon Progo.2013 [dikutip 5 Mei 2023]. Reference Source\n\nAkman C, Bakirdogen S, Akman C, et al.: The Impact of Serum Creatinine, Albumin, Age, and Gender on the Development of Contrast-Induced Nephropathy in Patients Exposed to Contrast Agent Upon Admission to the Emergency Department. Cureus. 20 Oktober 2020 [dikutip 13 Juni 2023]; 12(10). Publisher Full Text Reference Source\n\nOhwada H, Nakayama T, Kanaya Y, et al.: Serum albumin levels and their correlates among individuals with motor disorders at five institutions in Japan. Nutr. Res. Pract. 26 Januari 2017 [dikutip 13 Juni 2023]; 11(1): 57–63. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nKhairun Nisa F, Farhat Y; Gizi Politeknik Kesehatan Kemenkes Banjarmasin Jl Haji Cokrokusumo No J et al.: Hubungan Cita Rasa Makanan, Jenis Kelamin Dan Lama Hari Rawat dengan Sisa Makanan Pasien Rumah Sakit. J. Ris. Pangan dan Gizi. 1 Maret 2018 [dikutip 13 Juni 2023]; 1(1). Publisher Full Text Reference Source\n\nYulianti I: Sisa Makanan dan Kepuasan pada Pasien Rawat Inap Kelas III di Rumah Sakit Swasta di Gresik.2013 [dikutip 13 Juni 2023]. Reference Source" }	[ { "id": "351120", "date": "23 Jan 2025", "name": "Guduro Beriso Ware", "expertise": [ "Reviewer Expertise My research Areas Includes food security", "livelihood", "gender", "technology adoption", "and climate change." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study addresses a significant concern regarding the nutritional status of elderly individuals, particularly focusing on the unique health challenges faced by women. By employing a quantitative cross-sectional design, the research collects measurable data that offers clear insights into the health indicators and nutritional status of the participants. It emphasizes important health indicators, such as serum albumin levels and nutritional status, which are essential for evaluating the overall health of older adults. By analysing the differences in nutritional status and serum albumin levels between men and women, the study enhances our understanding of gender disparities in health among the elderly. Conducted within a specific cultural and geographic context (Surabaya, Indonesia), this research provides valuable insights that could inform local healthcare practices and policies. However, the quantitative approach may overlook the personal experiences and perceptions of elderly individuals regarding their nutrition and health, potentially missing valuable contextual insights.\nTherefore, I Approve this paper for indexing, with the suggestion that the authors acknowledge the limitations of their study and encourage future researchers to address these gaps in their work.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-376
https://f1000research.com/articles/13-375/v1	23 Apr 24	{ "type": "Systematic Review", "title": "The Model and Efficacy of Online Nurse-led on the Clinical Outcome of Diabetic Foot Ulcers: A Systematic Review of Randomized Controlled Trials", "authors": [ "Maria Komariah", "Juan Alessandro Jeremis Maruli Nura Lele", "Audrey Gunawan", "Keyzha Amartya Adammayanti", "Dewa Vighneswara", "Karlos Berlusconi Sihaloho", "Hesti Platini", "Sidik Maulana", "Shakira Amirah", "Joue Abraham Trixie", "Juan Alessandro Jeremis Maruli Nura Lele", "Audrey Gunawan", "Keyzha Amartya Adammayanti", "Dewa Vighneswara", "Karlos Berlusconi Sihaloho", "Hesti Platini", "Sidik Maulana", "Shakira Amirah", "Joue Abraham Trixie" ], "abstract": "Background: The most frequent consequence for those with diabetes mellitus is diabetic foot ulcers. Diabetic ulcer treatment must be done properly and on time. The development of online-based intervention by nurses, such as messaging health, may improve the clinical outcome of diabetic foot ulcers by providing easier access, more convenience, and cost-effectiveness, especially for patients in rural areas.\nObjective: This study aimed to perform a systematic review and meta-analysis the models and efficacy of online nurse-led intervention on clinical outcomes of diabetic foot ulcers.\nMethods: Randomized Controlled Trials were searched by using PubMed, Scopus, and Google Scholar. The final inclusion study analyzed and synthesized by tabulation, clusterization, contextual and thematic approach, and assessed risk of bias by using RoB 2.0. The study used Mantel Haenszel method.\nResults: Five randomized controlled trials with 1399 total number of participants were included. There are three studies with some concerns and two studies with low risk of bias. The nurse-led model for diabetic foot ulcer care consists of phone and web-based that conducted by nurse (community nurses and clinical nurses) and doctor specialists are involved in the service. The meta-analysis for amputation outcome showed that telehealth has more favor amputation number with RR 0.6 (95 % CI 0.43 - 0.84; p = 0.003). For healing wounds and mortality outcome, telehealth with RR 1.07 (95% CI 0.99 - 1.16; p = 0.11) and RR 1.37 (95 % CI 0.78 - 2.40; p =0.28), respectively.\nConclusions: Phone and web-based may improve clinical outcome of diabetic foot ulcers in terms of amputation outcome, but standard care still more favor in higher wound healing outcome and significantly lower mortality rate.", "keywords": [ "diabetic foot ulcers", "amputation outcome", "healing wound", "mortality outcome" ], "content": "Introduction\n\nDiabetes mellitus is a chronic disease caused by unbalance of insulin production or sensitivity, and a higher level of blood glucose.1 Complications caused by diabetes can affect the function of the heart and blood vessels, kidneys, nerves, and foot ulcers that occur in 40 to 60 million diabetic patients globally.2 Diabetic ulcers are one of the most common complications experienced by diabetes mellitus.3 The increase in diabetes mellitus patients has an impact on increasing the incidence of diabetic ulcers because 15% of patients with diabetes mellitus have diabetic ulcers.4\n\nThe prevalence of diabetes is expected to increase from 9.3% (463 million) in 2019 to 10.2% (578 million) in 2030 and 10.9% (700 million) in 2045.5 Treatment of diabetic ulcers must be done correctly and on time. Inadequate treatment can lead to lower extremity amputation with approximately 85% incidence.4,6 Standard care in the management of diabetic ulcers is usually through appointments with multiple health professionals depending on the severity. This can burden patients to get treatment.7 In areas where access to health care is challenging but has a good network, telehealth can be a solution. Telehealth is a health service that is accessed through telecommunication which is adapted from conventional practice. Telehealth can reduce potential healthcare disparities.8 Telehealth has a role in dealing with diabetic ulcers because long-distance treatment can provide easier access, more convenience, and cost-effectiveness, especially for patients in rural areas.7\n\nM-Health is an interactive mobile health application developed for behavioral modification and well-being interventions.9 M-Health is designed for a specific health condition to summarize the healthcare interventions accurately and reliably.10 The use of m-Health in diabetes education, exercise tracking by a fitness tracker, manual dietary tracking, incorporating blood glucose readings, diabetes education, and communication with healthcare providers can reduce A1C by 0.3% in type 1 diabetes mellitus and 0.8% in type 2 diabetes mellitus after 12 months of m-Health intervention when compared with the standard care.11 Research is growing with the delivery of health care remotely via an application on a mobile device (called mobile health or m-Health). Mobile phones are ubiquitous in society, and several software platforms, especially web-based and software applications, have been developed for diabetes self-management. Besides, m-health is improving the outcome of care, and the role of nurses is also important in integrating the foot ulcer care model. There has been a previous meta-analysis of telehealth for diabetic foot ulcer care.12 However, included studies of study just only three RCTs studies and does not discuss the related models of online-based intervention for foot ulcer care. In this regard, the study focused to perform a systematic review and meta-analysis of the effect of telehealth on clinical outcomes of diabetic foot ulcers.\n\nTherefore, the aim of telehealth interventions across the diabetic foot ulcer care continuum is to assess the efficacy of telehealth-based technologies that can substantially modify DFU risk factors such as screening and identifying loss of protective sensation, monitoring for lesions, palpation, and auscultation in individuals with DM foot during follow-up appointments so as to develop lower limb amputation prevention strategies, improve patient quality of life and reduce economic burden.12–14 Here, we conducted a systematic review and meta-analysis of all available studies to assess the efficacy of telehealth in diabetic foot ulcers.\n\nNurses play an important role in preventing and controlling diabetic foot ulcers (DFU) across the continuum of care. As a result, they can modify DFU risk factors such as screening and identifying loss of protective sensation, monitoring the presence of a lesion, palpation, and auscultation in individuals with DM foot during follow-up appointments.12,13 By educational initiatives, risk assessment, and diabetes foot care, nurses’ knowledge of DFU is crucial in preventing foot ulcers and lower limb amputations. It has been found that nurses who were knowledgeable and had a pleasant attitude were more likely to participate in ulcer care.13,14\n\n\nMethods\n\nPRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) statement rules were used to conduct a systematic review.15,35 Searches for included studies were conducted on databases including PubMed, Cochrane, and Google Scholar. We conducted a search using the terms (diabetic foot ulcer OR diabetes) AND (web OR phone OR telemedicine) AND (clinical outcome OR amputation OR healing OR mortality. The details of the search strategy can be seen in the Extended data.35\n\nThe eligibility criteria for inclusion and exclusion in this review were established based on the PICO (Population, Intervention, Comparison, and Outcome) framework. The population of interest consisted of patients with diabetic foot ulcers diagnosed based on clinical presentation, physical examination, and other diagnostic tests such as X-ray, MRI, or biopsy. The interventions included were randomized controlled trials that examined the effects of online nurse-led interventions on the clinical outcomes of diabetic foot ulcers. The comparison intervention was standard or usual care, which is care that is provided solely through face-to-face interaction and not through telehealth. The eligible studies assessed clinical outcomes such as wound healing, amputation, and mortality rate through validated clinical and laboratory measures. The outcomes were assessed by trained healthcare professionals who were blinded to the intervention allocation. Moreover, the exclusion criteria include articles that have not undergone peer review, were published before 2010 for relevantion, articles that were not in English, and were not randomized controlled trial (RCT).\n\nThe main results to show the efficacy of phone and web-based telehealth for clinical outcomes of patients with diabetic foot ulcers were amputation, healing wounds, and mortality. The results were analyzed and synthesized through a qualitative approach in the form of tabulation, clusterization, thematic analysis, and contextual descriptions. The data items that will be visualized including author and year, mean or median of age, study design, country of the study, participant characteristics, number of participants, type of telehealth, and outcome data.\n\nMeta-analysis was performed by using the Review Manager 5.4 statistical package (Cochrane Collaboration, Oxford, UK). The clinical outcome of the dichotomous data was reported as a risk ratio (RR), and an appropriate 95% confidence interval (95% CI) was calculated. Pooled effect estimates were generated using the Mantel-Haenszel method formula in the form of a risk ratio (RR) with their corresponding 95% confidence intervals (CI). The inconsistency index (I2) and subgroup analysis using the Chi-square test were utilized to explore potential sources of heterogeneity. A p-value of less than 0.05 and an I2 of more than 50% were considered significant for heterogeneity. To account for interstudy variability, a random-effects model was utilized regardless of the heterogeneity in the studies. We considered a two-tailed p-value with statistical significance set at p ≤ 0.05.\n\nThe Revised Instrument for Risk of Bias in Randomized Trials (RoB 2.0), which has five domains for initiative studies, was used to assess the risk of bias in the final inclusion studies. The authors used the Cochrane algorithm to assess risk of bias. The results are then added to the domain file bias (.xlsx). The file will then be uploaded to his ROBVIS website and the output data will be displayed properly.\n\n\nResults\n\nBased on the results of the article search in the main sources (PubMed, ScienceDirect, and Google Scholar), 632 articles were identified. Of these, nine of them are duplicate studies. Thirty-eight studies were excluded at the screening stage because they were grey literatures. Nine studies didn’t have the same context as PICO that has been proposed. In detail, four studies did not have the same population, one study had different interventions, two different comparison studies, and two had different primary and secondary outcomes (see Figure 1).\n\nThere were five final articles that matched the inclusion or eligibility criteria with 1399 total participants. Four final inclusion studies were classified as having blinding techniques and one study with open-label techniques.16–19 The types of online nurse-led interventions used were telephone and web-based. The participants involved were diabetic patients with complications of diabetic foot ulcers.\n\nThe included studies were all randomized controlled trials (RCTs). These studies were conducted in five different countries, including Norway (2), Denmark (2), and Australia (1), with a total of 1094 patients diagnosed with diabetes foot ulcers. The interventions used in the studies included an interactive web-based ulcer record and a mobile phone in two of the studies, a mobile phone in two other studies, and a software-based system in one study. The interventions were all online nurse-led, with the aim of improving the clinical outcomes of patients with diabetic foot ulcers (see Table 1).\n\nThe online nurse-led model utilizes both a mobile application and a web-based application. It involves community nurses and clinical nurses, as well as specialist doctors. Table 2 and Figure 2 show the model of an integrated online nurse-led foot ulcer care system. The diagram illustrates that nursing activities are conducted through online interventions by a community nurse who performs assessments and interventions. The assessment results are reported by community nurses via the web, and the planning is carried out in interprofessional collaboration involving specialist nurses and doctors. Specialist nurses review the results and provide feedback that can be discussed through a mobile phone or email. Additionally, specialist nurses conduct home visits at least once a week. This model enables integrated care across different health sector levels and has the potential to be implemented in rural areas.\n\nWithin five final inclusion studies, there was just data from Rasmussen et al. (2015)18 in mortality and Manuel (2012)20 in healing outcome statistically significant with p = 0.0001, respectively (Table 3).\n\n* Significant.\n\nIn this study, we recommend interactive telehealth. Interactive telehealth makes the relationship between doctors and patients better through two-way communication.18 Where doctors do not need to meet in real time but respond to the transmission of information from patients in real time. Meanwhile, non-interactive telehealth is the opposite. Patients act more passively and nurses and doctors are more active. Thus, interactive telehealth is much more recommended because there is better communication between doctors and patients.19\n\nAll five studies were included in the amputation analysis, four studies in healing wounds, and five studies in mortality analysis. The meta-analysis for amputation outcomes showed that the online nurse-led intervention group has a higher number of events with a Risk Ratio (RR) of 0.66 (p = 0.01; 95% CI 0.47-0.92). A funnel plot is a graphical representation of individual studies precision and effect size in a meta-analysis (see Figure 3). In a meta-analysis investigating the effectiveness of telemedicine treatments for amputation outcomes. The distribution of studies in the funnel plot appears homogenous, suggesting that there is little or no publication bias and the studies are similar in terms of their precision and effect size. This indicates that the studies are comparable and the results of the meta-analysis are robust. A homogenous funnel plot also suggests that the overall estimate of treatment effect is likely to be reliable (see Figure 4).\n\nThe Mantel-Haenszel analysis for healing wound outcome showed that standard care has more favor than the online nurse-led intervention group with RR 1.02 (p = 0.61; 95% CI 0.94-1.11). A funnel plot is a graphical representation of individual studies’ precision and effect size in a meta-analysis (see Figure 5). In a meta-analysis investigating the effectiveness of telemedicine treatments for DFU. The distribution of studies in the funnel plot appears homogeneous, if the plot is symmetrical, such as an inverted V, this is interpreted as indicating that there may be no publication bias. If the plot is asymmetric, the interpretation is likely to be publication bias. In this funnel plot, the data is shown to be homogeneous indicating that the overall estimate of the treatment effect tends to be reliable (see Figure 6).\n\nThe Mantel-Haenszel analysis for mortality outcome showed that standard care is not statistically significant. Standard care group with RR 1.48 (p = 0.30; 95% CI 0.70-3.12). nurse-led care group these data indicate that standard care usage is more recommended for reducing the mortality rate (see Figure 7). The distribution of studies in the funnel plot may appear heterogeneous, but there may be one study, Rasmussen et al. (2015), that appears as an outlier (see Figure 8). This outlier study may have reported a substantially larger effect size or a smaller standard error compared to the other studies in the meta-analysis.\n\nThere are two studies with a low risk of bias, three studies with some concern, and zero research with a high risk of bias, according to the risk of bias assessment performed using RoB 2.0. D5 dominated the bias risk domain with some level of concern (bias in the selection of the reported result). Whereas D1 (bias occurring in the randomization process), D3 (bias due to missing outcome data), and D4 (bias due to incomplete outcome data) dominated the risk of bias domain with a low-risk level (bias in the measurement of the outcome) (see Figure 9 and Figure 10).\n\n\nDiscussion\n\nChronic foot ulcers are a common complication of diabetes. These boils can last for months or even years. They can have a significant negative impact on an individual’s quality of life, are expensive to treat, and can lead to amputation of the affected limb.21 Treatment of diabetic ulcers must be carried out correctly and promptly. Inadequate treatment can lead to lower extremity amputation.4,6 Standard care in the management of diabetic ulcers is usually through appointments with several health professionals depending on the severity.22 The long-distance that is often traveled is the reason, and the slow follow-up is the main factor for the situation to worsen and can burden the patient to get treatment.23\n\nMobile health (m-Health) uses mobile technology to provide monitoring and interaction across multiple functions. Through this technology, patients can be more involved in their diabetes management, improve their diet, achieve better glycemic control, lose weight, and achieve better health outcomes while maintaining constant patient-provider communication.11 When compared to standard care, m-health is more efficient in remote care, providing more accessible, more convenient, and cost-effective access, especially for patients in rural areas.7 Telehealth can be a solution to improving health services, including the treatment and prevention of diseases.24,25 This service can improve health services in Indonesia, especially in areas with difficult access to health services.\n\nIn research conducted by Farmer, Blood glucose values were manually entered, and motivational messages (unrelated to blood glucose levels) were automatically sent to the phone via SMS by a server. The telehealth system offers a platform with the benefit of basing management on real-time data transfer, shared information between clinicians and patients, and the ability for quick data analysis to provide advanced decision assistance, in comparison to other systems.26 Online telehealth web-based technology can help avoid crowds in a pandemic situation. In one study, Huurne et al. conducted research on web-based technologies to improve healthcare services for individuals with chronic eating disorders. In the study he used a web-based treatment program to improve health care services, 54% of participants completed all tasks and programs to significantly improve BMI, physical, mental health, and quality of life.27,28\n\nThe current review showed that phone and web-based telehealth have has no better effect on wound healing than standard care. This is contradictory to research conducted by Stern et al., where the probability of healing for the control period was estimated to be 35.0%, and for the intervention, period to be 53.4%.29 This difference is not statistically significant as the two confidence intervals overlap. However, in a study conducted by Santamaria et al., intervention group patients had a positive healing rate of 6.82% per week. In contrast, controls had a negative rate of -4.90% per week (p = 0.012).30 The data has also shown the same indication for amputation outcomes. A meta-analysis conducted by Yammine K and Estephan M in 2021 showed the same result as our discussion (p = 0.003, RR 0.6). Telehealth services were proven to prevent amputation (p = 0.007, OR = 0.48), but not with wound healing rate (p = 0.4, OR = 1.35) and mortality (p = 0.2, OR = 1.66).31 However the study by Chumbler showed there was longer survival for the intervention group (telehealth) versus the control group (mean survival time 1348 vs 1278 days; p = 0.015). A multivariate analysis indicated that the telemonitoring program was associated with reduced 4-year all-cause mortality (p = 0.013, HR = 0.7, 95% CI 0.5–0.9). This data is contradictory to our result.32\n\nTelehealth is generally regarded favorably by both patients and clinicians, particularly as an adjunct to face-to-face care.7,8 Digital imaging, one of the m-Health facilities, has similar reliability to live assessment for assessing ulcers.7 The existence of technological developments allows telehealth to continue to implement health services according to the community’s needs by increasing the advances of the designed applications.33 Areas, where there is still a shortage of medical personnel, can apply telehealth services for diabetic wound control.\n\nThe findings of our integrative systematic review and meta-analysis have significant implications for practice in nursing and other healthcare professions, particularly in the management of diabetic foot ulcers. Our study highlights the potential benefits of online nurse-led interventions in improving the clinical outcomes of patients with diabetic foot ulcers. This model can be easily accessible, cost-effective, and can provide support to patients in remote or underserved areas.\n\nThe implication for nursing practice is significant, as it emphasizes the need for nurse-led interventions to be incorporated into the care plan of patients with diabetic foot ulcers. This can improve patient satisfaction, enhance patient education, and improve the quality of care provided. Furthermore, the online platform provides opportunities for nurses to practice in a more autonomous and innovative manner, resulting in better job satisfaction and improved professional development.\n\nThe study findings also have implications for other healthcare professions such as podiatry, wound care, and endocrinology. The integration of online nurse-led interventions can complement and enhance the care provided by other healthcare professionals, resulting in improved patient outcomes. It also highlights the need for multidisciplinary collaboration in the management of diabetic foot ulcers. Platini et al, also mentioned that telecoaching has the potential to enhance clinical and self-care outcomes for people with diabetes mellitus during COVID-19 and similar pandemics.34\n\nThe local government needs to conduct a more in-depth study of telehealth services and the local health office. Only patients with controlled diabetic ulcers can apply wound control through telehealth services. Thus, the patient does not need to come to a health facility just for control. However, if the wound has not been controlled, the patient still needs to visit a health facility. In addition to proposing telehealth services, the government still has to improve health service facilities in the regions.\n\nThis study has several limitations points: there was a potential heterogeneity caused by difference follow-up times in each study, the difficulty in finding several similar articles, and none of the studies discussed pharmacological therapy and lifestyle interventions. In addition, the heterogeneity in mortality outcomes was high.\n\n\nConclusion\n\nPhone and web-based telehealth can reduce the amputation rate of diabetic foot ulcers, but it has no better effect on wound healing and mortality rate than standard care. However, there are still debate about the method of telehealth usage, in-appropriate guideline for its usage, and real-time interaction needed. In the case of diabetic ulcer foot, the author would recommend interactive telehealth usage for a better outcome.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nZenodo: The model and efficacy of online nurse-led on the clinical outcome of diabetic foot ulcers: an integrative systematic review and meta-analysis of randomized controlled trials. https://zenodo.org/record/8309776. 35\n\nThis project contains the following extended data:\n\n- Appendix.docx (search strategy)\n\n- Extraction data telemedicine for diabetic foot ulcers.xlsx\n\nZenodo: PRISMA checklist for ‘The model and efficacy of online nurse-led care on the clinical outcome of diabetic foot ulcers: an integrative systematic review and meta-analysis of randomized controlled trials’. https://zenodo.org/record/8309776. 35\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe authors appreciated Universitas Padjadjaran, Bandung, West Java, Indonesia, for facilitating the database search to this scoping review.\n\nThe abstract for this study has been published in the Padjadjaran International Nursing Conference Book of Abstracts (http://pinc.fkep.unpad.ac.id/Book_of_Abstract.pdf).\n\n\nReferences\n\nSapra A, Bhandari P: Diabetes Mellitus. Stat Pearls; 2022.\n\nInternational Diabetes Federation: Diabetes Complications. International Diabetes Federation; 2020. Reference Source\n\nBekele F, Berhanu D: “Loss of a limb is not loss of a life”. Knowledge and attitude on diabetic foot ulcer care and associated factors among diabetic mellitus patients on chronic care follow-up of southwestern Ethiopian hospitals: A multicenter cross-sectional study. Ann Med Surg (Lond). 2021; 72: 103140. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcGuire J, Thomson A, Kennedy PG: The Biomechanics of Diabetic Foot Amputation [published online ahead of print, 2021 Apr 14]. Wounds. 2021; WNDS20210414-2.\n\nSaeedi P, Petersohn I, Salpea P, et al.: Global and regional diabetes prevalence estimates for 2019 and projections for 2030 and 2045: Results from the International Diabetes Federation Diabetes Atlas, 9th edition. Diabetes Res. Clin. Pract. 2019; 157: 107843. PubMed Abstract \| Publisher Full Text\n\nNagoba B, Gavkare A, Rayate A, et al.: Role of an acidic environment in the treatment of diabetic foot infections: A review. World J. Diabetes. 2021; 12(9): 1539–1549. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDrovandi A, Wong S, Seng L, et al.: Remotely Delivered Monitoring and Management of Diabetes-Related Foot Disease: An Overview of Systematic Reviews. J. Diabetes Sci. Technol. 2023; 17(1): 59–69. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKichloo A, Albosta M, Dettloff K, et al.: Telemedicine, the current COVID-19 pandemic and the future: a narrative review and perspectives moving forward in the USA. Fam. Med. Community Health. 2020; 8(3): e000530. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShanbehzadeh M, Kazemi-Arpanahi H, Kalkhajeh SG, et al.: Systematic review on telemedicine platforms in lockdown periods: Lessons learned from the COVID-19 pandemic. J. Educ. Health Promot. 2021; 10: 211.\n\nVarshney U, Singh N, Bourgeois AG, et al.: Review, Assess, Classify, and Evaluate (RACE): a framework for studying m-health apps and its application for opioid apps. J. Am. Med. Inform. Assoc. 2022; 29(3): 520–535. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Badri M, Hamdy O: Diabetes clinic reinvented: will technology change the future of diabetes care? Ther. Adv. Endocrinol. Metab. 2021; 12: 2042018821995368. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMishra SC, Chhatbar KC, Kashikar A, et al.: Diabetic foot. BMJ. 2017; 359: j5064. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbate TW, et al.: Nurses’ knowledge and attitude towards diabetes foot care in Bahir Dar, North West Ethiopia. Heliyon. 2020; 6(11): e05552. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbdullah WH, et al.: Capacity Building for Nurses’ Knowledge and Practice Regarding Prevention of Diabetic Foot Complications. Int. J. Nurs. Sci. 2017; 7(1): 1–15. Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021; 372: n71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFasterholdt I, Gerstrøm M, Rasmussen BSB, et al.: Cost-effectiveness of telemonitoring of diabetic foot ulcer patients. Health Informatics J. 2018; 24(3): 245–258. PubMed Abstract \| Publisher Full Text\n\nIversen MM, Igland J, Smith-Strøm H, et al.: Effect of a telemedicine intervention for diabetes-related foot ulcers on health, well-being and quality of life: secondary outcomes from a cluster randomized controlled trial (DiaFOTo). BMC Endocr. Disord. 2020; 20(1): 157. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRasmussen BS, Froekjaer J, Bjerregaard MR, et al.: A Randomized Controlled Trial Comparing Telemedical and Standard Outpatient Monitoring of Diabetic Foot Ulcers. Diabetes Care. 2015; 38(9): 1723–1729. PubMed Abstract \| Publisher Full Text\n\nSmith-Strøm H, Igland J, Østbye T, et al.: The Effect of Telemedicine Follow-up Care on Diabetes-Related Foot Ulcers: A Cluster-Randomized Controlled Noninferiority Trial. Diabetes Care. 2018; 41(1): 96–103. PubMed Abstract \| Publisher Full Text\n\nManuel P: A prospective, interventional study of the effectiveness of digital wound imaging, remote consultation and podiatry offloading devices on the healing rates of chronic lower extremity wounds in remote regions of Western Australia. Wound Practice & Research. 2012; 20(2): 103–109.\n\nKantor J, Margolis D: Expected Healing Rates for Chronic Wounds. Wounds. 2000; 12: 155–158.\n\nHicks JP, Allsop MJ, Akaba GO, et al.: Acceptability and Potential Effectiveness of eHealth Tools for Training Primary Health Workers From Nigeria at Scale: Mixed Methods, Uncontrolled Before-and-After Study. JMIR Mhealth Uhealth. 2021; 9(9): e24182. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSyed ST, Gerber BS, Sharp LK: Traveling towards disease: Transportation barriers to health care access. J. Community Health. 2013; 38(5): 976–993. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKomariah M, Maulana S, Platini H, et al.: A Scoping Review of Telenursing’s Potential as a Nursing Care Delivery Model in Lung Cancer During the COVID-19 Pandemic. J. Multidiscip. Healthc. 2021; 14: 3083–3092. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaulana S, Trisyani Y, Mirwanti R, et al.: The Potential of Cardiac Telerehabilitation as Delivery Rehabilitation Care Model in Heart Failure during COVID-19 and Transmissible Disease Outbreak: A Systematic Scoping Review of the Latest RCTs. Medicina (Kaunas). 2022; 58(10): 1321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFarmer A, Gibson O, Hayton P, et al.: A real-time, mobile phone-based telemedicine system to support young adults with type 1 diabetes. Inform. Prim. Care. 2005; 13(3): 171–177. PubMed Abstract \| Publisher Full Text\n\nAntor MB, et al.: Development of a Web-Based Telemedicine System for Covid-19 Patients. Intell. Autom. Soft Comput. 2021; 30(3): 899–915. Publisher Full Text\n\nTer Huurne ED, de Haan HA , Postel MG, et al.: Long-term effectiveness of web-based cognitive behavioral therapy for patients with eating disorders. Eat. Weight Disord. 2021; 26(3): 911–919. PubMed Abstract \| Publisher Full Text\n\nStern A, Mitsakakis N, Paulden M, et al.: Pressure ulcer multidisciplinary teams via telemedicine: A pragmatic cluster randomized stepped wedge trial in long term care. BMC Health Serv. Res. 2014; 14(1): 1–13.\n\nSantamaria N, Ogce F, Gorelik A: Healing rate calculation in the diabetic foot ulcer: Comparing different methods. Wound Repair Regen. 2012; 20(5): 786–789. PubMed Abstract \| Publisher Full Text\n\nYammine K, Estephan M: Telemedicine and diabetic foot ulcer outcomes. A meta-analysis of controlled trials. Foot (Edinb.). 2022; 50: 101872. PubMed Abstract \| Publisher Full Text\n\nChumbler NR, Chuang HC, Wu SS, et al.: Mortality risk for diabetes patients in a care coordination, home-telehealth programme. J. Telemed. Telecare. 2009; 15(2): 98–101. PubMed Abstract \| Publisher Full Text\n\nTedeschi C: Ethical, Legal, and Social Challenges in the Development and Implementation of Disaster Telemedicine. Disaster Med. Public Health Prep. 2021; 15(5): 649–656. Publisher Full Text\n\nPlatini H, Lathifah A, Maulana S, et al.: Systematic Review and Meta-Analysis of Telecoaching for Self-Care Management among Persons with Type 2 Diabetes Mellitus. Int. J. Environ. Res. Public Health. 2022; 20(1): 237. Published 2022 Dec 23. Publisher Full Text\n\nKomariah M, Lele JAJMN, Gunawan A, et al.: The model and efficacy of online nurse-led on the clinical outcome of diabetic foot ulcers: an integrative systematic review and meta-analysis of randomized controlled trials.2023. Publisher Full Text" }	[ { "id": "278628", "date": "29 May 2024", "name": "Cesare Miranda", "expertise": [ "Reviewer Expertise Diabetic complications", "diabetic foot" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Systematic Review is on a topic of relevance and general interest to the readers of the journal.\nI found that paper is well written and the study well thought .\nI believe there are other limitations that the authors should underline: for example the ethnicity of the studies included, the level of education of the patients etc.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [] }, { "id": "305255", "date": "27 Jul 2024", "name": "Marissa J. Carter", "expertise": [ "Reviewer Expertise Wound care research", "biostatistics", "clinical trial design", "systematic reviews' health economics", "epidemiology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a potentially interesting systematic review and meta-analysis in regard to telehealth (nurse-led interventions) vs standard of care approaches. However there are a number of problems with this studies, some of which are detailed below.\nThe manuscript would greatly benefit from two additional process: (a) a review by a statistician to sort out many of those problems; and (b) editing by a medical writer.\nIntroduction\nThe last paragraph beginning “Nurses play an important role…” Please insert this as a new paragraph after the sentence “ Besides, m-health is improving the outcome of care, and the role of nurses is also important in integrating the foot ulcer care model.” Then start a new paragraph with the sentence beginning “There has been a previous meta-analysis of telehealth for diabetic foot ulcer care.” That will allow for a better flow of the Introduction. You indicate that reference 12 is the systematic review/meta-analysis but this publication is neither. Please insert the correct reference. Since I do not know the systematic review the authors are referring to I cannot confirm that it included only 3 RCTs. You indicate that “Here, we conducted a systematic review and meta-analysis of all available studies to assess the efficacy of telehealth in diabetic foot ulcers.” I assumed that this would mean all kinds of studies, but in your eligibility criteria state that only RCTs qualify. This inconsistency must be fixed. In addition, why are you therefore conducting a similar systematic review compared to the previous one? Did the authors learn that new studies have since been published? This must be mentioned. Also, why restrict studies only to RCTs? Is there no value in including other types of studies?\n\nMethods and Results\n“The outcomes were assessed by trained healthcare professionals who were blinded to the intervention allocation.” Do you mean members of your study team? (It is also helpful in a systematic review to describe at the end what the members of your study team did in regard to this study.) “relevantion” Unclear. This sentence needs some rewriting for comprehension. It would be good to have further data on the patients (where available); for example, duration of diabetes I am a bit concerned about combining the studies for meta-analysis (were the study lengths different? (Nothing reported in your tables.) Are the interventions substantially different? Please comment and or justify your meta-analysis in the Discussion. “In this study, we recommend interactive telehealth. Interactive telehealth …” This paragraph would be better placed in the Methods section. “A funnel plot is a graphical representation of individual studies precision and effect size in a meta-analysis (see Figure 3).” Mention of using a funnel plot should be in the Methods section. Figure 3 is a forest plot. This needs fixing and I would add that to the figure legend. I see the same problem with your other outcomes and this needs fixing. There are also numerous other problems with your forest/funnel plots regarding mortality in terms of description; for example, in Fig 7 it looks as though the intervention groups are wrongly labelled in the diagram. (I would dispense with the funnel plots for mortality and wound healing.) “All five studies were included in the amputation analysis, four studies in healing wounds, and five studies in mortality analysis. The meta-analysis for amputation outcomes showed that the online nurse-led intervention group has a higher number of events with a Risk Ratio (RR) of 0.66.” First, you have 4 studies in your forest plot and second the higher events are in the standard of care group. “and zero research with a high risk of bias” Should be stated as no studies with a high risk of bias.\n\nDiscussion.\nChronic foot ulcers are not boils! “Our study highlights the potential benefits of online nurse-led interventions in improving the clinical outcomes of patients with diabetic foot ulcers.” That conclusion is not warranted. Amputation rates are better but there’s no conclusion regarding healing rates and mortality. There may be several reasons why your study appears to contradict the literature and this needs some additional in-depth discussion. Another limitation is the geography of the countries involved in the studies you reviewed. There also needs to be a serious discussion on the types of studies used as evidence. Why did you restrict the studies to RCTs? You quote extensive literature findings but many of these are not RCTs. It's not straightforward to compare results of different study types.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-375
https://f1000research.com/articles/13-374/v1	23 Apr 24	{ "type": "Research Article", "title": "Effect of radiotherapy on microhardness and surface morphology of pretreated primary teeth with silver diamine fluoride: an in vitro study", "authors": [ "Simran Das", "Nilima Thosar", "Anurag Luharia", "Swaroop Narayan Mohanty", "Nishi Malviya", "Rutuja Ragit", "Nilima Thosar", "Anurag Luharia", "Swaroop Narayan Mohanty", "Nishi Malviya", "Rutuja Ragit" ], "abstract": "Abstract Background: Children with head and neck cancer undergo radiation therapy, which has proved to be a successful treatment option. One of the common side effect of radiation therapy has been radiation induced caries. This is not as a result of the decreased salivary flow, but rather as a result of the direct impacts of these harmful rays on the enamel of the teeth. Silver diamine fluoride (SDF) is an effective remineralising agent for initial carious lesions and prevents demineralisation of the already deep carious agent. Various studies have also proved its effectiveness in improving the microhardness of the teeth. Hence, the objective of this study was to evaluate whether radiotherapy causes changes in the microhardness and surface morphology of enamel in primary teeth pretreated with SDF. Method: 22 primary teeth samples were divided into two groups with 11 samples in each group. The study group samples were pretreated with SDF and in the control group no pretreatment was done. Both groups were subjected to radiotherapy of 60 Gy radiation for a duration of 30 days. The samples were tested using the Vickers microhardness test and scanning electron microscope (SEM) analysis for surface morphological changes post radiotherapy. Results: It was found that there was a statistically significant difference (p<0.001) in mean microhardness values between the two groups. The mean microhardness of the SDF group (254.07 ± 35.84) was significantly higher that the control group (88.18 ± 6.79). SEM image of enamel of control teeth displayed loss of smooth homogeneous surface and more amorphous structures were seen which was very evident in comparison to the SDF group. Conclusion: Following radiation therapy, SDF application led to greater microhardness of the enamel surface and less morphological alteration in the surface enamel of primary teeth.", "keywords": [ "Head and neck cancer in children", "Radiation therapy", "Primary teeth", "Silver diamine fluoride", "Microhardness of primary teeth" ], "content": "Introduction\n\nA large number of children around the world suffer greatly from cancer, and it is considered one of the most fatal diseases known to mankind (more information here).\n\nAlthough head and neck tumours in children are very uncommon, they have been on the rise in the recent years and becoming more and more common.1 Head and neck cancers (HNC) make for 5% of all pediatric cancers.1 Radiation therapy (RT) is a crucial component of the multimodality approach to treating HNC in children.1 Complex considerations in treatment planning may be necessary depending on a number of variables, such as the location, tumour size, and molecular features.1 Treatment results in direct and indirect harmful effects on the oral cavity, one of the most severe being radiation induced caries.2\n\nPost-radiation caries advance quickly and are quite damaging to the dental tissue.3 All the common side effects can manifest within the first three months of RT.3 Xerostomia induced due to radiation of the head and neck is one of the most common adverse effects seen which causes alteration in the saliva production which in turn affects the oral flora causing increase in the incidence of caries.3\n\nThe increased amount of caries incidence could also be due to the direct effect on the mechanical and physical properties of the teeth.2 Surface hardness, mineral and organic contents of enamel and dentine respectively with carbonate, phosphate, hydrocarbons and amide are all shown to be reduced after RT.2 The rods in primary teeth are thinner and denser, there are many micro porosities, some of the rods are exposed, and there is a significant amount of carbonate addition. Due to all of these circumstances, primary teeth are extremely vulnerable to radiation caries and develop severe carious lesions.2 Therefore, all efforts to manage such type of patients with severe caries should be redirected towards prevention. Effective preoperative dental care, routine dental examination, and regular topical fluoride administration can help in solving this problem.4\n\nSDF is an effective agent in remineralising initial carious lesions and arresting advanced caries.5 Streptococcus mutans and lactobacilli respond favourably to its antibacterial activity, demonstrating its anticariogenic effects.5 Its mechanism of action includes piercing the bacterial cell wall causing the impairment of deoxyribonucleic acid (DNA) replication and cell wall damage by the silver nitrate nanoparticles. Hence it prevents further demineralization of the already carious lesion.5 Staining caused by SDF on the tooth and adjacent structures is a significant drawback.6 However, SDF has been proved to increase the microhardness of the tooth in various in vivo and in vitro studies.5,7\n\nChildren with HNC have to undergo frequent radiation exposure compromising the oral health and causing extensive carious lesions.2 For such patients comprehensive dental treatment may be required. Due to such issues, primary teeth enamel of such children can be protected by pre-treating with SDF application prior to radiation exposure. Considering the beneficial effects of SDF the current study was undertaken to evaluate and compare the effect of RT on microhardness and surface morphology of pre-treated primary teeth with SDF and without any pre-treatment.\n\n\nMethods\n\nThe sample size was calculated using 95% probability, showing a statistically significant difference using the alpha level and power 80% by using nMaster software (Version 2.0), Rstudio (RRID:SCR_000432) may be able to perform similar tasks and is available for free. It was calculated using the formula for Qualitative data with the mean and standard deviation obtained from previous research. The formula utilised z∝+zβ2δ12+δ22kΔ2 where Zα is the level of significance at 5% level of significance i.e. 95% confidence interval, Zβ is the power of test, the δ1is the standard deviation of control group,δ2is the standard deviation of SDF group and Δbeing the difference between the mean of the two groups. According to this formula n was determined as 10.35 per group. So, the minimum sample size calculated was 11 for each group and total 22 samples were taken.\n\nInclusion criteria was caries free primary teeth and primary teeth nearing exfoliation. Exclusion criteria was carious primary teeth and primary teeth with developmental defects and cracks. Tooth samples were collected from the patients who visited the department of Pediatric and Preventive Dentistry and had to undergo extraction. Teeth were not specifically extracted for this study but which were indicated for extraction. Written informed consent was taken from the parents of the patients before extraction. Out of these, samples which met the inclusion criteria were included in the study.\n\nA total of 22 freshly extracted or exfoliated primary teeth were taken from children ranging in the age of 6-12 yrs. 5.25% sodium hypochlorite (Prime dental) was used to clean the primary teeth by soaking for one minute and then ultrasonic scaling (Woodpecker UDS-P ultrasonic scaler) was performed to remove any debris on the surface of the teeth. The samples were kept immersed in distilled water for no more than three months before the study was carried out.\n\nThe tooth samples were divided randomly into two groups of 11 samples each. Group 1: the SDF group and group 2: the control group. The primary teeth samples were cut 2mm below the cemento-enamel junction (CEJ) with diamond disks (Brasseler USA, Savannah, GA) and high speed handpiece (Air Rotor) (NSK, Japan). They were then mounted in self-cure acrylic resin using circular metallic moulds of 1.5-centimeter (cm) diameter and 1.5 cm height (Circle Frame Die Cut, Topiky), and the buccal surfaces of the teeth were exposed. An area of 5 × 5 mm was exposed on the buccal surface of all the samples. Polishing of the mounted teeth was carried out using silicon carbide paper of 200, 600, 800, and 1200-grit sequentially for one minute each to obtain a smooth surface on all sides except on the exposed buccal surface of the primary teeth. They were then stored in artificial saliva of pH7.0 containing 0.9 mM PO4, 1.5 mM Ca and 150 mM KCl in 20 mM Tris buffer for 37 c. To achieve this ratio 122.48 milligram (mg) of monopotassium phosphate (KH2Po4),220.53 mg of calcium chloride (CaCl2), 11.175 gram (gm) of KCl and 2.422 g of Tris buffer was used in 100 ml of deionized water. All the quantities were measured using balanced weighing machine (ADVENTURER ANALYTICAL, AX124/E, OHAUS). The pH of the artificial saliva was adjusted to 7 using digital pH meter. Standardized instructions were followed from the manufacturer for SDF (Kids-e-Dental) application before radiation therapy.\n\nAll the 22 samples were exposed to a daily fraction of 2 Gy each day for five days, followed by a two-day interval for six weeks resulting in a total dose of 60 Gy. A total of 30 daily fractions were completed. This protocol was developed in the “American College of Radiology (ACR)” and is traditionally used for patients suffering from Hodgkin’s lymphoma.8\n\nThe irradiation process was carried out in a cancer hospital with the facility of RT. The samples were irradiated on a Vital Beam (Life saving radiotherapy linear accelerator) (Varian Medical System international, India) with photon energy of 6 megavolt (MV) at a distance of 100 cm from the surface of the samples with 15X15 cm2 field size. The monitor units were calculated for 2 Gy per fraction (Figure 1 and 2). A uniform irradiation was received by all the samples of both the groups. After every fraction of 2 Gy of radiation, the samples were placed in new artificial saliva which was renewed daily. All the samples were then transferred in an incubator (Sesw 28 L bacteriological incubator) at 37o C to stimulate the normal body temperature of an individual.\n\nSurface microhardness (SMH) of the samples was tested by a Vickers microhardness testing machine (MITUTOYA, Japan) under a load of 50 grams for 10 seconds. The microhardness for each sample was assessed at five different sites within the sample, 300 μm apart from each other and their mean was considered as the final microhardness for that particular sample. Two representative samples from each group were prepared to be evaluated using a SEM (JEOL JSM-6380A). The samples were scanned at power of 100X, 500X and 1000X magnification and photomicrographs were taken to observe the structural changes in the enamel.\n\nDescriptive and analytical statistics were done. The data was represented in mean, median and standard deviation. The normality of continuous data was analyzed by Shapiro-Wilk test. A nonparametric test called the Mann-Whitney U test was used which enables two groups to be compared without assuming that the data are regularly distributed. SPSS software (Statistical Package for Social Sciences) Version 24.0 (IBM Corporation, Chicago, USA) (RRID:SCR_002865) was used. The p value <0.05 was considered to be statistically significant.\n\n\nResults\n\nIn Figure 3 the mean microhardness values after RT of the control and SDF group is compared27,28. It was found that there was statistically significant difference (p<0.001) in mean microhardness values between the two groups. The mean microhardness of the SDF group (254.07 ± 35.84 Vickers pyramid number) was significantly higher that the control group (88.18 ± 6.79 Vickers pyramid number).\n\nSEM images29 of SDF samples at 100X (Figure 4) revealed a surface that was smooth and had less dentine collagen fiber exposed. At 500 X (Figure 5), some amount of surface roughness was seen. At 1000X (Figure 6) showed dense granular structures of spherical grains. Such appearance is visible only in sample viewed under high power magnification. No evident discontinuity was observed on the enamel surface.\n\nSEM images of the control group samples at 100X (Figure 7) showed discontinuity of the buccal contour due to exposure from radiation. At 500X (Figure 8) showed progressive morphological alterations on the enamel surface. The enamel surface showed surface irregularities and cracks. SEM images of the control group samples at 1000X (Figure 9) indicated that the peritubular structure was gradually destroyed, which caused the tubules to gradually get obliterated. It also showed amorphous structures. After comparing Figure 6 and Figure 9, it was found that the SEM image of the enamel of the control teeth displayed loss of smooth homogeneous surface which was very evident in comparison to the SDF group. More amorphous structures were seen in the SEM images of the control group than the SDF group.\n\n\nDiscussion\n\nTopical fluorides to prevent radiation caries in patients HNC has been suggested by various authors.9,10 Kielbassa AM et al (1997)11 and Fränzel W et al (2006)12 recommended the biannual or quarterly use of 1.25% and 5.6% of NaF varnish respectively. Use of 1% neutral NaF gel has been suggested by Dreizen S et al (1977)9. Together, these studies showed how fluoride therapy can be used to prevent radiation caries, and dentists should always recommend its use while dealing with patients of HNC. The positive results obtained from the present study that is the mean microhardness of the SDF group being significantly higher from the control group suggest fluoride application in the form of SDF in preventing radiation caries in children.\n\nBoth an antibacterial and remineralising agent, SDF is a solution consisting of silver nitrate and fluoride. By lowering biofilm counts and preventing collagen deterioration, the product encourages the remineralization of enamel and dentin, halting the spread of caries which in turn arrests the carious lesion and its progression.13 In cases where other options aren't accessible, SDF can be used to control caries. To combat fear and anxiety in very young children to extensive dental treatment, SDF which is a low-cost simple method, can be used as a conservative treatment. It has therefore grown its acceptance in caries management.13\n\nChu CH et al (2008)7 in his ex vivo study found that SDF aided in prevention of progression of arrested coronal caries in primary teeth of preschool children and it also showed potential to promote enamel SMH, decrease enamel surface mineral loss, and inhibit cariogenic growth.7 Their results are in accordance to the current study in which the enamel SMH of the SDF group were greater than the control group. Findings from the study of Prakash M et al (2021)14 suggested that single application of SDF treated tooth is beneficial in increasing the microhardness of dentin surfaces as compared to non-SDF treated surfaces. But in their study SDF in combination with Potassium iodide (KI) was used which could improve carious dentin microhardness closer to that of a sound dentin surface in comparison to 38% SDF.14 However, in the present study a single application of commercially available SDF solution was used without the combination of KI.\n\nA tooth's mineral composition has a direct impact on the changes seen in the microhardness.15 It was reported in the study of Li YJ et al (1984)16 that the microhardness of demineralized enamel and dentine increased after SDF treatment. When treated with SDF, silver chloride and silver phosphate were reportedly almost completely insoluble or only slightly soluble and were found on the dentine surface from various studies.16 These precipitates suggest that a layer of insoluble protection was formed to stop demineralization of enamel and dentine also further losing calcium and phosphorus. Another ex vivo study by Mei ML et al (2014)17 reported that after the application of SDF, a dense and highly remineralized surface layer was discovered that was abundant in calcium and phosphate.17 This is how SDF treatment hardened the surface of the arrested lesions.\n\nConsidering the beneficial effects of SDF towards the microhardness of the teeth. The present study had planned to pretreat the surfaces of primary teeth before exposure to RT.\n\nSeveral studies have been conducted using permanent teeth to evaluate the effect of radiation exposure in the context of oral cancer.3 But in the present study primary teeth were considered as children are likely to undergo radiation exposure at 6-12 years old. For such an age group both sets of teeth are present in the oral cavity.2 The primary teeth have thin and aprismatic enamel with irregular enamel rods which further can get affected with structural disturbances while undergoing radiation exposure.2 Hence only primary teeth were selected for the study.\n\nLu H et al (2019)18 and Gonçalves LMN et al (2014)19 observed a reduction in the enamel microhardness close to the dentinoenamel junction region, while de Siqueira Mellara T et al (2014)20 observed, first, a decrease and then an increase in microhardness. No changes have been reported by some studies,21,22 while others recorded an increase in microhardness,19,20 and some have reported decreases in microhardness21,22 after RT. In the current study, a statistically significant difference (p<0.001) was observed in the enamel of primary teeth pretreated with SDF compared to the control group where no pretreatment with SDF was done. A 188.12 % increase in microhardness was seen with SDF group when compared to control group after RT.\n\nAfter six weeks treatment of radiation exposure primary teeth pretreated with SDF samples had values of 254.07 mean Vickers pyramid number which is more when compared to a study by Mante FK et al (2022).23 Variation in results with respect to study by Mante FK et al (2022)23 is because in their study they had used permanent teeth samples. But the present study had used primary teeth samples. The difference in microhardness values can be attributed to morphological differences in primary teeth enamel as compared to permanent teeth enamel.\n\nContrary to other studies on permanent teeth, which either found that the microhardness of irradiated enamel is lower than that of nonirradiated enamel24 or that the microhardness is unaffected by radiation.22,10 The current study, however used primary teeth, and it is possible that they would react to RT differently. Ionizing radiation may cause mineralized tissues' crystal structures to reorganize, which would change their physical properties, including structural microhardness, according to studies using permanent teeth.20\n\nSDF is said to form a coating with a high silver content when applied on enamel, deposits of silver were discovered on the surface penetrating into a depth of 20–40μm.25 Other researchers have shown that SDF treatment causes silver to be incorporated into hydroxyapatite, and it may help to enhance surface hardness.12,17 Surface hardness may rise as a result of rapid production of fluorohydroxyapatite due to SDF's high fluoride content (44,800 ppm).17 The ability of teeth treated with SDF to resist demineralization, stop the progression of caries, and simultaneously inhibit the development of new caries can be explained by the significant increase in enamel hardness. Because of this, SDF is more effective than other caries preventative treatments in preirradiated patients, such fluoride gels containing 5% NaF (22600 ppm) and stannous fluoride (1,100 ppm).23 However, the blackish stain formed after the application of SDF may encourage its application only on the posterior teeth.23\n\nThe orientation of the prisms that make up tooth enamel determines its anisotropic performance and impacts its mechanical properties. As previously documented for bovine teeth,22 SEM revealed morphological changes in the enamel structure, which were characterized by a more disordered prismatic structure as the cumulative dosage of radiation grew to 60 Gy. This change in the crystalline structure of the enamel is one of the possible reasons for the increased risk of dental caries following RT.20 Taking these changes in consideration, SDF application was done in the current study to prevent these ill effects from occurring which was not done in the previous studies.\n\nThe SEM images of the enamel surface of the SDF pre-treated tooth samples showed a relatively smooth surface with few dentine collagen fibres exposed. Dense granular structures of spherical grains were found at higher magnification of 1000X. The control group's contour discontinuity was more obvious than it was in the SDF group. The SDF-pretreated enamel showed no obvious discontinuity. Prisms were clearly structured and surrounded by interprismatic zones in the enamel of the SDF samples.\n\nThe buccal contour was disrupted in the enamel without any previous treatment. Images obtained through SEM examination revealed both enamel and dentin to have undergone gradual morphological changes. After 60 Gy, superficial fractures on the enamel surface were visible. The tubules were gradually destroyed as a result of the peritubular structure degrading over time. Loss of smooth homogeneous surface is very evident in comparison to the SDF group. It also showed amorphous structures.\n\nThe interprismatic area of enamel, is where the initial radiation damage exposes itself, despite the fact that the majority of the enamel's composition is inorganic. Hydrogen peroxide and hydrogen free radicals are created during the oxidation of water molecules, and they denature the organic components.26 As a result, the integrity and mechanical characteristics of the enamel are impacted. The prismatic structure of the enamel was shown to have been affected by irradiation in the current investigation, suggesting that changes to both the organic and inorganic chemicals in the enamel are what cause the clinically recognizable radiation effects. Nevertheless, the measured abnormalities in the tissue's mechanical and physical properties in the current study imply that the disturbance of the enamel and its SMH is a contributing component in the clinically reported alterations.\n\nSeveral limitations exist in this study as evaluation of the SMH would have hampered the SDF application on the samples for example: SMH before RT and after application of SDF was not evaluated, change in SMH after each interval of weekly radiation exposure within six weeks schedule was not evaluated, change in the ionic concentration such calcium, phosphate and bicarbonate ions after RT and SDF application was not evaluated.\n\n\nConclusions\n\nBased on the observations and results of the current study it can be drawn that the SMH of primary teeth pretreated with SDF after RT was significantly higher than normal primary teeth without any pretreatment. SEM analysis of primary teeth pretreated with SDF after RT revealed smooth homogeneous surface and well-formed enamel prism. Within the limitation of the study, it can be concluded that SDF significantly improved the SMH and morphology of the primary teeth. Therefore, it is recommended that more research be done in order to completely understand how fluoride treatments work to support the restoration of the physical properties of teeth following RT for oral cancer.\n\nIn the current in-vitro study institutional ethical committee clearance was obtained from “Datta Meghe Institute of Higher Education and Research (Deemed to be University), Sawangi (Meghe), Wardha” with reference number DMIMS (DU)/IEC/2020-21/9413. Written informed consent for study and data publication was taken from the parents of the patients whose tooth samples were used for the study.", "appendix": "Data availability\n\nZenodo: Microhardness for SDF group after Radiation Therapy. https://doi.org/10.5281/zenodo.7744176. 27\n\nThis project contains the following underlying data:\n\n- SDF group samples.csv\n\nZenodo: Microhardness of control group teeth after Radiation Therapy. https://doi.org/10.5281/zenodo.7744252. 28\n\nThis project contains the following underlying data:\n\n- Control group samples.csv\n\nZenodo: SEM image of control group and SDF treated teeth after radiation therapy\n\nhttps://doi.org/10.5281/zenodo.8072843. 29\n\nThis project contains the following underlying data:\n\n- 1 CONTROL 1000X.jpg\n\n- 10 CONTROL 100X.jpg\n\n- 11 CONTROL 300X.jpg\n\n- 12 CONTROL 500X.jpg\n\n- 13 CONTROL 1000X.jpg\n\n- 14 CONTROL 5000X.jpg\n\n- 15 CONTROL 100X.jpg\n\n- 16 CONTROL 500X.jpg\n\n- 17 CONTROL 1000X.jpg\n\n- 2 CONTROL 500X.jpg\n\n- 3 CONTROL 1000X.jpg\n\n- 4 CONTROL 500X.jpg\n\n- 5 CONTROL 100X.jpg\n\n- 6 CONTROL 500X.jpg\n\n- 7 CONTROL 1000X.jpg\n\n- 8 CONTROL 5000X.jpg\n\n- 9 CONTROL 27X.jpg\n\n- SDF 1000X 16.jpg\n\n- SDF 1000X 4.jpg\n\n- SDF 1000X 6.jpg\n\n- SDF 100X 1.jpg\n\n- SDF 100X 9.jpg\n\n- SDF 300X 2.jpg\n\n- SDF 5000X 5.jpg\n\n- SDF 500X 7.jpg\n\n- SEM 1000X 11.jpg\n\n- SEM 100X 10.jpg\n\n- SEM 100X 13.jpg\n\n- SEM 300X 14.jpg\n\n- SEM 500X 12.jpg\n\n- SEM 500X 15.jpg\n\nZenodo: STROBE Checklist. https://doi.org/10.5281/zenodo.7766253. 30\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThis research was supported by Datta Meghe Institute of Higher Education and research, Sawangi (Meghe), Wardha. Various facilities like RT and central laboratory containing incubator were utilised in the institution.\n\n\nReferences\n\nFrankart AJ, Breneman JC, Pater LE: Radiation Therapy in the Treatment of Head and Neck Rhabdomyosarcoma. Cancers (Basel). 2021 Jul 16; 13(14): 3567. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarangoni-Lopes L, Rovai-Pavan G, Steiner-Oliveira C, et al.: Radiotherapy Reduces Microhardness and Mineral and Organic Composition, and Changes the Morphology of Primary Teeth: An in vitro Study. Caries Res. 2019; 53(3): 296–304. PubMed Abstract \| Publisher Full Text\n\nGupta N, Pal M, Rawat S, et al.: Radiation-induced dental caries, prevention and treatment - A systematic review. Natl. J. Maxillofac Surg. 2015; 6(2): 160–166. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMonteiro DR, Gorup LF, Takamiya AS, et al.: Silver distribution and release from an antimicrobial denture base resin containing silver colloidal nanoparticles. J. Prosthodont. 2012 Jan; 21(1): 7–15. PubMed Abstract \| Publisher Full Text\n\nMohammadi N, Farahmand Far MH: Effect of fluoridated varnish and silver diamine fluoride on enamel demineralization resistance in primary dentition. J. Indian Soc. Pedod. Prev. Dent. 2018 Sep; 36(3): 257–261. PubMed Abstract \| Publisher Full Text\n\nRosenblatt A, Stamford TCM, Niederman R: Silver diamine fluoride: A caries “silver-fluoride bullet.”. J. Dent. Res. 2009 Feb; 88(2): 116–125. PubMed Abstract \| Publisher Full Text\n\nChu CH, Lo ECM: Microhardness of dentine in primary teeth after topical fluoride applications. J. Dent. 2008 Jun; 36(6): 387–391. PubMed Abstract \| Publisher Full Text\n\nDuruk G, Acar B, Temelli Ö: Effect of different doses of radiation on morphological, mechanical and chemical properties of primary and permanent teeth-an in vitro study. BMC Oral Health. 2020 Sep 1; 20(1): 242. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDreizen S, Brown LR, Daly TE, et al.: Prevention of xerostomia-related dental caries in irradiated cancer patients. J. Dent. Res. 1977 Feb; 56(2): 99–104. PubMed Abstract \| Publisher Full Text\n\nMeyerowitz C, Featherstone JD, Billings RJ, et al.: Use of an intra-oral model to evaluate 0.05% sodium fluoride mouthrinse in radiation-induced hyposalivation. J. Dent. Res. 1991 May; 70(5): 894–898. PubMed Abstract \| Publisher Full Text\n\nKielbassa AM, Beetz I, Schendera A, et al.: Irradiation effects on microhardness of fluoridated and non-fluoridated bovine dentin. Eur. J. Oral Sci. 1997 Oct; 105(5P1): 444–447. PubMed Abstract \| Publisher Full Text\n\nFränzel W, Gerlach R, Hein HJ, et al.: Effect of tumor therapeutic irradiation on the mechanical properties of teeth tissue. Z. Med. Phys. 2006; 16(2): 148–154. PubMed Abstract \| Publisher Full Text\n\nZaffarano L, Salerno C, Campus G, et al.: Silver Diamine Fluoride Efficacy in Arresting Cavitated Caries Lesions in Primary Molars: A Systematic Review and Metanalysis. Int. J. Environ. Res. Public Health. 2022 Oct 9; 19(19): 12917. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrakash M, Kang YH, Jain S, et al.: In-vitro Assessment of Silver Diamine Fluoride Effect on Natural Carious Dentin Microhardness. Front. Dent. Med. 2021; 2: 811308. Publisher Full Text\n\nZhao IS, Gao SS, Hiraishi N, et al.: Mechanisms of silver diamine fluoride on arresting caries: a literature review. Int. Dent. J. 2018 Apr; 68(2): 67–76. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi YJ: Effect of a silver ammonia fluoride solution on the prevention and inhibition of caries. Zhonghua Kou Qiang Ke Za Zhi. 1984 Jun; 19(2): 97–100. PubMed Abstract\n\nMei ML, Ito L, Cao Y, et al.: An ex vivo study of arrested primary teeth caries with silver diamine fluoride therapy. J. Dent. 2014 Apr; 42(4): 395–402. PubMed Abstract \| Publisher Full Text\n\nLu H, Zhao Q, Guo J, et al.: Direct radiation-induced effects on dental hard tissue. Radiat. Oncol. 2019 Jan 11; 14(1): 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGonçalves LMN, Palma-Dibb RG, Paula-Silva FWG, et al.: Radiation Therapy alters microhardness and microstructure of enamel and dentin of permanent human teeth. J. Dent. 2014 Aug; 42(8): 986–992. PubMed Abstract \| Publisher Full Text\n\nde Siqueira MT , Palma-Dibb RG, de Oliveira HF , et al.: The effect of Radiation Therapy on the mechanical and morphological properties of the enamel and dentin of deciduous teeth--an in vitro study. Radiat. Oncol. 2014 Jan 22; 9: 30. Publisher Full Text\n\nMeredith N, Sherriff M, Setchell DJ, et al.: Measurement of the microhardness and Young’s modulus of human enamel and dentine using an indentation technique. Arch. Oral Biol. 1996 Jun; 41(6): 539–545. PubMed Abstract \| Publisher Full Text\n\nMarkitziu A, Gedalia I, Rajstein J, et al.: In vitro irradiation effects on hardness and solubility of human enamel and dentin pretreated with fluoride. Clin. Prev. Dent. 1986; 8(4): 4–7. PubMed Abstract\n\nMante FK, Kim A, Truong KN, et al.: Effect of Preirradiation Fluoride Treatment on the Physical Properties of Dentin. Int. J. Dent. 2022; 2022: 1–8. Publisher Full Text\n\nJansma J, Buskes JA, Vissink A, et al.: The effect of Xray irradiation on the demineralization of bovine dental enamel. A constant composition study. Caries Res. 1988; 22(4): 199–203. PubMed Abstract \| Publisher Full Text\n\nWillershausen I, Schulte D, Azaripour A, et al.: Penetration Potential of a Silver Diamine Fluoride Solution on Dentin Surfaces. An ex vivo Study. Clin. Lab. 2015; 61(11): 1695–1701. PubMed Abstract\n\nJoyston-Bechal S: The effect of X-radiation on the susceptibility of enamel to an artificial caries-like attack in vitro. J. Dent. 1985 Mar; 13(1): 41–44. PubMed Abstract \| Publisher Full Text\n\nDas S: Microhardness for SDF group after Radiation Therapy. [Data]. Zenodo. 2023. Publisher Full Text\n\nDas S: Microhardness of control group teeth after Radiation Therapy. [Data]. Zenodo. 2023. Publisher Full Text\n\nDas S: SEM images of control and SDF treated teeth after radiation therapy. [DATA]. Zenodo. 2023. Publisher Full Text\n\nDr. Das. S : STROBE Checklist. Zenodo. 2023. Publisher Full Text" }	[ { "id": "285277", "date": "04 Jun 2024", "name": "Md Sofiqul Islam", "expertise": [ "Reviewer Expertise Operative dentistry", "Dental materials", "Caries", "Esthetic dentistry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe reviewer appreciates the effort of the author in accomplishing the article. overall the manuscript is well written however after careful review the reviewer came up with several recommendations.\n\nThe introduction section can be improved by adding more information regarding the literature background, problem statement, and rationale of the study. The objectives of this study need to be added. The reviewer recommends adding a methodological diagram rather than individual images in the methodology section. The caption for the figure 9 is wrong. Please revise\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-374
https://f1000research.com/articles/13-373/v1	23 Apr 24	{ "type": "Case Report", "title": "Case Report: Giant bronchogenic cyst compressing the pericardium and the lung hilum", "authors": [ "Mahdi Abdennadher", "Amani Ben Mansour", "Hazem Zribi", "Mouna Mlika", "Amina Abdelkebir", "Hedia Bellali", "Sarra Zairi", "Fatma Tritar", "Adel Marghli", "Hazem Zribi", "Mouna Mlika", "Amina Abdelkebir", "Hedia Bellali", "Sarra Zairi", "Fatma Tritar", "Adel Marghli" ], "abstract": "Introduction: The bronchogenic cyst is a congenital anomaly of the trachea and the bronchi resulting in a malformation that develop in the bronchial tree, most often in the middle mediastinum. It is a benign pathology, often asymptomatic, however in the case of a large bronchogenic cyst, signs of compression of the intra-thoracic organs appear and early surgery is necessary to avoid complications. Case presentation: A 49-year-old patient was referred to our department with dry cough, dyspnea and chest tightness progressing for six months. Radiological exploration concluded that a giant bronchogenic cyst, 90 mm in diameter, was very probable. Surgery was performed via a right posterolateral thoracotomy. Intraoperatively, there was a large cystic formation 100mm80 mm of the middle mediastinum in intimate contact with the origin of the right pulmonary artery, the lower right pulmonary vein as well as the right atrium exerting a compressive effect on the bronchi. The lesion was firmly adhered to the pericardium. The cystic was ‘en bloc’ resected in totality. The postoperative course was uncomplicated. Histological examination confirmed diagnosis of a bronchogenic cyst. The patient was asymptomatic throughout the follow-up period. Clinical discussion: Apart from the possibility of malignant degeneration, a bronchogenic cyst can increase in size and become huge causing serious complications. Despite the predictive diagnostic value of imaging, definitive diagnosis of a bronchogenic cyst is confirmed by surgical excision and pathological examination. Conclusions: Surgery is almost obligatory especially if the cyst is above a certain size (about 60 mm) and in the case of giant bronchogenic cysts.", "keywords": [ "giant bronchogenic cysts", "surgical excision", "complications", "case report" ], "content": "Introduction\n\nBronchogenic cysts (BCs) are defined as uncommon congenital anomalies.1 They account for 60% of mediastinal cyst lesions.1 Mediastinal BCs have often been described arising from an abnormality in tracheobronchial tree budding between the third and sixth weeks of gestation.2,3 In adult patients, BCs are frequently asymptomatic2,4–6 and are often randomly discovered during a chest X-ray.2 Whenever they become symptomatic, surgical resection becomes highly recommended. Typically, BCs are oval in shape, of diameter between 20 to 120 mm.2\n\nThe aim of our case, which was operated on in The Public Hospital of Abdarrahman Mami, Tunis, is to insist in the good timing of surgery of BCs in order to avoid compressive complications due to increasing size and to ensure easier operation.\n\n\nCase report\n\nA 49-year-old patient was referred to the Thoracic Surgery Department of Abderrahmane Mami Hospital in April 2021 with a dry cough, dyspnea and chest tightness progressing for six months. The patient had a medical history of diabetes mellitus, and arterial hypertension. She had no surgical history or family history of bronchogenic cysts.\n\nPhysical examination revealed no abnormalities.\n\nChest radiography showed a mass overlapping the cardiac silhouette (Figure 1). A computed tomography (CT) scan of the chest revealed a round homogeneous cystic mass 96 mm 80 mm in diameter, occupying the middle mediastinum between the aortic arch and right pulmonary artery in sub-carine of liquid density not enhanced after injection of a contrast product. Thoracic magnetic resonance imaging (MRI) showed a cystic formation of homogeneous signal with thin wall in T2 hypo signal, evoking a bronchogenic cyst (Figure 2).\n\nSurgery was performed via a right posterolateral thoracotomy. Intraoperatively, there was a large cystic formation 100 mm*80 mm of the middle mediastinum in intimate contact with the origin of the right pulmonary artery, the lower right pulmonary vein as well as the right atrium exerting a compressive effect on the adjacent organs especially the pericardium (Figure 3A). After aspiration of a yellow liquid content and viscous consistency, the cystic was ‘en bloc’ resected in totality (Figure 3B).\n\nThe postoperative course was uncomplicated with removal of the drains on the fourth post-operative day. The patient was discharged from the hospital on May 16, 2021, on the fifth postoperative day. Histological examination confirmed diagnosis of a bronchogenic cyst. The patient was asymptomatic throughout the follow-up period.\n\n\nDiscussion\n\nBCs are relatively uncommon.1 They occur not only in pediatric patients, but also in adults.2 BCs are typically found near the large airways in the mediastinum, often just posterior to the carina, although they may be attached to the oesophagus or even inside the pericardium.3 BCs are thought to originate early in lung bud development, before bronchus formation.3 BCs contain clear fluid or less commonly, haemorrhagic secretions or air. Cases of intra-pericardial BCs are very rare in the literature.5 We present a distinctive case in which a giant BC was discovered compressing the pulmonary artery and pericardium in a very important way.\n\nBCs are diagnosed incidentally because patients do not show symptoms.5–6 However, when BCs are huge, they sometimes bring about life-threatening complications including rupture, infections, an haemorrhage and compression of the surrounding structures.6–8 Those complications can be suggested by the presence of symptoms such as cough, fever, haemoptysis, dyspnea and chest pain. If the cyst is giant with invasion of the pericardium, there is an imminent risk of intra-pericardial rupture and pericardial effusion that can lead to cardiac tamponade and exacerbation of the initial symptoms.5\n\nOn radiography, BCs appear as a spherical opacity, non-calcified, with smooth outlines.2 A CT scan is very useful in preoperative diagnosis of BCs to ascertain the precise size and in order to show the relationship of the cyst to adjacent mediastinal structures.2–9 Thus, it shows homogeneous, smooth, solitary, round or ovoid masses usually located in middle mediastinum. The CT scan density of BCs can vary from typical water density to high density related to increased calcium content, anthracotic pigment, blood, or greater protein content of the fluid.9 MRI may provide specific diagnostic confirmation in regard to BCs and allows the limits within the pericardium and the large vessels to be specified.9 In Tunisia, hydatid cysts are common, and they are the first differential diagnosis to be suggested. In such contentious cases, only surgery associated with histological examination can affirm one of the two diagnoses.\n\nSurgical resection is the most approved treatment option of BCs.6–8 The evolutionary possibilities of the cyst justify the legitimacy and the need of complete removal of this lesion.4 Despite the predictive diagnostic value of imaging, definitive diagnosis of BCs is confirmed by surgical excision and pathological examination.9 Different authors suggest various approaches such as CT guided or mediastinoscopic drainage, video-assisted thoracic surgery (VATS) or open thoracotomy. The choice of one or the other is according to the condition of the patient and characteristics of malformation (e.g., size, extension).1,6 Generally, considering the risk of serious complications and even malignancy degeneration, BCs require complete resection and should be performed every time when the diagnosis is suspected especially since the patient’s follow up is uncertain.1,5 Specifically, for giant BCs, surgical resection is recommended as early as possible in order to avoid serious complications due to the increasing size.5 In cases where there is a close relationship between the BC and the pericardium, it is important to consider emergency surgery in order to avoid a sudden rupture of the cyst in the pericardium that can lead to tamponade or acute pericarditis.10 The prognosis after complete excision is excellent.8 Incomplete excision will lead to a high recurrence rate and to the potential for more serious sequelae.8 Trans-tracheal and percutaneous drainage of the cyst are proposed by some authors as alternatives to surgery, but they are not widely accepted because of possible cyst recurrence.8\n\nIn our case, surgery was laborious because the cyst was firmly adhered to the pericardium, right pulmonary artery, and the lower right pulmonary vein with a very important compression of the bronchi. The surgical challenge was to do a radical excision without injuring the vascular and bronchial elements. We succeeded in performing this by dissecting the wall of the cyst step by step and we had the choice of approaching the patient with open thoracotomy.\n\n\nConclusions\n\nApart from the progressive malignant potential, BCs can increase in size becoming huge cysts and causes serious complications. Surgical excision is almost obligatory especially when the cyst is a certain size and in the case of giant BCs. The advent of VATS increasingly supports the idea of adhering to surgical treatment choice in the event of a bronchogenic cyst whatever the size. A careful analysis of the radiologic appearance allows us to better assess the limits of the BC and in order to prepare for sometimes laborious surgery. Incomplete surgical excision is associated with high late recurrence of the cyst.\n\nGiven the rarity of the BC, limited data exist on the surgical treatment of a giant BC and management is based on expert opinion. However, our study is limited to one case report and we haven’t significant information as would be the case with a series of patients.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nKouerinis IA, Zografos GC, Exarchos DN, et al.: A huge posteromedial mediastinal cyst complicated with vertebral dislodgment. World J. Surg. Oncol. 2006 Aug 22; 4: 56. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBasoglu A, Celik B, Sengul AT: Giant parenchymal bronchogenic cyst mimicking hydropneumothorax. J. Thorac. Cardiovasc. Surg. 2003; 126(4): 1201–1202. PubMed Abstract \| Publisher Full Text\n\nSomwaru LL, Midgley FM, Di Russo GB: Intrapericardial Bronchogenic Cyst Overriding the Pulmonary Artery. Pediatr. Cardiol. 2005; 26: 713–714. PubMed Abstract \| Publisher Full Text\n\nWorsnop CJ, Teichtahl H, Clarke CP: Bronchogenic cyst: a cause of pulmonary artery obstruction and breathlessness. Ann. Thorac. Surg. 1993 May; 55(5): 1254–1255. PubMed Abstract \| Publisher Full Text\n\nUgurlucan M, Sayin OA, Felten M, et al.: Intrapericardial bronchogenic cyst: an unusual clinical entity. Case Rep. Med. 2014; 2014: 651683. Epub 2014 Dec 15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHan SJ, Cho HJ, Kang MW, et al.: A Life-Threatening Bronchogenic Cyst. Korean J. Thorac. Cardiovasc. Surg. 2018 Feb; 51(1): 69–71. Epub 2018 Feb 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAgha RA, Franchi T, Sohrab C, et al.: The CARE 2020 guideline: updating consensus Surgical Case Report (CARE) guidelines. International Journal of Surgery. 2020; 84(1): 226–230. PubMed Abstract \| Publisher Full Text\n\nSarper A, Ayten A, Golbasi I, et al.: Bronchogenic cyst. Tex Heart Inst J. 2003; 30(2): 105–108. PubMed Abstract\n\nLimaïem F, Ayadi-Kaddour A, Djilani H, et al.: Pulmonary and mediastinal bronchogenic cysts: a clinicopathologic study of 33 cases. Lung. 2008 Jan-Feb; 186(1): 55–61. Epub 2007 Dec 7. PubMed Abstract \| Publisher Full Text\n\nLu Q, Yang E, Wang W, et al.: Spontaneous rupture of a giant intrapericardial bronchogenic cyst. Ann. Thorac. Surg. 2013 Nov; 96(5): e109–e110. PubMed Abstract \| Publisher Full Text" }	[ { "id": "271904", "date": "29 May 2024", "name": "Manoj Madhusudan", "expertise": [ "Reviewer Expertise Pediatric Pulmonology", "Interventional Pulmonology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The authors have mentioned that physical examination was completely normal. Is that the case with a huge BC compressing the pericardium and hilum? 2. Was a per-op lung function or an echocardiogram performed? 3. Can the authors specify any reason why an MRI was done over a CT? 4. The authors mention that hydatid cyst is the most common diagnosis for a mediastinal cyst in the authors region. However the pre-surgery diagnosis was BC. Was there a radiological finding that suggested a Hydatid cyst over a BC? 5. Could the authors add histopathology images? 6. The sentence ' they occur not only in pediatric patients, but also in adults' should be re-phrased. They don't 'occur' in adults, they can remain undiagnosed till adulthood.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-373
https://f1000research.com/articles/13-372/v1	23 Apr 24	{ "type": "Software Tool Article", "title": "Bruco: a video game to learn the periodic table", "authors": [ "Dhanalakshmi Vadivel", "Diego Savio Branciforti", "Daniele Dondi", "Diego Savio Branciforti", "Daniele Dondi" ], "abstract": "Background: Elements symbols, groups, periods, and other periodic table-related topics are of fundamental importance in science, but it can be a bit of a taxing subject to learn at times. By combining video games with teaching, the topic could be turned into fun. Methods: In this regard we decided to write a program under the basis of the universally known game snake, called periodic caterpillar (in Italian called BRUCO). The gameplay is intended to help students cooperate. In this purpose, we also designed a joystick interface which is more comfortable for primary-grade students. Use case: Teaching in the classroom by game-based learning is the major usage of this research. We present the usage of this game in two different ways. One student/person play alone to understand their own proficiency with a periodic table. Another one is a group of students/people who can participate and play to exhibit their interpersonal skills. Conclusions: Bruco could prove highly useful for teaching chemistry to school students in a cooperative way. It may also be useful as a refreshment in a research laboratory-like environment and in the classroom.", "keywords": [ "video game", "periodic table", "chemical education", "young students", "chemistry" ], "content": "Introduction\n\nIn chemistry, learning and remembering the periodic table is an important target1 for beginners and is fundamental for science students in general.\n\nHuman bonding through interpersonal relationship commonly takes place among family members and friends also achieved among groups sporting and people spend time together.2 This type of bonding in the working atmosphere is really needed, especially in research, where emotional support and trust are valuable.3\n\nGame-based education4–6 is an up-coming field and its application in teaching is investigated and valued positively.7 When compared to traditional methods, game-based teaching in a playful way gives better results8 because it helps the users to balance the subject matter with their real world for example with their friends and colleagues. Most of the research on digital games9 focused on comparison between traditional methods of learning and media-based studies. In fact, an essential aspect to investigate is how the theoretical design of game influences the learning in a broad diversity of learners in the classroom.10\n\nIn recent years, very few video games for chemistry were released, we will discuss on some of the most known. Cheminoes is a colourful game, where students can learn relations between concepts such as chemical element, valence, atomic number, and chemical symbol for the first 36 elements of the periodic table.11 In the Time Bomb Game, designed by Júnior and co-workers, students must deactivate a time bomb by correctly answering questions taken randomly from a database.12 Some video games are related to organic chemistry, such as Chairs!13 a mobile app to make aware of the ring flip of cyclohexane.\n\nIn the computer game “Say My Name” by Josè Nunes da Silva Junior et al., players can improve their knowledge on nomenclature of organic compounds through answering up to 600 questions distributed in three difficulty levels.14 In the same way, Chemical Nomenclature, created by Mary Anne Sousa Lima et al., helps students to learn chemistry answering up 700 questions directly on their smartphone15 (Android and iOS).\n\nOther video games are intended to allow students to experiment in a virtual chemistry laboratory. Some examples are, Chem Crafter, an iPad app allows users to build their own lab. It can also measure the energy released and in critical conditions the program shows fire and smoke. Digital games like Collisions are useful to teach and explain important concepts such as information on atoms, ions, bonding information, acid-base concepts, and phase change.\n\nOur video game, “periodic caterpillar” is inspired by Snake, one of the most important titles on the international video game scene. The original Snake game was designed in seventies with the arcade title Blockade,16 but it became very famous in the nineties during the large diffusion of mobile phone games. Snake was based on a very simple gameplay that was implemented on many types of gaming platforms. During the game, the player must guide a “digital snake” inside an area, using the standard directions like Up, Down, Left and Right. By eating the food that appears randomly on the screen, the length of the snake is increased. The game is over is when the snake bites itself.\n\n\nMethods\n\nThe program was written by using the Processing v.3.5.4 integrated development environment (IDE).10 Processing is a free software useful for visual arts programming and the programs written could work on different platforms. Processing is compatible with the several programming languages, from Java to HTML5. Our program is written in Java 9 and it works by using the built in 2D renderer without additional libraries. The main characteristics of this environment is the presence of a startup() function, called once at the beginning of the game, and a draw() function, called automatically at every cycle respecting the framerate. The game board is represented internally by a square matrix and the caterpillar is drawn each frame by using simple drawing routines such as circles and lines. The number of horizontal squares grid is calculated by dividing the horizontal resolution by 50. The screen is updated with a framerate of 15 frames per second in full screen mode. This framerate is chosen in order to have a balance between speed and playability. The minimum requirements for a smooth game is a PC with an output resolution of 1920×1080 pixels (Windows 10 with 2 GHz central processing unit (CPU) and 8 Gb of rapid access memory (RAM)). The program automatically sets the number of grid squares for different screen resolutions but at higher resolution the number of empty squares overtake the filled thus rendering the game less appealing due to the time needed to reach elements. When the program starts the image start.png is shown together with the list of the top 10 players in an arcade-style. This allows the customization of the starting image, but remembering that the central part will be overwritten by the game while printing the list of players.\n\nThe possibility to have the score indicated in the top 10 list is intended to increase the motivation of the players to achieve better and better results. The introduction page of the game together to the top 10 can be seen below in the Figure 1.\n\nSome variables could be used to change the game appearance such as grid size (in pixels) and are commented in the code. Players can control the caterpillar by using the letters w, a, s, d for, respectively, up, left, down and right directions.\n\nThe arcade joystick with microswitches (Tongmisi 8 Way Arcade Joystick with Microswitch for Arcade Game Console) was connected to the Arduino Leonardo directly on four digital inputs, D9-D12. The pin “D9” was used to emulate “d”, “D10” was used to emulate “a”, “D11” was used to emulate “s”, “D12” was used to emulate “w”. The schematic representation of Joystick is shown in Figure 2, while the firmware code is inserted in a public repository.18\n\nAfter having recognized an element as it appears on the periodic table or as a part of a group or period, we hope that the player tends to remember the answer even in the following sessions. In this present work, the specialty of the game is that it could be potentially applied for team building purposes on different levels, from the encouragement to team working in school classes and/or with students, to different areas of interest as it could be a lab environment, in which members must learn or to improve their ability to work in teams or small groups.\n\n\nUse case\n\nThe video game presented here is more relevant to chemical elements with their placement in periodic table. It is also classroom-oriented and competitive. The gameplay is so simple that the game can be played by children of any age. For this reason, we also designed a simple joystick interface. The game also gives higher scores to players those who are faster in identifying elements. This enhances the game spirit and competition among players.\n\nThe game begins with a small caterpillar that starts moving on the screen. The player can control it across all the board. During the game, element symbols appear randomly on the screen. At this point, a sentence appears at the bottom of the screen, requesting that the player “eats” a specific element. The request could correspond to an element symbol, period, group, block (s, p, d, f orbitals) and type (alkaline, alkaline-earth, etc.). In the bottom-left corner a graphical representation of the periodic table helps to find the required element. While eating the elements, the caterpillar grows longer and longer. Compliments17 like: ‘good’, ‘great’, ‘beautiful’, ‘keep it up’, ‘yum’, ‘nice shot’, ‘very well’, ‘go strong’, ‘prominent’ and ‘you’re myth’, for each correct answer is designed to promote pleasure when the correct element is taken which are shown in Figure 5.\n\nThe game also comments for wrong elements like: ‘oh no’, ‘ops’, ‘caution’, ‘look what is required’, ‘watch out’, ‘error’, ‘this was not to eat’, ‘mistaken’, ‘concentrated’ and ‘look at the table well’. In the latter case, one life is decreased from the starting five. These remarks are designed to help the player to be the best.\n\nAfter each element is eaten, from one to three new elements appear on the board. Thus, the probability to find the correct element decreases while the probability of failure increases. Every five elements taken the game speed increases up to a maximum when the elements taken are 15, rendering the playability more and more difficult. The faster the correct elements are taken by the player, the higher the probability that a life bonus appears on the board. This happens if we collected at least two elements since the last bonus and random(300)>float (time Bonus/elements Since Last Bonus).\n\nWhen time between successes is greater than 1500 cycles (about 100 seconds), correct elements are highlighted. This helps beginners (people new to periodic table) to go ahead in the game but they have a reduced life bonus (see Figure 5, bonus lives) probability. The game ends when the player finishes the lives, or the caterpillar bites itself.\n\nThis game is very versatile and can be exploited in many ways. For example, a good method to use periodic caterpillar game with students is divide the class into groups that contains 2 to 4 players and give to them a periodic table (see Figure 4). One team member controls the caterpillar, and the others help him suggest the right elements to eat. Each group will be able to play until the “game over”, finishing all their available lives. The team that achieves the highest score win the game.\n\nThe purpose of the game is simple: to explore the periodic table. Finding the chemical elements location, their groups, periods, symbols and in some cases their mere existence are parts of this exploration (see Figure 3).\n\nThe team play, especially with two players, where the one controlling the caterpillar and the other suggesting elements (with the help of a periodic table). For example, in a specific case, the student could move the caterpillar with the help of a joystick under the suggestion of an adult.\n\nThe video game was shown during the European Researchers’ night held in Pavia (Italy) on 27th September 2019. People were attracted while seeing the graphic of the game and they immediately liked the gameplay. The number of players increased quickly because this game is kind of magnetic that will rush you to help your friends with suggestions. The important point we observed is that it is not limited only to some groups of known friends, even complete strangers started to help each other during the match without being familiar.\n\n\nConclusion\n\nIn the present work, we succeeded in making a video game for school students targeted at making their learning of chemistry cooperative. In fact, this software gives each member of a group, a specific role by increasing the compatibility between them. Furthermore, the game promotes their level of interest in science since the periodic table has a key role in research in physics, chemistry, and life sciences. In this aspect we move forwards youngsters towards science with compliments and appreciation. When users commit mistakes while choosing elements, they are informed in a soft manner with five life chances for every play. This video game had a good influence with research scholars of the same department and students from various schools as we received good feedback during the European Researchers’ nights held at Pavia (Italy) in 2019 and 2021. In all, we believe that this mutually beneficial way of teaching can be of broader application, also in non-chemistry related curriculum.\n\n\nAuthor contribution\n\nDhanalakshmi Vadivel: Methodology, Visualization, Data curation Writing - review & editing Diego Savio Branciforti: Investigation, new inputs and Daniele Dondi: Supervision, Validation, Conceptualization.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nCOLAVER s.r.l.-Vimodrone (Milan, Italy) Laboratory Glassworks and ENDEAVOUR ENERGIA s.r.l are strongly acknowledged for their support during researchers’ night display of periodic table at Pavia. All the research scholars, students of university of Pavia and teachers of various school who gave the feedback after playing this video game.\n\n\nReferences\n\nBierenstiel M, Snow K: Periodic Universe: A Teaching Model for Understanding the Periodic Table of the Elements. J. Chem. Educ. 2019; 96(7): 1367–1376. Publisher Full Text\n\nChu LC: Impact of Providing Compassion on Job Performance and Mental Health: The Moderating Effect of Interpersonal Relationship Quality: Providing Compassion, Performance, and Mental Health. J. Nurs. Scholarsh. 2017; 49(4): 456–465. PubMed Abstract \| Publisher Full Text\n\nReblin M, Uchino BN: Social and emotional support and its implication for health. Curr. Opin. Psychiatry. 2008; 21(2): 201–205. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVergne MJ, Simmons JD, Bowen RS: Escape the Lab: An Interactive Escape-Room Game as a Laboratory Experiment. J. Chem. Educ. 2019; 96(5): 985–991. Publisher Full Text\n\nEdmonson LJ, Lewis DL: Equilibrium Principles: A Game for Students. J. Chem. Educ. 1999; 76(4): 502. Publisher Full Text\n\nCarney JM: Retrosynthetic Rummy: A Synthetic Organic Chemistry Card Game. J. Chem. Educ. 2015; 92(2): 328–331. Publisher Full Text\n\nCruz-Cunha MM, editor. Handbook of Research on Serious Games as Educational, Business and Research Tools. IGI Global; 2012. Publisher Full Text\n\nClark DB, Tanner-Smith EE, Killingsworth SS: Digital Games, Design, and Learning: A Systematic Review and Meta-Analysis. Rev. Educ. Res. 2016; 86(1): 79–122. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmerica’s Lab Report: Investigations in High School Science. National Academies Press; 2005; 11311. Publisher Full Text\n\nDarling-Hammond L, Flook L, Cook-Harvey C, et al.: Implications for educational practice of the science of learning and development. Appl. Dev. Sci. 2020; 24(2): 97–140. Publisher Full Text\n\nMoreno LF, Hincapié G, Alzate MV: Cheminoes: A Didactic Game To Learn Chemical Relationships between Valence, Atomic Number, and Symbol. J. Chem. Educ. 2014; 91(6): 872–875. Publisher Full Text\n\nda Silva Júnior JN , Santos de Lima PR, Sousa Lima MA, et al.: Time Bomb Game: Design, Implementation, and Evaluation of a Fun and Challenging Game Reviewing the Structural Theory of Organic Compounds. J. Chem. Educ. 2020; 97(2): 565–570. Publisher Full Text\n\nWinter J, Wentzel M, Ahluwalia S: Chairs!: A Mobile Game for Organic Chemistry Students To Learn the Ring Flip of Cyclohexane. J. Chem. Educ. 2016; 93(9): 1657–1659. Publisher Full Text\n\nda Silva Júnior JN , Nobre DJ, do Nascimento RS , et al.: Interactive Computer Game That Engages Students in Reviewing Organic Compound Nomenclature. J. Chem. Educ. 2018; 95(5): 899–902. Publisher Full Text\n\nSousa Lima MA, Monteiro ÁC, Melo Leite Junior AJ, et al.: Game-Based Application for Helping Students Review Chemical Nomenclature in a Fun Way. J. Chem. Educ. 2019; 96(4): 801–805. Publisher Full Text\n\nLoguidice B, Barton M, Todeschini C, et al.: Vintage games: La storia di Grand Theft Auto, Super Mario e dei piu influenti videogiochi di tutti i tempi. Raganella; 2009.\n\nDondi D: Bruco. Zenodo. [Code]. 2023. Publisher Full Text\n\nDondi D: joystick for bruco videogame. Zenodo. [Code]. 2023. Publisher Full Text" }	[ { "id": "270789", "date": "06 Jun 2024", "name": "Aliyu Hassan", "expertise": [ "Reviewer Expertise Chemistry Education", "Computational Thinking", "HOTs", "Game-based Learning", "Virtual Learning", "and Learning Management System" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author(s) conducted awesome research. The development of the software tool looks great, as does its description. But the rationale for developing the software was not clearly justified. For example, the author should have presented similar software that chemistry experts used in teaching and learning that area of chemistry and explained it limitations that necessitated the development of the current software.\n\nThe author should have used additional assessment tools rather than relying on mere observation.\n\nOn a final note, the research work is great and surely it content will attract many schorlars.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [] }, { "id": "290883", "date": "17 Jun 2024", "name": "Angelo Mark Walag", "expertise": [ "Reviewer Expertise Chemistry education", "game-based learning", "gamification", "inquiry-based learning", "educational innovations" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript attempts to develop an instructional material by integrating video-game elements in the learning of periodic table-related properties. This was utilized in a class to evaluate its effectiveness. While the paper demonstrates utility, it can be improved by addressing the following comments.\n1. The abstract's background can still be improved by providing a context of why game-based elements are necessary in the learning of concepts as this topic is quite simple to learn. I disagree with the authors that it is taxing. There must be strong justification why innovating instruction with the use of video game is necessary. 2. The abstract can also be reviewed in terms of correct English grammar and syntax rules. 3. In the introduction, the first paragraph consists of just one sentence. This can still be improved by adding more literature of why games must be integrated in the learning of chemistry or science in general. 4. The second paragraph of the introduction seems off. It is not clear how it connects to the first paragraph. Coherence and story-telling must be employed in writing the introduction so readers would understand the context of the work. 5. Aside from enumerating the existing video games for chemistry, discuss also their strengths and weaknesses. This would allow the authors to identify existing gap in the literature that would justify the novelty of the work. 6. End the introduction with your research objectives. What would be the practical utility of the game? How would it be used by teachers in a class? When should teachers use it? Is this a supplementary material? What competencies are targeted? 7. Where is the discussion on the usage of the game? It would help establish the utility of the game if students who played it evaluated in terms of certain criteria. 8. The conclusion of \"learning of chemistry cooperative\" is not justified by the results. It seems that the study only developed a game. There was no testing and the paper did not show any results to support the conclusion of \"promotes their level of interest\"\nThese concerns must be addressed to establish the utility, effectiveness, and scientific rigor of the paper.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No", "responses": [] }, { "id": "290886", "date": "03 Jul 2024", "name": "Dylan P. Williams", "expertise": [ "Reviewer Expertise Chemistry education", "pedagogy", "nanotechnology", "physical chemistry" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors should be congratulated for developing a novel chemistry learning game based on a very well established game format. The game is likely to support pupils at school level familiarise themselves with the periodic table. The game is primarily focused on supporting learners in memorising the periodic table so it's applications will be largely focused on the early stages of chemistry education. The game definitely has the potential to be adopted by other instructors but a number of additions and modifications are needed in order to facilitate that.\nMy primary concerns are related to the lack of evidence in support of the authors' conclusions. The authors claim that the game promotes the level of interest of students but there is no explanation of how this was measured. Some discussion of the experimental methodologies used to establish student levels of interest along with the relevant data and an analysis of this data. The manuscript describes an implementation of the game held during European Researchers' nights in 2019 and 2021. This part of the manuscript briefly refers to positive feedback from participants but there is no discussion of how this feedback was solicited or what participants actually fed back. Again, there needs to be some discussion of the methodology (including characteristics of the pilot group and sample sizes) used to collect this feedback, some presentation of the data (e.g. quotes from participants, charts of Likert data, etc.) along with an appropriate analysis of this data. The authors should also be encouraged to discuss the limitations of piloting the game with a group of people who are distinct from the primary target group (i.e. the researchers attending these events are likely to already have a good understanding of the topic and are likely to already be motivated to learn chemical/scientific topics). This may vary significantly from the primary target group (school pupils).\n\nThe manuscript needs some very careful proof reading. There are numerous sentences that don't follow the conventions of English writing which makes some sections of the manuscript difficult to read. I have made some suggestions for how the abstract could be made clearer below but a similar analysis of the rest of the manuscript is also needed.\n\nThe following section describes a number of specific presentation and structure comments related to the manuscript:\n- You could open the background of the abstract with a statement like \"The structure and content of the periodic table are of fundamental...\" - The phrase \"but it can be a bit of...\" could be replaced with something like \"but it can be one that some students may find challenging\" - The phrase \"the topic could be turned into fun\" could be rephrased as \"a fun and engaging learning experience could be developed\" - Replace \"In this purpose...\" with \"To facilitate this...\" - You could open the Use case subsection of the abstract with \"This study is focused on the implementation of game-based learning in the classroom environment\" - In conclusions section of abstract, replace \"refreshment\" with \"as a refresher activity\" - The second paragraph of the introduction seems out of place. This needs to be placed in context. - The statement that game-based learning supports \"better results\" than traditional methods is a very significant claim. You need to define what type of results you are considering (i.e. student attainment or something else?) and present a substantial body of evidence to support such a large claim. Any limitations in the literature findings need to be clearly described here. - It would be helpful to know how the games discussed in the introduction work. We don't need a lot of detail but it would be helpful to know the basis of how they support student learning. - In the sixth paragraph of the introduction, it would be very useful to know what type of energy release is modelled by this game. - What evidence is there to support the effectiveness of any of the games described in the introduction? There needs to be some introduction of how their effectiveness has been measured. What are the limitations of these game-based approaches? - The introduction section needs to end with a clear statement of your aims. Outline your research questions and use this to set-up the methodology section where you will describe how you set-up and ran your experiments. - The description of how the game was created works well. - You need some further discussion of how the game is used in the classroom setting. Perhaps a timeline showing how this fits in with other curricular activities would be helpful? The goal here should be to produce something that would be easy for other instructors to adopt in their own teaching so add any instructor guidance that you feel would help them do this. - I would strongly encourage you to develop a set of tutor notes that could be uploaded as SI alongside the paper itself. This would make it easier for other instructors to adopt your game. - The Methods section needs an additional sub-section focused on how you evaluated the effectiveness of the game. What research methodologies did you use (and why?). What would other researchers need to do in order to repeat your work and obtain consistent findings? - The Arduino is mentioned for the first time on page 3. Presumably this should have been introduced earlier in the manuscript. - The sub-heading \"Superiority of periodic caterpillar game\" needs to be changed. You haven't explained what you believe the game is superior to and you haven't presented any evidence of the effectiveness of the game (see earlier comments on further details of research methodology, evidence collected and analysis of this evidence. - How do players score points? Is it one point per element that the caterpillar eats? - Avoid using male pronouns to describe the person playing the game (or add other pronouns).\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No", "responses": [] } ]	1	https://f1000research.com/articles/13-372
https://f1000research.com/articles/13-370/v1	23 Apr 24	{ "type": "Brief Report", "title": "Studies on variability in mode of infection by the isolates of leaf pathogens isolated from diseased leaves of Musa paradisiaca from Uttar Dinajpur District", "authors": [ "Debarati Das", "Papan Chowhan", "Parimal Mandal", "Arka Pratim Chakraborty", "Debarati Das", "Papan Chowhan", "Parimal Mandal" ], "abstract": "Banana is (Musa sp) one of the most exoteric and materialistic fruit crop of many tropical and subtropical areas in India. Banana leaf diseases, caused by several fungal pathogens are one of the major diseases. Among the fungi causing banana leaf diseases, Curvularia sp/C. lunata is one of the main causal organisms causing leaf spot disease in banana plant. Two fungal isolates- MUSLF-2, MUSLF-3 and one fungal isolate- MUSLF-1 were isolated from the infected leaf from Ramganj and Gotgaon locations. Based on light microscopic and scanning electron microscopic studies, MUSLF-2 and MUSLF-3 were identified as Curvularia sp. After Koch’s postulate, three fungal isolates- MUSLF-2, MUSLF-3 [Curvularia sp] and MUSLF-1 were applied in banana field along with foliar spray of spore suspensions. The symptoms were similar to those observed in the in vitro detached leaf inoculation technique. The present research work depicts about the severity of leaf spot diseases of Musa paradisiaca and the nature of mode of infections exhibited by the fungal pathogens.", "keywords": [ "Curvularia sp.", "Leaf spot diseases", "Musa paradisiaca", "Koch’s postulate", "Scanning electron microscopy", "Transmission electron microscopy" ], "content": "Introduction\n\nBetween December 2022 and January 2023, leaf spot disease was observed on leaves of field-grown banana plants in the Uttar Dinajpur District, West Bengal. Diseased leaf samples were collected from Ramganj (Lat - 25.64855° long - 88.430628°), Gotgaon (Lat - 25.646622° long - 20 88.440895°) and Kaluhar ((Lat - 25.637923° long - 88.444335°) places. Symptoms first appeared as yellowish-brown spots in the middle and margin of leaves. Symptoms range from a few lesions scattered across leaves to lesions densely covering large sections of leave (Figure 1).\n\nTwo fungal isolates - MUSLF-2, MUSLF-3 and one fungal isolate - MUSLF-1 were isolated from the infected leaf from Ramganj and Gotgaon locations onto potato dextrose agar amended with Monocef. Based on light microscopic and scanning electron microscopic studies, MUSLF-2 and MUSLF-3 were identified as Curvularia sp. (Figures 2 & 3). Koch’s postulate was successfully established for Curvularia sp. causing leaf spot disease in banana. Disease symptoms were developed within seven days on inoculated detached leaves and in inoculated leaf surfaces, conidial germination was observed. Curvularia sp. was reisolated from the infected spots. Leaf diseases by Curvularia sp. or Curvularia lunata or other species of Curvularia were reported by previous researchers (Addrah et al., 2021; Manzar et al., 2021) in support of our research findings.\n\nMycelial invasion of the pathogen in infected leaf was confirmed through the section of leaves under light microscope with cotton blue staining (Figures 4 & 5). The surface morphology of healthy and Curvularia sp. inoculated leaves were studied by scanning electron microscopy (Figures 6 & 7). Changes in internal structures of healthy and Curvularia sp. inoculated leaves were observed through transmission electron microscopy (Figure 8). Role of Curvularia in causing leaf spots in other crop plants was studied by researchers (Khoo et al., 2022; Bandara et al., 2022).\n\nAfter Koch’s postulate, three fungal isolates- MUSLF-2, MUSLF-3 [Curvularia sp.] and MUSLF-1 grown in sand maize meal media were applied in banana field along with foliar spray of spore suspensions (1×103 conidia/ml). Although the method of inoculation was somewhat artificial, the symptoms were similar to those observed in the in vitro detached leaf inoculation condition (Figures 9 & 10). Similar finding on first report of Curvularia lunata causing leaf spots in banana plant from Uttar Dinajpur District is in support of our present research (Chowhan and Chakraborty, 2022).\n\nIn a nutshell, the research finding focuses on the nature of symptoms of leaf spot diseases of banana and role of Curvularia sp. in establishment of leaf spot through Koch’s postulate in detached leaf technique as well as in field condition.", "appendix": "Data availability\n\nNo data is associated with the research.\n\n\nAcknowledgements\n\nAuthors take this opportunity to express earnest gratefulness to the Director of USIC - Scanning Electron Microscopy Unit, University of North Bengal for taking the scanning electron microscopic photographs and the Director of USIC-AIIMS, New Delhi for taking the transmission electron microscopic photographs.\n\n\nReferences\n\nAddrah ME, Shi B, Li H, et al.: First report of sunflower leaf spot caused by Curvularia lunata in China. J. Plant Pathol. 2021; 103: 1363. Publisher Full Text\n\nBandara KMCS, Ferdinandez HS, Manamgoda DS, et al.: The first report of Curvularia senegalensis causing leaf and floral spots on Zinnia elegans in Sri Lanka. Ceylon J. Sci. 2022; 51: 73–77. Publisher Full Text\n\nChowhan P, Chakraborty AP: First report of Curvularia lunata (ON246070) causing leaf spot disease of banana from Raiganj, West Bengal, India. Plant Health Progress. 2022; 24: 32–36. Publisher Full Text\n\nKhoo YW, Rosina B, Amiruddin S, et al.: First report of Curvularia lunata causing leaf spot on Oryza sativa in Sabah, Malaysian Borneo. Plant Dis. 2022. PubMed Abstract \| Publisher Full Text\n\nManzar N, Kashyap AS, Sharma P, et al.: First report of leaf spot of Maize caused by Curvularia geniculata in India. Plant Dis. 2021; 105: 4155. Publisher Full Text" }	[ { "id": "275397", "date": "28 May 2024", "name": "Ying Wei Khoo", "expertise": [ "Reviewer Expertise Plant Pathology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. replace \"crop\" with \"crops\" 2. replace \"plant\" with \"plants\" 3. Which one do you want to refer to, Curvularia sp or C. lunata? 4. Please restructure this sentence: “Two fungal isolates- MUSLF-2, MUSLF-3 and one fungal isolate- MUSLF-1 were isolated from the infected leaf from Ramganj and Gotgaon locations.” 5. Without molecular results, how can you confirm the isolates are either Curvularia sp. or Curcularia lunata based on macroscopic and microscopic characterization? 6. Remove “about” before “the severity” 7. Add “the” before “mode” 8. A scale bar should be added to the figure In cases where a figure has multiple parts or panels, it is better to label each with a letter: A, B, C, etc. in lowercase or upper-head letters depending on the journal’s guidelines. 9. Figures no.5, 7, and 8 Figure 2 are not clear, same goes for some figures in Figures 3, 4, 9, and 10. 10. Your identification of the fungi lacks strong evidence to support its accuracy.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/13-370
https://f1000research.com/articles/13-369/v1	23 Apr 24	{ "type": "Review", "title": "A review of common methods used in the analysis of human microbiome sequencing data", "authors": [ "Patrick Hannan", "Mark Nicol", "Maia Lesosky", "Mark Nicol", "Maia Lesosky" ], "abstract": "The past two decades have seen a rapid rise in the development and use of sequencing technologies. The advent of high-throughput sequencing (HTS) has allowed scientists sequence the genomic content of entire microbial communities rapidly and affordably. Methods for data management, visualization, and analysis of this microbiome sequencing data are now widespread in open and closed source software tools. In this review, we identify common analysis methods used in microbiome sequencing studies, including methods for normalisation of abundance table data, visualization of high-dimensional microbiome data and the analysis of longitudinal microbiome sequencing data. In particular we find that a very small proportion of metagenomic studies made use of compositional data analysis methods and none that made use of compositional methods for longitudinal microbiome data.", "keywords": [ "human microbiome", "review", "compositional data" ], "content": "Author summary\n\nThe rapid decrease in the cost of sequencing large amounts of genomic material has led to an equally rapid increase in the number of studies sequencing entire microbial communities. There is increasing awareness in the literature that microbiome datasets generated by next generation or high-throughput sequencing (HTS) are compositional due to the arbitrary read count total. In this study, we investigated the methods used to analyse microbiome data generated by HTS machines and the adoption of methods that take into account the compositional nature of microbiome data. A specific focus of this study was to investigate compositional methods in the analysis of longitudinal microbiome sequencing data.\n\nAlthough recent studies were more likely to make use of compositional methods or employ software tools that account for compositionality such as ANCOM or ALDeX2, we find that a very small proportion of metagenomic studies made use of compositional data analysis methods and none that made use of compositional methods for longitudinal microbiome data.\n\n\nIntroduction\n\nIt has long been known that plant and animal species are also host to a wide variety of microbial life (Luckey, 1972; Savage, 1977). These microbes, generally known as the “host-associated microbiota” play a variety of roles in the development and biology of the associated host from necessary activity, such as immune function modulation and homeostasis (Chervonsky, 2010; Muniz et al., 2012), to coincidental activity. There is at least one estimate that the number of these “host-associated microbes” that reside on or within the human body roughly equal the number of human somatic and germ cells that make-up an average human body (Sender et al., 2016a, 2016b). Together, the genomes of these microbial organisms (collectively defined as the human microbiome, the human metagenome, or the human microbiota) provide services to humans, and in some cases, may play a role in disease progression or severity (Garrett, 2015; Paun et al., 2017).\n\nThe first widespread technology for sequencing of genomic material, such as that used by the Human Genome Project (Lander et al., 2001), was performed using a technique known as Sanger sequencing. Sanger sequencing sequences multiple copies of the same fragment of DNA at a time and is considered a low-throughput sequencing method (Sanger et al., 1977). More modern sequencing technologies are now well established and are capable of sequencing millions of strands of DNA in parallel. Collectively the group of modern sequencers capable of such high-volume parallel genomic sequencing are known as high-throughput sequencing (HTS) or “next generation” sequencing technologies. The technology to sequence millions of strands of DNA in parallel allows large comprehensive genomic datasets to be generated, which can be analysed for insights into the genomic make-up of whole microbial communities.\n\nHost microbial composition is typically investigated using two main sequencing methodologies, 16S ribosomal RNA (rRNA) amplicon sequencing or whole metagenome shotgun (WMGS) sequencing. 16S rRNA sequencing amplifies specific ribosomal subunit genes found only in bacteria, while WMGS sequencing amplifies and sequences all DNA in a given sample including Archaeal and Viral genetic material. While the focus of this review is not on the differences in microbial sequencing pipelines, it is important to note that decisions made during sequencing and quality control can significantly impact the results obtained after analysis (Caporaso et al., 2010; Dahlberg et al., 2019; McMurdie and Holmes, 2014; Schloss et al., 2009; Straub et al., 2019; Thorsen et al., 2016). Furthermore, the location from which samples are obtained as well as the manner in which they are stored can alter the reported microbial community composition and lead to the inclusion of contaminant DNA (Dahlberg et al., 2019; Drengenes et al., 2019; Salter et al., 2014). The final output of the sequencing and quality control pipelines is a table of read counts assigned to each sample that is grouped by DNA sequence similarity of a specific taxonomic marker gene or reference genomic sequence, the resultant group is known as an operational taxonomic unit (OTU), and the resultant table is therefore known as an OTU table or abundance table. Abundance tables that relate OTU or sequence abundance produced at the end of both sequencing pipelines to sample data are typically analysed using similar statistical approaches (Calle, 2019).\n\n\nCompositionality of metagenomic data\n\nThe final sequence abundance output of HTS experiments are then analysed under the assumption that the output, such as abundance or OTU tables, provides independent counts of organisms or reads within each given sample (Robinson et al., 2016), similar to how a birder would count species of birds on a beach, however there are issues with this perspective for microbiome data. Researchers are increasingly drawing attention to the fact that HTS machines have a maximum number of total reads that can be sequenced in a given run, also known as their throughput or maximum throughput (Morey et al., 2013; Quince et al., 2017; Reuter et al., 2015). The consequence of a fixed maximum throughput in HTS machines means that the read counts generated by such experiments are constrained by an arbitrary constant sum, implying statistical non-independence in the individual OTU counts. The read count returned from a HTS run can therefore be thought of as a fixed-size random sample of the relative abundance of the genetic material in the underlying ecosystem (Gloor, Macklaim et al., 2017). A further issue is the amplification process for 16S sequencing which preserves ratios but changes absolute abundances. For example, a library sequenced on an Illumina MiSeq could return approximately 25 million reads, whereas the same library sequenced on an Illumina HiSeq could return approximately 300 million reads. Constrained data of this nature are known as compositional data (CoDa). Compositional data are vectors of non-negative elements constrained to a constant sum. This constrained sum limitation inherent in HTS technology extends to all fixed capacity sequencing machines regardless of the number of taxa identified or analysed (Gloor, Macklaim et al., 2017).\n\nA further problem relevant to metagenomic data and inherent in compositional data is that spurious correlation occurs when a dataset is subset into composition with fewer parts than the original composition, known as a subcomposition. This is particularly problematic because metagenomic sequencing experiments are always subcompositions of the full metagenomic environment (Calle, 2019; Gloor, Wu et al., 2016). Decisions made in the sequencing quality control pipeline (Bolyen et al., 2019; Schloss et al., 2009), as well as the maximum throughput of the HTS machine itself mean that not all OTUs present in the environment are present in the output results.\n\nGiven the compositional nature of microbiome sequencing data, metagenome experiments alone cannot quantify the absolute number of organisms present within a given sample, but only provide data about the relative differences in abundance. HTS data is implicitly treated as compositional data when researchers choose to use microbiome data as relative abundance values, normalised counts, or rarefied count values (Weiss et al., 2017). This review will investigate what statistical methods and approaches are being used to analyse and make inference from such metagenomic data.\n\n\nMethods\n\nThe following electronic databases were searched using the relevant keywords and search syntax appropriate to each database. The bibliographies of the articles were hand searched to identify additional studies.\n\n1. PubMed (January 2000 to January 2022)\n\n2. Scopus (January 2000 to January 2022)\n\n3. Embase (January 2000 to January 2022)\n\nOnly primary articles in the English language were considered. The search used a combination of the following search terms:\n\n(microbiota OR metagenom* OR microbiom* OR “microbiota”[MeSH])\n\nAND (16S ribosomal RNA OR 16S rRNA OR WMGS OR NGS OR shotgun sequencing OR “High-Throughput Nucleotide Sequencing”[MeSH])\n\nAND (analysis OR analyse*) NOT (protocol OR comparative study [pt] OR systematic review [ti] OR review [ti] OR review [pt]).\n\nA total of 6100 studies were extracted from electronic databases. Of the 6100 abstracts included, 381 were randomly selected to be assessed by the author to determine the study population, type of metagenomic sequencing used and analysis methods. To further assess the types of methods used in metagenomic studies an R script was written to extract keywords from all abstracts returned by the search strategy in order to determine sequencing methods and possible analysis methods for the studies that were not selected to be reviewed. All text extraction and analyses were performed in R (version 4.1.2) (R Core Team, 2020). The full text of an additional five randomly selected abstracts was reviewed for each section of the review (normalisation methods, diversity metrics, and, inferential statistics for microbiome data). For full text review, 18 papers that discussed methods for compositional data in their abstracts were included. In total the full text of 38 randomly selected articles was reviewed.\n\n\nResults\n\nOf the 15 articles randomly selected from the full list of abstracts included in this review seven used rarefying in order to normalize abundance table count (Azad et al., 2016; Craig et al., 2018; Ding et al., 2019; Hantsoo et al., 2019; Piyathilake et al., 2016; Sugita et al., 2016; Zhu et al., 2019). One article did not normalise the data prior to analysis, however the Bayesian model the authors developed included the use of a modelling offset to adjust a parametric generalized linear model (GLM) for fluctuating library size (Pendegraft et al., 2019). Five articles did not normalise the microbiome data prior to analysis (Chaudhari et al., 2019; Eren et al., 2015; Shi et al., 2020; Sjödin et al., 2019; Zhang et al., 2015). One did not perform any form of normalisation as only the quality of the reads was studied (Ram et al., 2011). One article did not investigate the microbiome, instead performing RNA-seq on strains from a single bacteria species (Hansen et al., 2011).\n\nOf the 381 abstracts evaluated for inclusion, 144 (37 %) included calculation of either an alpha or beta diversity metric in the abstract. Five papers that included an alpha or beta diversity metric were randomly selected for full text review in order to demonstrate the variety of approaches and use of diversity metrics in the metagenomic literature.\n\nThe Shannon diversity index is one of the most common methods of presenting information about intra-sample diversity in the literature. Shannon diversity is typically calculated for the groups or subgroups of interest and then compared using standard statistical tests. For example, comparison of Shannon diversity across two groups was done using a Mann-Whitney U test (Depner et al., 2017), and a t-test (Dickson et al., 2015). In order to investigate the differences in Shannon diversity in more than two categories some researchers make use of boxplots and test for differences using ANOVA (Dickson et al., 2015).\n\nIn four of the articles randomly selected to evaluate diversity metrics a beta diversity metric was also calculated and used to perform clustering or comparison of the diversity between samples. One paper did not report any alpha diversity metric, however unweighted UniFrac distances were calculated as beta diversity metrics and group differences in beta diversity compared using a Mann-Whitney U test (Iwauchi et al., 2019). Similarly, Depner et al. (2017) calculated UniFrac distances and compared differences in beta diversity between individuals with asthma and controls using Wilcoxon test. One randomly selected paper presented the visualized UniFrac distances after applying Principal Coordinates Analysis (PCoA) as an ordination method, and then performed clustering via partitioning around medoids for a number of distance metrics (Koren et al., 2013). Finally unweighted and weighted UniFrac distances were compared between groups using Permutational Multivariate Analysis of Variance (PERMANOVA), and a novel method, known as MiRKAT, developed by the study authors (Zhao et al., 2015).\n\nA wide variety of methods are used to analyse microbiome data, however testing for differences in diversity and testing for differential abundance are the most common goals of microbiome sequencing analyses. Of the five papers randomly selected to investigate analysis methods used in microbiome sequencing studies, one paper made use of the “standard QIIME pipeline” and ANOVA to test for differentially abundant bacterial genera from 16S rRNA sequencing (Chaudhari et al., 2019). One paper used linear discriminant analysis (LDA) effect size (LEfSe) to identify Blautia oligotypes that show statistically significant differential abundances among groups of human and sewage samples versus animals (Eren et al., 2015). LEfSe determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance (Segata et al., 2011). Another common software tool for differential abundance analysis is DESeq2. DESeq2 was originally developed to analyse data from RNA-seq experiments, however it has been advocated for use in other experiments that generate sequence count data (Calgaro et al., 2020). One randomly selected paper used DESeq2 to investigate relative changes in gut microbiota between allergic and nonallergic children over time (Sjödin et al., 2019). One of the randomly selected papers created a novel Bayesian hierarchical negative binomial model to investigate differentially abundant OTUs found in metagenomic sequencing (Pendegraft et al., 2019). One paper made use of generalized linear models to assess differential mean abundance between samples from women who had adverse childhood experiences and those that had not; multiple tests were corrected with the Benjamini-Hochberg method (Hantsoo et al., 2019).\n\nOf the 6100 abstracts searched, only 19 (0.54%) abstracts included compositional data analysis methods, one of these papers provided an example and walkthrough of a metagenomic analysis using available compositional data software tools in the R programming language (Macklaim and Gloor, 2018), six of these papers focussed on development of methods for cross-sectional compositional data (Fang et al., 2015; Friedman and Alm, 2012; Kurtz et al., 2015; Quinn et al., 2018; Weiss et al., 2017; Woloszynek et al., 2019) and one paper investigated novel methodology for longitudinal compositional data (Äijö et al., 2018). These 7 papers combined explored the development of a range of problems in compositional data analysis including the creation of networks from compositional data, probabilistic approaches to model overdispersion and sampling zeros using Gaussian Processes, and modelling types of zeroes present in microbiome data, but were all focussed on the development of novel methods. The remaining 12 (63%) papers that used compositional data analysis methods focussed on application of CoDa methods for metagenomic data.\n\n\nDiscussion\n\nComparison between samples within microbiome sequencing experiments is challenging because it is often very difficult to collect the same number of reads for each sample even if the same sample is sequenced multiple times. Differences in sample read count can arise from differences in the sequencing machine, difficulties in loading the same molar amounts of the sequencing libraries, or because of random variation (Gloor, Macklaim et al., 2017). The total read depth is a strong confounder for any distance or diversity metric used and is thus also a strong confounder for any downstream analyses that make use of these distance or diversity metrics (McMurdie and Holmes, 2014).\n\nInitially “rarefying” was a common method of normalising read counts between samples, however McMurdie and Holmes (2014) question the validity of rarefying because “although rarefying does equalise variances, it does so only by inflating the variances in all samples to the largest (worst) value among them at the cost of discriminating power (increased uncertainty)”. The prevalence of rarefying in microbiome sequencing studies is likely to due to software pipelines for analysing microbiome data that implement rarefying as the default method for dealing with large differences in read counts between samples. A variety of alternative normalisation strategies for metagenomic data have been proposed and are found in the literature. Commonly used alternatives to rarefying include the trimmed mean of M-values (TMM) (McCarthy et al., 2012; Robinson and Oshlack, 2010), and the normalisation scaling factor calculated by DESeq2 (Love et al., 2014). The utility of count normalisation strategies in general has also been questioned, as the number of counts returned by sequencing instruments do not contain information on the absolute number of molecules in the original environment due to the already described constraint to a fixed total number of reads. Researchers using a compositional data analysis approach normalise the data prior to analysis when sequence count data are converted to log-ratios (Gloor, Macklaim et al., 2017).\n\nThe choice of normalisation method can dramatically alter the ability of methods to distinguish signal from noise depending on the methods used (Lin et al., 2016; Weiss et al., 2017). For example, the choice of normalisation methods can alter conclusions drawn from community comparisons using beta diversity metrics (McKnight et al., 2019). Some normalisation methods, such as TMM normalisation, can give different results depending on how low abundance reads get removed from the dataset.\n\nA key scientific objective of many metagenomic sequencing experiments is to investigate if a particular microbial composition is associated with a given outcome. For example, investigating if the diversity in a sample from an individual with a particular disease differs from that of a comparable healthy control. Microbiome sequencing studies have been used to investigate questions in a wide range of research areas including epidemiology (Willner et al., 2009), clinical diagnostics, and as potential treatments for certain diseases (Rossen et al., 2015).\n\nOne common way this is done in the literature is to calculate a summary measure of the diversity present in a given sample, typically an alpha diversity measure, and then compare the mean species diversity between the two groups representing those samples. These diversity metrics are then often used in further downstream analyses, such as ordination or regression. Beta diversity, a measure of the dissimilarity of microbial communities between samples, is also commonly calculated in microbiome studies. Beta diversity dissimilarity matrices are used for ordination, such as principal coordinates analysis (PCoA) or principal component analysis (PCA), or classification depending on the research question. These methods allow for the visualization of complex high-dimensional dissimilarity matrices in lower dimensional spaces. Ordination plots can then be supplemented by the inclusion of sample metadata to visualize any possible sample clustering based on the metadata, for example PCA plots can be generated and coloured by sample disease status. Although the total number of reads in a sample is a strong confounder for dissimilarity-based methods (McMurdie and Holmes, 2014), dissimilarity matrices generated after the data has been normalised may still provide useful information about sample dissimilarity. Three such dissimilarity matrices are commonly used in the literature; Bray-Curtis dissimilarity, Jensen-Shannon distance, and UniFrac distance (Lozupone et al., 2011).\n\nThe use of these diversity metrics in metagenomic studies has been criticised as inappropriate for compositional data, as the dissimilarity metrics do not take into account the compositional nature of microbiome data. Beta diversity metrics are sensitive to the total sequencing read depth of a sample, and many distance or dissimilarity methods discriminate between samples largely based on the most relatively abundant features in the samples, not on the features that are necessarily the most variable between samples (Gorvitovskaia et al., 2016; Wong et al., 2016). This can lead to a substanial shift in the location of included samples in an ordination depending on included and excluded dataset features (Gloor, Macklaim et al., 2017; Wong et al., 2016). Alternatives for compositional data such as Aitchison distance and adjustments to UniFrac distances have been proposed (Wong et al., 2016) that do account for the compositional nature of the data.\n\nAlpha and beta diversity metrics provide useful descriptive summaries of the microbial diversity present in a given sample. However, in many microbiome studies the aim is not merely to determine if samples are more or less diverse than one another but rather to determine which microbes are differentially abundant between the comparison groups of interest. In compositional data structures, when the proportion of one microorganism increases, the proportions of the other microorganisms in the sample must by definition decrease to allow for the standardised proportion of all OTUs to sum of 1 (Aitchison, 1986; Gloor, Wu et al., 2016). Furthermore, microbiome data is sparse and high-dimensional, typically containing many more features than there are samples and many OTUs are either not detected in all samples or are removed during data quality control and pre-processing pipelines (Paulson et al., 2013). Count distributions arising from microbiomes sequencing data are also known to be overdispersed (McMurdie and Holmes, et al., 2014; Richards, 2008). The combination of these features of microbiome sequencing data makes determining true differences in microbial composition challenging and calls for the use of specialized analytic methods.\n\nIdentifying differentially abundant features in microbiome data is a common goal of microbiome sequencing studies. As such there are a number of methods that have been applied to detecting differentially abundant features. Although not appropriate for compositional data, classical statistical methods such as parametric statistical tests (for example, two sample t-tests, Wilcoxon rank sum tests, and ANOVA) and measures of correlation, including Spearman’s rank correlation, and Pearson correlation are frequently used to investigate differentially abundant organisms and microbial networks. More sophisticated methods have been developed to assess differentially abundant features between samples by taking into account the nature of microbiome data as well as the number of hypothesis tests performed during differential abundance analysis. For example, one of the most common methods for performing differential abundance analyses on an entire microbiome sequencing dataset at once is implemented in the R package DESeq2 (Love et al., 2014). Given the challenges associated with metagenomic data and multiple testing, methods for detection of differentially abundant organisms in microbiome sequencing studies are an active area of research. The two most common software pipelines for bioinformatic processing of metagenomic sequencing data are QIIME2 (Bolyen et al., 2019) and mothur (Schloss et al., 2009), both of these software pipelines include tools to prepare, quality control, and analyse data from metagenomic experiments. Failing to account for compositionality of metagenomic data means that findings for microbiome analysis carried out with these methods are particularly sensitive to negative correlation bias. Furthermore, many current methods for differential abundance analysis in microbiome studies have been shown to have unacceptably high false discovery rates. In some cases, depending on the method and data pre-processing pipeline the false discovery rates exceeded 80% (Hawinkel et al., 2019; Weiss et al., 2017).\n\nAn important step in microbiome sequencing projects is visualization of the high-dimensional abundance tables. Typically, this is done by reducing the dimensionality of the data via PCoA, and then plotting the resulting principal coordinates. In the compositional data analysis framework, the equivalent of the PCoA plot is the variance-based compositional principal component (PCA) biplot (Aitchison and Greenacre, 2002). Compositional alternatives for investigating the relative abundance of OTUs between groups have also been developed to replace traditional differential abundance analysis methods. For example, the ALDEx2 R package provides compositional methods for estimation of differential expression by performing statistical tests on the centered log-ratio (CLR) values from a modelled probability distribution of the dataset and reports the expected values of parametric and non-parametric statistical tests along with estimate of effect-size (Fernandes, Macklaim et al., 2013; Fernandes, Reid et al., 2014). The ANCOM R package offers an alternative to ALDEx2 for differential abundance testing while taking into account compositionality. ANCOM performs statistical tests on point estimates of data transformed by an additive log-ratio (ALR) transformation, where invariant taxa are chosen as the reference for the ALR transformation (Mandal et al., 2015).\n\nAlthough not yet widely used in the literature, there exist statistical methods for the analysis of compositional microbial data from cross-sectional microbiome sequencing experiments (Gloor, Macklaim et al., 2017). For example, sequencing read counts are explicitly normalized across samples when analysed as compositional, because compositional analyses make use of log-ratio transformations of the abundance tables (Aitchison, 1986). Log-ratios have the important mathematical property that their sample space is the whole real number line, and thus many standard statistical analyses that have been developed for real random variables can be used in conjunction with log-ratios while appropriately taking into account the compositionality of the data. Similarly in some applications the Aitchison distance, defined as the Euclidean distance between two log-ratio points, can be used as the compositional alternative to common ecological distance measures, such as Bray-Curtis, UniFrac, and Shannon distances (Gloor, Macklaim et al., 2017). There are also proposed compositional alternatives to determine correlation and other measures of association for compositional data, such as the proportionality (Φ) (Lovell et al., 2015) and proportionality coefficient (p) (Erb and Notredame, 2016) metrics.\n\nThe 12 papers that analysed microbiome data using methods for compositional data can be broadly classified into two groups; studies that analysed data from longitudinal microbiome experiments (three papers) and studies that analysed data from cross-sectional microbiome sequencing experiments (nine papers). Of the papers that analysed cross-sectional microbiome data three papers did not fully utilise a compositional data analysis pipeline, instead only making use of ANCOM to evaluate differentially abundant OTUs (Chung et al., 2019; Iszatt et al., 2019; Lee et al., 2014). All other papers that were included in this review transformed the data via the CLR transform prior to performing statistical tests on the OTU tables. Although the utility of ecological diversity measures for metagenomic data is debated, three papers that utilised compositional methods reported conventional ecological diversity metrics, such as Shannon and UniFrac distances (Genco et al., 2019; Peters et al., 2017; San-Juan-Vergara et al., 2018), instead of the compositional alternatives such as Aitchison distance.\n\nOnly three studies used compositional methods to investigate the change in human microbial composition over time, a specific focus of this review, however all three of the studies evaluated time points independently from one another. For example, Dahl et al. (2018) investigated the gut microbiome in preterm infants at ten days, four months, and one year. The investigators performed a standard analysis of metagenomic data without accounting for compositionality, calculated traditional diversity metrics and evaluated differences in beta diversity using PERMANOVA. The authors then used ANCOM to test for differentially abundant OTUs at each time point separately. The other two papers that investigated the microbiome at two timepoints transformed all OTU counts via the centered log-ratio transformation. In the study by Dijkhuizen et al. (2019) zero values were dealt with by imputing the missing values using the robCompositions R package. Log ratio-transformed OTU relative abundances were then analysed using principal components analysis (PCA), and group difference in log-ratio transformed relative abundances were assessed with logistic regression. Notably, baseline, inactive disease, and persistent activity samples were analysed independently. Finally, Stanaway et al. (2016) measured exposure to seasonal pesticides during the spring-to-summer fruit-thinning season and the offseason. Prior to transformation into log-ratios alpha diversity measures were calculated, then OTU tables were then transformed using the CLR transform. The PCA on CLR transformed data was used as an exploratory examination of the beta diversity in spring/summer and winter samples separately. Group differences in PC1 scores from the PCA were compared using t-tests. The PCA data was then used to determine clusters in the spring/summer and winter season data respectively, in order to determine if a cluster with exposure to azinphos-methyl could be distinguished from non-exposure based on OTU table data.\n\nAn area of open research in compositional methods for microbiome data is the application of compositional analysis methods to data from longitudinal microbiome sequencing studies where we must assume there exist correlation within individuals. Theoretical methods for the analysis of some forms of longitudinal dependence in compositional data have been developed (Pawlowsky-Glahn et al., 2015), however these methods have not yet been applied or tested for use in microbiome sequencing studies.\n\n\nConclusion\n\nThis review had identified that many of the published analyses of microbiome sequencing data fail to account for the compositional nature of microbiome data, and the applicability of those methods to microbiome data. Given the rapid decrease in costs of sequencing entire microbial communities, it is likely that longitudinal studies of microbial communities will become more prevalent. Thus, longitudinal microbiome study designs and appropriate analysis methods will become critical for extracting useful information from microbiome data.\n\n\nData availability\n\nData and source code available from: https://github.com/luhann/lit-review-phd.\n\nThis project contains the following underlying data:\n\nlit_review.r. R script and code used to process literature review results. pubmed_results.xml. Xml file containing full text of all open access articles in PubMed Central. lit_review_anon.csv. Annotated csv file containing annotations for the 381 abstracts screened by authors.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAuthor contributions\n\nAll authors contributed equally from conception, design. PH was responsible for drafting of the manuscript and final approval for submission. ML and MN were responsible for supervision.", "appendix": "References\n\nÄijö T, Müller CL, Bonneau R: Temporal Probabilistic Modeling of Bacterial Compositions Derived from 16S rRNA Sequencing. Bioinformatics. Feb. 2018; 34(3): 372–380. PubMed Abstract \| Publisher Full Text\n\nAitchison J: The Statistical Analysis of Compositional Data. Monographs on Statistics and Applied Probability. GBR: Chapman & Hall, Ltd.;Aug. 1986.\n\nAitchison J, Greenacre M: Biplots of Compositional Data. Journal of the Royal Statistical Society: Series C (Applied Statistics). Oct. 2002; 51(4): 375–392. Publisher Full Text\n\nAzad MB, Konya T, Persaud RR, et al.: Impact of Maternal Intrapartum An-tibiotics, Method of Birth and Breastfeeding on Gut Microbiota during the First Year of Life: A Prospective Cohort Study. BJOG Int. J. Obstet. Gynaecol. May 2016; 123(6): 983–993. PubMed Abstract \| Publisher Full Text\n\nBolyen E, et al.: Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2. Nat. Biotechnol. Aug. 2019; 37(8): 852–857. PubMed Abstract \| Publisher Full Text\n\nCalgaro M, Romualdi C, Waldron L, et al.: Assessment of Statistical Methods from Single Cell, Bulk RNA-Seq, and Metagenomics Applied to Microbiome Data. Genome Biol. Dec. 2020; 21(1): 131–191. PubMed Abstract \| Publisher Full Text\n\nCalle ML: Statistical Analysis of Metagenomics Data. Genomics & Informatics. Mar. 2019; 17(1). PubMed Abstract \| Publisher Full Text\n\nCaporaso JG, Kuczynski J, Stombaugh J, et al.: QIIME Allows Analysis of High-Throughput Community Sequencing Data. Nat. Methods. May 2010; 7(5): 335–336. Publisher Full Text\n\nChaudhari D, Dhotre D, Agarwal D, et al.: Understanding the Association between the Human Gut, Oral and Skin Microbiome and the Ayurvedic Concept of Prakriti. J. Biosci. Sept. 2019; 44(5): 112. Publisher Full Text\n\nChervonsky AV: Influence of Microbial Environment on Autoimmunity. Nat. Immunol. Jan. 2010; 11(1): 28–35. Publisher Full Text\n\nChung Y-CE, Chen H-C, Chou H-CL, et al.: Exploration of Microbiota Targets for Major Depressive Disorder and Mood Related Traits. J. Psychiatr. Res. Apr. 2019; 111: 74–82. PubMed Abstract \| Publisher Full Text\n\nCraig SJC, Blankenberg D, Parodi ACL, et al.: Child Weight Gain Trajectories Linked To Oral Microbiota Composition. Sci. Rep. Sept. 2018; 8(1): 14030. PubMed Abstract \| Publisher Full Text\n\nDahl C, Stigum H, Valeur J, et al.: Preterm Infants Have Distinct Microbiomes Not Explained by Mode of Delivery, Breastfeeding Duration or Antibiotic Exposure. Int. J. Epidemiol. Oct. 2018; 47(5): 1658–1669. Publisher Full Text\n\nDahlberg J, Sun L, Waller KP, et al.: Microbiota Data from Low Biomass Milk Samples Is Markedly Affected by Laboratory and Reagent Contamination. PLoS One. June 2019; 14(6): e0218257. PubMed Abstract \| Publisher Full Text\n\nDepner M, Ege MJ, Cox MJ, et al.: Bacterial Microbiota of the Upper Respiratory Tract and Childhood Asthma. J. Allergy Clin. Immunol. Mar. 2017; 139(3): 826–834.e13. PubMed Abstract \| Publisher Full Text\n\nDickson RP, Erb-Downward JR, Freeman CM, et al.: Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography. Ann. Am. Thorac. Soc. Mar. 2015; 12(6): 821–830. PubMed Abstract \| Publisher Full Text\n\nvan Dijkhuizen EHP , Chierico FD, Malattia C, et al.: Microbiome Analytics of the Gut Microbiota in Patients With Juvenile Idiopathic Arthritis: A Longitudinal Observational Cohort Study. Arthritis Rheum. May 2019; 71(6): 1000–1010. PubMed Abstract \| Publisher Full Text\n\nDing M, Qi C, Yang Z, et al.: Geographical Location Specific Composition of Cultured Microbiota and Lactobacillus Occurrence in Human Breast Milk in China. Food Funct. Feb. 2019; 10(2): 554–564. PubMed Abstract \| Publisher Full Text\n\nDrengenes C, Wiker HG, Kalananthan T, et al.: Laboratory Contamination in Airway Microbiome Studies. BMC Microbiol. Dec. 2019; 19(1): 1–13. PubMed Abstract \| Publisher Full Text\n\nErb I, Notredame C: How Should We Measure Proportionality on Relative Gene Expression Data?. Theory Biosci. June 2016; 135(1): 21–36. PubMed Abstract \| Publisher Full Text\n\nEren AM, Sogin ML, Morrison HG, et al.: A Single Genus in the Gut Microbiome Reflects Host Preference and Specificity. ISME J. Jan. 2015; 9(1): 90–100. PubMed Abstract \| Publisher Full Text\n\nFang H, Huang C, Zhao H, et al.: CCLasso: Correlation Inference for Compositional Data through Lasso. Bioinformatics. Oct. 2015; 31(19): 3172–3180. PubMed Abstract \| Publisher Full Text\n\nFernandes AD, Macklaim JM, Linn TG, et al.: ANOVA-like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq. PLoS One. July 2013; 8(7): e67019. PubMed Abstract \| Publisher Full Text\n\nFernandes AD, Reid JN, Macklaim JM, et al.: Unifying the Analysis of High-Throughput Sequencing Datasets: Characterizing RNA-Seq, 16S rRNA Gene Sequencing and Selective Growth Experiments by Compositional Data Analysis. Microbiome. May 2014; 2(1): 15. Publisher Full Text\n\nFriedman J, Alm EJ: Inferring Correlation Networks from Genomic Survey Data. PLoS Comput. Biol. Sept. 2012; 8(9): e1002687. PubMed Abstract \| Publisher Full Text\n\nGarrett WS: Cancer and the Microbiota. Science. Apr. 2015; 348(6230): 80–86. PubMed Abstract \| Publisher Full Text\n\nGenco R, LaMonte M, McSkimming D, et al.: The Subgingival Microbiome Relationship to Periodontal Disease in Older Women. J. Dent. Res. Aug. 2019; 98(9): 975–984. PubMed Abstract \| Publisher Full Text\n\nGloor GB, Macklaim JM, Pawlowsky-Glahn V, et al.: Microbiome Datasets Are Compositional: And This Is Not Optional. Front. Microbiol. Nov. 2017; 8. PubMed Abstract \| Publisher Full Text\n\nGloor GB, Wu JR, Pawlowsky-Glahn V, et al.: It’s All Relative: Analyzing Microbiome Data as Compositions. Annals of Epidemiology. The Microbiome and Epidemiology. May 2016; 26(5): 322–329. PubMed Abstract \| Publisher Full Text\n\nGorvitovskaia A, Holmes SP, Huse SM: Interpreting Prevotella and Bacteroides as Biomarkers of Diet and Lifestyle. Microbiome. Apr. 2016; 4(1): 15. PubMed Abstract \| Publisher Full Text\n\nHansen EE, Lozupone CA, Rey FE, et al.: Pan-Genome of the Dominant Human Gut-Associated Archaeon, Methanobrevibacter Smithii, Studied in Twins. Proc. Natl. Acad. Sci. Mar. 2011; 108(Supplement 1): 4599–4606. PubMed Abstract \| Publisher Full Text\n\nHantsoo L, Jašarević E, Criniti S, et al.: Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress during Pregnancy. Brain Behav. Immun. Jan. 2019; 75: 240–250. PubMed Abstract \| Publisher Full Text\n\nHawinkel S, Mattiello F, Bijnens L, et al.: A Broken Promise: Microbiome Differential Abundance Methods Do Not Control the False Discovery Rate. Brief. Bioinform. Jan. 2019; 20(1): 210–221. Publisher Full Text\n\nIszatt N, Janssen S, Lenters V, et al.: Environmental Toxicants in Breast Milk of Norwegian Mothers and Gut Bacteria Composition and Metabolites in Their Infants at 1 Month. Microbiome. Feb. 2019; 7(1): 34. PubMed Abstract \| Publisher Full Text\n\nIwauchi M, Horigome A, Ishikawa K, et al.: Relationship between Oral and Gut Microbiota in Elderly People. Immunity, Inflammation and Disease. July 2019; 7(3): 229–236. PubMed Abstract \| Publisher Full Text\n\nKoren O, Knights D, Gonzalez A, et al.: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. PLoS Comput. Biol. Jan. 2013; 9(1): e1002863. PubMed Abstract \| Publisher Full Text\n\nKurtz ZD, Müller CL, Miraldi ER, et al.: Sparse and Compositionally Robust Inference of Microbial Ecological Networks. PLoS Comput. Biol. May 2015; 11(5): e1004226. PubMed Abstract \| Publisher Full Text\n\nLander ES, et al.: Initial Sequencing and Analysis of the Human Genome. Nature. Feb. 2001; 409(6822): 860–921. Publisher Full Text\n\nLee SC, Tang MS, Lim YAL, et al.: Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota. PLoS Negl. Trop. Dis. May 2014; 8(5): e2880. PubMed Abstract \| Publisher Full Text\n\nLin Y, Golovnina K, Chen Z-X, et al.: Comparison of Normalization and Differential Expression Analyses Using RNA-Seq Data from 726 Individual Drosophila Melanogaster. BMC Genomics. Dec. 2016; 17(1): 1–20. Publisher Full Text\n\nLove MI, Huber W, Anders S: Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2. Genome Biol. Dec. 2014; 15(12): 550–550. PubMed Abstract \| Publisher Full Text\n\nLovell D, Pawlowsky-Glahn V, Egozcue JJ, et al.: Proportionality: A Valid Alternative to Correlation for Relative Data. PLoS Comput. Biol. Mar. 2015; 11(3): e1004075. PubMed Abstract \| Publisher Full Text\n\nLozupone C, Lladser ME, Knights D, et al.: UniFrac: An Effective Distance Metric for Microbial Community Comparison. ISME J. Feb. 2011; 5(2): 169–172. PubMed Abstract \| Publisher Full Text\n\nLuckey TD: Introduction to Intestinal Microecology. Am. J. Clin. Nutr. Dec. 1972; 25(12): 1292–1294. Publisher Full Text\n\nMacklaim JM, Gloor GB: From RNA-Seq to Biological Inference: Using Compositional Data Analysis in Meta-Transcriptomics. Methods in Molecular Biology (Clifton, N.J.). Oct. 2018; 1849: 193–213. Publisher Full Text\n\nMandal S, Treuren WV, White RA, et al.: Analysis of Composition of Microbiomes: A Novel Method for Studying Microbial Composition. Microb. Ecol. Health Dis. Dec. 2015; 26(1): 27663. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcCarthy DJ, Chen Y, Smyth GK: Differential Expression Analysis of Multifactor RNA-Seq Experiments with Respect to Biological Variation. Nucleic Acids Res. May 2012; 40(10): 4288–4297. PubMed Abstract \| Publisher Full Text\n\nMcKnight DT, Huerlimann R, Bower DS, et al.: Methods for Normalizing Microbiome Data: An Ecological Perspective. Methods Ecol. Evol. Mar. 2019; 10(3): 389–400. Publisher Full Text\n\nMcMurdie PJ, Holmes S: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. PLoS Comput. Biol. Apr. 2014; 10(4): e1003531. PubMed Abstract \| Publisher Full Text\n\nMorey M, Fernández-Marmiesse A, Castiñeiras D, et al.: A Glimpse into Past, Present, and Future DNA Sequencing. Molecular Genetics and Metabolism. Special Issue: Diagnosis. Sept. 2013; 110(1): 3–24. Publisher Full Text\n\nMuniz LR, Knosp C, Yeretssian G: Intestinal Antimicrobial Peptides during Homeostasis, Infection, and Disease. Front. Immunol. Oct. 2012; 3. PubMed Abstract \| Publisher Full Text\n\nPaulson JN, Stine OC, Bravo HC, et al.: Differential Abundance Analysis for Microbial Marker-Gene Surveys. Nat. Methods. Dec. 2013; 10(12): 1200–1202. PubMed Abstract \| Publisher Full Text\n\nPaun A, Yau C, Danska JS: The Influence of the Microbiome on Type 1 Diabetes. J. Immunol. Jan. 2017; 198(2): 590–595. Publisher Full Text\n\nPawlowsky-Glahn V, Egozcue JJ, Tolosana-Delgado R: Modeling and Analysis of Compositional Data. John Wiley & Sons;Feb. 2015; 273.\n\nPendegraft AH, Guo B, Yi N: Bayesian Hierarchical Negative Binomial Models for Multivariable Analyses with Applications to Human Micro-biome Count Data. PLoS One. Aug. 2019; 14(8): e0220961. PubMed Abstract \| Publisher Full Text\n\nPeters BA, Wu J, Pei Z, et al.: Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers. Cancer Res. Dec. 2017; 77(23): 6777–6787. PubMed Abstract \| Publisher Full Text\n\nPiyathilake CJ, Ollberding NJ, Kumar R, et al.: Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses. Cancer Prev. Res. May 2016; 9(5): 357–366. Publisher Full Text\n\nQuince C, Walker AW, Simpson JT, et al.: Shotgun Metagenomics, from Sampling to Analysis. Nat. Biotechnol. Sept. 2017; 35(9): 833–844. Publisher Full Text\n\nQuinn TP, Crowley TM, Richardson MF: Benchmarking Differential Expression Analysis Tools for RNA-Seq: Normalization-Based vs. Log-Ratio Transformation-Based Methods. BMC Bioinformatics. Dec. 2018; 19(1): 1–15. PubMed Abstract \| Publisher Full Text\n\nR Core Team: R: A Language and Environment for Statistical Computing. manual. Vienna, Austria:R Foundation for Statistical Computing;2020.\n\nRam JL, Karim AS, Sendler ED, et al.: Strategy for Microbiome Analysis Using 16S rRNA Gene Sequence Analysis on the Illumina Sequencing Platform. Syst Biol Reprod Med. June 2011; 57(3): 162–170. Publisher Full Text\n\nReuter JA, Spacek D, Snyder MP: High-Throughput Sequencing Technologies. Mol. Cell. May 2015; 58(4): 586–597. PubMed Abstract \| Publisher Full Text\n\nRichards SA: Dealing with Overdispersed Count Data in Applied Ecology. J. Appl. Ecol. Feb. 2008; 45(1): 218–227. Publisher Full Text\n\nRobinson CK, Brotman RM, Ravel J: Intricacies of Assessing the Human Microbiome in Epidemiologic Studies. Annals of Epidemiology. The Microbiome and Epidemiology. May 2016; 26(5): 311–321. PubMed Abstract \| Publisher Full Text\n\nRobinson MD, Oshlack A: A Scaling Normalization Method for Differential Expression Analysis of RNA-Seq Data. Genome Biol. Mar. 2010; 11(3): R25–R29. PubMed Abstract \| Publisher Full Text\n\nRossen NG, MacDonald JK, de Vries EM , et al.: Fecal Microbiota Transplantation as Novel Therapy in Gastroenterology: A Systematic Review. World J Gastroenterol: WJG. May 2015; 21(17): 5359–5371. PubMed Abstract \| Publisher Full Text\n\nSalter SJ, Cox MJ, Turek EM, et al.: Reagent and Laboratory Contamination Can Critically Impact Sequence-Based Microbiome Analyses. BMC Biol. Nov. 2014; 12: 87. PubMed Abstract \| Publisher Full Text\n\nSan-Juan-Vergara H, Zurek E, Ajami NJ, et al.: A Lachnospiraceae-Dominated Bacterial Signature in the Fecal Microbiota of HIV-Infected Individuals from Colombia, South America. Sci. Rep. Mar. 2018; 8(1): 1–13. PubMed Abstract \| Publisher Full Text\n\nSanger F, Nicklen S, Coulson AR: DNA Sequencing with Chain-Terminating Inhibitors. Proc. Natl. Acad. Sci. U. S. A. Dec. 1977; 74(12): 5463–5467. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSavage DC: Microbial Ecology of the Gastrointestinal Tract. Annu. Rev. Microbiol. Oct. 1977; 31(1): 107–133. Publisher Full Text\n\nSchloss PD, Westcott SL, Ryabin T, et al.: Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Appl. Environ. Microbiol. Dec. 2009; 75(23): 7537–7541. PubMed Abstract \| Publisher Full Text\n\nSegata N, Izard J, Waldron L, et al.: Metagenomic Biomarker Discovery and Explanation. Genome Biol. June 2011; 12(6): R60–R18. PubMed Abstract \| Publisher Full Text\n\nSender R, Fuchs S, Milo R: Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell. Jan. 2016a; 164(3): 337–340. Publisher Full Text\n\nSender R, Fuchs S, Milo R: Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. Aug. 2016b; 14(8): e1002533. PubMed Abstract \| Publisher Full Text\n\nShi Z, Qiu Y, Wang J, et al.: Dysbiosis of Gut Microbiota in Patients with Neuromyelitis Optica Spectrum Disorders: A Cross Sectional Study. J. Neuroimmunol. Feb. 2020; 339: 577126. Publisher Full Text\n\nSjödin KS, Hammarström M-L, Rydén P, et al.: Temporal and Long-Term Gut Microbiota Variation in Allergic Disease: A Prospective Study from Infancy to School Age. Allergy. Jan. 2019; 74(1): 176–185. PubMed Abstract \| Publisher Full Text\n\nStanaway IB, Wallace JC, Shojaie A, et al.: Human Oral Buccal Micro-biomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure. Appl. Environ. Microbiol. Dec. 2016; 83(2): e02149–e02116. PubMed Abstract \| Publisher Full Text\n\nStraub D, Blackwell N, Fuentes AL, et al.: Interpretations of Microbial Community Studies Are Biased by the Selected 16S rRNA Gene Amplicon Sequencing Pipeline. bioRxiv. Dec. 2019; p. 2019.12.17.880468. Publisher Full Text\n\nSugita T, Yamazaki T, Makimura K, et al.: Comprehensive Analysis of the Skin Fungal Microbiota of Astronauts during a Half-Year Stay at the International Space Station. Med. Mycol. Mar. 2016; 54(3): 232–239. PubMed Abstract \| Publisher Full Text\n\nThorsen J, Brejnrod A, Mortensen M, et al.: Large-Scale Benchmarking Reveals False Discoveries and Count Transformation Sensitivity in 16S rRNA Gene Amplicon Data Analysis Methods Used in Microbiome Studies. Microbiome. Nov. 2016; 4: 62. PubMed Abstract \| Publisher Full Text\n\nWeiss S, Xu ZZ, Peddada S, et al.: Normalization and Microbial Differential Abundance Strategies Depend upon Data Characteristics. Microbiome. Mar. 2017; 5: 27. PubMed Abstract \| Publisher Full Text\n\nWillner D, Furlan M, Haynes M, et al.: Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals. PLoS One. Oct. 2009; 4(10): e7370. PubMed Abstract \| Publisher Full Text\n\nWoloszynek S, Mell JC, Zhao Z, et al.: Exploring Thematic Structure and Predicted Functionality of 16S rRNA Amplicon Data. PLoS One. Dec. 2019; 14(12): e0219235. PubMed Abstract \| Publisher Full Text\n\nWong RG, Wu JR, Gloor GB: Expanding the UniFrac Toolbox. PLoS One. Sept. 2016; 11(9): e0161196. PubMed Abstract \| Publisher Full Text\n\nZhang F, He S, Jin J, et al.: Exploring Salivary Microbiota in AIDS Patients with Different Periodontal Statuses Using 454 GS-FLX Titanium Pyrosequencing. Front. Cell. Infect. Microbiol. July 2015; 5: 55. PubMed Abstract \| Publisher Full Text\n\nZhao N, Chen J, Carroll IM, et al.: Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test. Am. J. Hum. Genet. May 2015; 96(5): 797–807. PubMed Abstract \| Publisher Full Text\n\nZhu X, Xiang S, Feng X, et al.: Impact of Cyanocobalamin and Methylcobalamin on Inflammatory Bowel Disease and the Intestinal Microbiota Composition. J. Agric. Food Chem. Jan. 2019; 67(3): 916–926. PubMed Abstract \| Publisher Full Text" }	[ { "id": "278219", "date": "30 May 2024", "name": "Yi-Juan Hu", "expertise": [ "Reviewer Expertise Biostatistics", "bioinformatics", "microbiome analysis" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript aims to identify common analysis methods used in microbiome sequencing studies, including methods for data normalization and visualization, and compositional methods for association testing, with a focus on compositional methods in the analysis of longitudinal microbiome data. It was found that a very small proportion of microbiome studies made use of compositional data analysis methods.\n\nMajor Comments:\n-. Timeliness of Literature Search: The manuscript limited the search of literature to studies published before January 2022, which was two and a half years ago. This approach misses a large number of more recent publications and fails to serve as a timely review of the literature.\n-. Clarity of Search Terms: The search terms should be explained in plain language rather than computer code to improve readability and accessibility.\n-. Summary Table: It would be more readable and informative to provide a table that summarizes the type of analysis, common methods for the analysis, and proportions of papers that used these methods.\n-. Scope of Review: The review was limited to a very small proportion of the articles (e.g., 381 abstracts, 38 full articles) that satisfied the search criteria. It would be more informative to expand the review to include more articles.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] }, { "id": "294971", "date": "22 Jul 2024", "name": "Christopher A. Lowry", "expertise": [ "Reviewer Expertise Dr. Lowry’s research program focuses on understanding stress-related physiology and behavior with an emphasis on the microbiome-gut-brain axis", "a program designed to lead to novel", "microbiome-based interventions for the prevention of anxiety disorders", "mood disorders", "and trauma- and stressor-related disorders", "such as posttraumatic stress disorder (PTSD)." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript provides an assessment of analysis methods for 16S rRNA gene and metagenomic sequencing data based on a sample of studies published during a 22-year period between January 2000 and January 2022. The article is well-written and provides a useful account of how microbiome data, including measures of alpha diversity, beta diversity, and community composition, have been analyzed using statistical approaches. The article will be useful, particularly to researchers new to the microbiome field, in understanding many of the pitfalls of microbiome analysis, and may also be useful in courses and workshops designed to introduce trainees to microbiome analysis methods. The article highlights the need for continued development of statistical methods that are designed to analyze microbiome data, particularly longitudinal compositional data, statistical methods that have rarely been used during the period covered by the review. The microbiome field, including analysis tools, is rapidly evolving and, consequently, some new tools for analysis of compositional data, e.g., analysis of composition of microbiomes with bias correction (ANCOM-BC),1 and its application2, are not mentioned. It is possibly worth highlighting efforts to establish reporting guidelines for microbiome research, such as the STORMS checklist.3 Increased use of such reporting guidelines has potential to enhance the reproducibility of microbiome research and to enhance efforts to document, in the future, how microbiome analysis methods will undoubtedly continue to evolve as new tools become available.\nReferences: (Lin H, et al., 2020 [Ref 1]), (Lin H, et al., 2024 [Ref 2]), (Mirzayi C, et al., 2021 [Ref 3])\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-369
https://f1000research.com/articles/13-366/v1	23 Apr 24	{ "type": "Research Article", "title": "Digital nursing promotion has increased ethics digital literacy: Program improvement", "authors": [ "Rr Tutik Sri Hariyati", "Hanny Handiyani", "Tsania Ayu Zaharany", "Rona Cahyantari Merduaty", "Andi Amalia Wildani", "Shanti Farida Rachmi", "Dewi Gayatri", "Laode Abdul Rahman", "Nami Kobayashi", "Hanny Handiyani", "Tsania Ayu Zaharany", "Rona Cahyantari Merduaty", "Andi Amalia Wildani", "Shanti Farida Rachmi", "Dewi Gayatri", "Laode Abdul Rahman", "Nami Kobayashi" ], "abstract": "Introduction Digital technology plays a positive role in helping nursing services work more effectively and efficiently. This study reports on a competency improvement program based on the promotion of digital literacy.\n\nMethods This study applies the Assessment, Development and Design Program, Implementing and Evaluation (ADDIE) approach, which consists of five stages. The first is a study of gap assessment needs to increase digital literacy and an analysis using a Fishbone Diagram. The second to fifth stages are development, program design, implementation, and evaluation. The participants consisted of 10 nurses for the initial assessment using Focus Group Discussion. The sample for evaluating digital literacy pre- and post-implementation consisted of 25 nurses selected via purposive sampling. Nurses included in the evaluation stage are those who participated in digital literacy promotion. The instrument used was the “Person-Centered Digital Literacy” questionnaire, the validity of which was in the range of 0.497–0.897, with a reliability value of 0.975.\n\nResults In the first stage, the fishbone analysis recommended developing a program promoting digital literacy. Implementation was delivered to nurses after the flow and learning materials were developed and confirmed by nursing experts. The program increased perceptions (20%) of ethical attitude, awareness of data confidentiality and security, and use of social media with wisdom.\n\nConclusion The promotion of digital literacy with ADDIE model is needed to improve the competency of nurses in digital technology.", "keywords": [ "ADDIE", "Ethical Attitude", "Digital Literacy", "Digital Promotion", "Nurse" ], "content": "Introduction\n\nDigital technology is important in supporting health services, including improving nursing care, education, and decision making.1–6 Digitalization provides convenience and has a positive impact on the health sector,1 which is currently experiencing demand for a fast and precise shift. The coronavirus disease 2019 (COVID-19) pandemic has also encouraged the acceleration of the use of digitalization in health services for reasons of physical restrictions.1,7,8 The use of digital technology in this era aims to reduce the speed of transmission of contact transmission of infection.8,9 Some of the developments in digitalization in the COVID-19 era include telemedicine and telenursing.9,10 Telenursing has had a positive impact and can be utilized in conducting health education, health consultations, and medical consultations in pre- and post-operating procedures.11–14\n\nMoreover, the development of digital technology is not only used to provide services to patients but also to improve the competency of health workers, including those in the nursing profession. Digital-based education can be conducted through websites, e-learning, webinars, or even material sharing through mobile communication media or social media.13–15 This competency improvement was very much needed at the beginning of the pandemic because the new disease resulted in many gaps in knowledge, including how to treat patients, how to use Personal Protective Equipment (PPE), how to reduce virus transmission, and how to improve physical and psychosocial endurance. Digital-based education is widely carried out in the era of COVID-19, considering that the workload of nurses is growing along with the increase in the number of patients, making conventional training activities difficult to carry out. On the other hand, a lot of information and materials are being developed and given out by various parties, which can sometimes be confusing. Therefore, the dissemination of information and learning materials must be managed so that they are useful in supporting nursing care and services.16\n\nThe ability to filter the validity and reliability of information is one of the digital literacy skills that nurses must have. Digital literacy comprises being able to find, evaluate, and utilize appropriately, ethically, wisely, intelligently, carefully, precisely, and lawfully.17 The use of digital-based education or digitalization in health sectors must be managed carefully, with organizations requiring an effective internal control mechanism.18 Organizations must accompany the digitalization transformation so that because of the presence of digitalization in the era of COVID-19. For it to have a positive impact, hospitals need to understand digital literacy and develop human resource competencies in digital technology. Digital literacy could improve services for the community so that they can become responsive, innovative, productive, effective, organized, and higher quality.18,19\n\nBased on the results of an interview with the head of the nursing division at a hospital in Jakarta, Indonesia, it was found that while the use of digital technology in nursing care has been implemented, it is still not optimal. During the pandemic, this hospital had a great impetus to learn information about how to treat COVID-19 patients, improve resilience, and enter a new era of adaptation. The busyness of shifts and the current limitations of physical learning have led to an agreement to use an electronic system to improve the competence of nurses, especially in the use of PPE, new treatment methods for COVID-19 patients, efforts to reduce anxiety, and psychosocial support for nurses. Digitalization has also been used to implement integrated reporting through online teleconferencing, which is expected to facilitate effective and collaborative communication.\n\nThe hospital does not yet have a policy on how to use digitalization technology in the field of nursing services. The absence of standard procedures raises the risk of misuse of the digital system and the violation of ethical principles. Digital literacy competence must also be improved so that there is no risk of system failure. This study reports on a digital literacy promotion program that aims to increase digital literacy competency in nurses, including improving the ability to use technology appropriately, filter information, and implement ethics in using digital media.\n\n\nMethods\n\nThis study used data from the improvement program that was implemented after permission from the hospital and ethical approval were obtained in May 2022, from Ethical Board of Faculty of Nursing, Universitas Indonesia (Number 138/UN2.F12. D1.2.1/PPM.00.02/2022), and all respondents have signed the written informed consent. The respondents understood the purpose, benefits and procedures of the study. The team respected the right of respondents to participate in the improvement program. The questionnaires were filled out anonymously, and participant names are hidden and replaced with code names such as P1, P2 etc. The team ensured confidentiality and explained the benefits of socializing the promotion of digital literacy, which include accompanying the change of service providers with better quality and prioritizing patient safety. In publishing data from the improvement study, the authors will also use ethical principles by maintaining data confidentiality as well as individual and organizational privacy.\n\nThis study reports on quality improvement programs that have been carried out in hospitals after the pandemic and the new post-pandemic era in May to July 2022. The activity was carried out for five weeks using an Assessment, Development and Design Program, Implementing and Evaluation (ADDIE) approach. The ADDIE approach was chosen because from previous studies it was concluded that ADDIE can make it easier for trainees and nurses to follow the directions in a structured manner and can improve their competency. ADDIE also improve clinical leadership of head nurse.20–22\n\nThe ADDIE approach starts with an assessment and then continues to problem analysis using The Fishbone approach. The FGD aims to identify the room’s readiness to use digitalization and the problems that arise when implementing digitalization in health services. Problem identification was carried out using structured interview techniques and assessment using digital literacy questionnaires at the person center. Interviews were conducted with nine heads of rooms and one manager of the nursing division.39 A purposeful sampling procedure was conducted. An invitation with information about the study was deliver to the heads of wards, and all participants knew the reasons for doing the research. All the participant the selected were from wards that have treated Covid-19 patients. Questions in the interview include42: 1) Does the hospital already have a policy on the use of digitalization? 2) What is the current competency of nurses in using digital technology? 3) What is the availability of infrastructure and staff support that helps and facilitates the implementation of digitalization in the hospital? Before carrying out the FGD, bracketing was carried out by carrying out interview practice. Bracketing aims to help researchers discuss emotionally charged research questions and topics.\n\nThe FGD was conducted in the meeting room to avoid disturbances that might arise during the process and was held for about 60 minutes. All information from the participants were recorded by tape recording. At the end of the meeting, a number of unclear questions were asked again. All data in this study have been verified and reached saturation at the end of the interview. The FGD ended when all questions were answered, and all participants submitted their information. Transcipts were read twice to catch any writing error, then the data were organised, extracted to find meaningful using fishbone tema approach. Data validity test were performed by checked from participant. A Fishbone diagram is created after the FGD data has been examined and is used to list the various root causes that may be associated with a problem. As a result, this diagram helps differentiate the root cause from the various contributing elements. The main application of this visual is in dispersion analysis. By analyzing additional causes of each primary cause and how they impact the quality attribute, dispersion analysis thoroughly investigates each of them. A cause-and-effect fishbone diagram focuses on a highlighted problem or symptom and shows the root cause. Through a Fishbone we can identify real problems and their underlying causes, thereby enabling the creation or selection of alternative action plans.\n\nThe second step of promotion programs consist of design and development programs. Designing and developing the program involved using a drafting procedure, producing learning materials, and then continue by nurse expert face validation. The development of learning media includes digital security, digital security, digital identity, and digital welfare.\n\nThe third step was implemented with face-to-face training in one day and continued with online simple share material learning by WhatsApp group communication. Every day, the nurse manager delivered reminders about the ethical conduct using digital health and open discussion for barrier in implementation digital for patient education and nursing electronic documentation.\n\nAn evaluation of the digital literacy competency of nurses was carried out using the original questionnaire developed by the researcher.41 The questionnaire was refered from “A Health and Care Digital Capabilities Framework” by NHS, London, which includes four sub-variables, namely, digital security literacy, digital well-being, digital security, and digital privacy. The six domains of digital literacy in person-centered care are communication, collaboration, and participation; teaching, learning, and self-development; information, data, and media literacy; creation, innovation, and scholarship; and technical skills.23 The validity of the questionnaire is in the range of 0.497–0.897, while the reliability value is 0.975. A purposeful and convenient sampling procedure was conducted. The questionnaire was filled out by 25 nurses who met the criteria, and the questionnaires were given before and after implementation. Analysis of before and after implementation using the Excel (MS Office Version 2020).41\n\n\nResults\n\nThe stages of the ADDIE digital literacy promotion approach were assessment, design and development, implementation, and evaluation (see Table 1).\n\nADDIE Approach of the literacy nurse digitalization.\n\n\n\n1. Assessment & analysis\n\n\n\n1. Interview FGD with a nurse manager39\n\n2. Deliver pre-test before program implementation using the modification of “digital literacy in person center care Questionare”41\n\n3. Develop the Guidance42 & Procedure Operating Standard for FGD43\n\n4. Analysis40\n\n\n\n1. Fishbone analysis\n\n2. Statement Problem\n\n\n\n2. Design & development\n\n\n\n5. Development plan of action\n\n6. Develop of Operating Standard (SOP) for PIE44\n\n7. Face validity & reviewed of SOP by nurse manager & nurse expert\n\n8. Learning material\n\n9. Reviewed of learning material by nurse manager & nurse expert\n\n\n\n3. SOP\n\n4. Learning material:\n\n• confidentiality data\n\n• data security\n\n• how to use digital technology for communication\n\n• increasing productivity, and innovation\n\n• improve the welfare and health of nurses\n\n\n\n3. Implementation digital literacy promotion\n\n\n\n10. Face to face socialization by champion leader team\n\n11. Deliver socialization by what-up group by the head nurse\n\n12. Reminder in everyday by the head nurse\n\n13. Record and report\n\n\n\n5. Implementation program\n\n\n\n4. Evaluation\n\n\n\n14. Post-test post implementation\n\n\n\n6. The short result of evaluation in the one unit in the Hospital\n\n7. Recommendation for continue of digitalization promotion\n\nFocus Group Discussions were conducted with nine head nurses, and one nursing division manager. All heads of rooms come from rooms that have treated Covid-19 patients and all participants have work experience of more than 20 years. Nine participants were female, and one nurse manager was male. Participants stated that hospitals already have the facilities and infrastructure to implement digitalization. Participants also said that nurses are ready to use some digitalization but need to improve digitalization literacy, such as ethical behavior and innovation competence. There were several participant statements, and all statements were analyzed based on the Fishbone root cause theme approach (Figure 1).\n\nManagement aspect\n\nParticipants discussed about regulations and plans for using technology. Several quotations related to participants’ answers were taken from verbatims, thematic analysis, and summarized as management aspect themes.\n\n“We have guide, a strategic plan for development digital technology in health system.” (P1, P2)\n\n“… have unit as management system information.” (P1) (P3)\n\n“We not yet have ethic guide for using technology.” (P1, P3)\n\n“Our leader support for digitalization development.” (P3. P4)\n\n“Military culture, so there have been direct instructions from superiors at that time, we will change according to instructions.” (P1, P2, P3, P4, P5, P7)\n\n“Leader monitors directly at morning and every day.” (P3)\n\n“For ethics for digitalization, there is still no regulation, so there must be develop and educate.” (P1)\n\nPeople and environmental aspects\n\nParticipants discussed the readiness of nurse staff for digital implementation in hospital, and below are conversations taken from the results of the discussion.\n\n“At Hospital, when it comes to digital systems, it does take time in terms of changes, adaptation and assistance for our nurses.” (P1, P3)\n\n“We seem to be lacking in digitalization capabilities compared to other large hospitals.” (P3).\n\n“We need to increase digital literacy.” (P3) (P4) (P5) (P9).\n\n“When it comes to computer systems, there are still many people who are confused, so they need further strengthening and training in terms.” (P1, P4)\n\nMaterial and equipment\n\nParticipants discussed about the readiness of infrasructure for digital implementation, and below are conversations taken from the results of the focus group discussion.\n\n“In our case, the digital system is still not optimal.” (P1, P2)\n\n“We have INFOLATA.” (P1, P2, P3, P4)\n\n“We have INFOLATA as the information, digitalization and technology management unit in the hospital.” (P1)\n\n“You can ask the Head of INFOLATA regarding the digital ecosystem. There is already hardware and software so there should be a digital ecosystem.” (P3)\n\n“At Hospital, the technology used is complete and high quality.” (P2) (P5) (P6) (P7) (P8)(P9)\n\n“The hospital has good infrastructure and internet connection.” (P3) (P7)\n\nFigure 1 shows the Fishbone assessment analysis of the need to increase digital literacy. The assessment was carried out to identify the readiness of human resources, management, methods, environment, facilities, and infrastructure. The results of the analysis indicate that there are supporting elements that are ready to accept digitalization. The hospital in this study is a large hospital in Jakarta, Indonesia, accredited by the Hospital Accreditation Board and already in possession of health digitalization facilities, with electronic medical records, internet connection facilities, and an information technology system manager that functions as a support system if there are problems related to digital technology. Things that still need to be improved include a lack of regulation on the use of digital technology in nursing services, the sub-optimal digital literacy competency of nurses, and the fact that there is no socialization that can improve digital literacy. The promotion of digital literacy is very necessary considering the era of COVID-19 and new adaptation, which demands the use of technology to make services more effective and efficient. Digital technology is used for collaboration, coordination, and improvement in services in the context of implementing social distancing and reducing transmission through direct contact. From the results of the assessment, it was concluded that hospitals need to improve their quality through the promotion of digital literacy.\n\nThe strategy used a design and development approach by the quality improvement program in order to anticipate the use of digital technology and new adaptations in the COVID-19 and new adaptation era. The grow and build strategy are an approach recently to market penetration and product promotion development. This strategy is following the condition of hospitals that already have nursing staff, information technology support staff, and adequate infrastructure. The strategy for improving the quality of nursing services includes strengthening management through the standardization of procedures for using digital technology when providing nursing services. Standard procedures, among others, contain provisions for the use of centralized communication media led by the head nurse.\n\nStandard procedures were also associated with using only information and education that came from the hospital, and not social media sources that caused confusion and increased nurses’ anxiety. In addition, educational materials for the promotion of digital literacy were prepared. The preparation and development of digital literacy were arranged according to the literature, namely by synthesizing the components of management tools, people-centered digital literacy, and ethics in using digital technology. Information on how to maintain patient confidentiality, data security, and how to use digital technology to improve communication, productivity, innovation, and the welfare and health of nurses was also taken into account. The development of standard procedures and learning media was carried out over two weeks and all standard procedures and learning materials were reviewed by validation experts.\n\nThe next activity was to disseminate standard procedures for using digital technology in nursing services, and education to promote digital literacy. Characteristics of champions in the digital literacy promotion trial in this study were nine head nurses with bachelor education backgrounds and more than five years of work experience. As for the evaluation before and after the implementation of digital promotion with the ADDIE model. The sample included were 25 nurse practitioners with bachelor’s degrees in nursing who had worked for more than one year in the ward. The face-to-face socialization was delivered by the campion and was carried out in one day. After socialization, the implementation continued with the sharing of learning media in a WhatsApp group. The implementation, facilitated by the campion leader, was carried out over two weeks. The head nurse gave reminders about implementation, provided positive motivation, and recorded the progress of the implementation.\n\nThe respondents selected in the digital promotion evaluation were all nurses who had experience working with health technology and had also worked in wards caring for COVID-19 patients. The demographics of the respondents were male nurses (10%) and female nurses (90%); 6 nurses aged 20-25 years, 13 people between 25-45 years, and 6 people aged more than 45 years. Respondents’ education was 10 percent bachelor nurse and 90 percent were still vocational with more than one year of work.\n\nEvaluation of digital literacy competency was carried out after two weeks after socializing standard procedures and promoting the use of digitalization in nursing services. Pre- and post-evaluation of the digitalization literacy promotion program was done using people-centered digital literacy instruments. There was an observed increase in the awareness attitude to behave in using digital technology, but technology skills, the use of technology for productivity, digital technology development, and innovation capacities did not change. Therefore, this digital literacy promotion program must be continued, and nursing managers must implement an action plan for continuous digital competency improvement.\n\nFigure 2 shows the differences in digital literacy competency before and after the promotion of the digital literacy program. The domains of person-centered digital literacy that scored less than 80% before the intervention to promote digital literacy were: skills in using information technology, attitude when using digital technology, self-development, and the use of digital-based innovation. There was an increase in digital attitude after the intervention of socializing standard procedures for using digital technology in nursing services and socializing digital literacy. Competence in data and information communication, informal learning, and the use of digital information is optimal. This study showed an increase in aspects of digital attitude, while skills in technology, skills in increasing productivity by using technology, and abilities in development and innovation did not improve within two weeks after promotion.\n\n\nDiscussion\n\nDigital literacy is a basic competency that must be possessed by nurses who use digital technology in nursing services. Digital literacy involves competence in using digital technology appropriately and wisely.18 The use of digital technology ideally increases productivity, improves communication and coordination, and increases innovation and creativity.2,4 Digital literacy is very much needed in the 4.0 digital era and also in the era of COVID-19. The results of the study at the beginning of the pandemic found that the use of digital technology in the treatment room was still minimal.7,11 However, following a surge in cases, digital technology became an important medium to improve the competency of nurses in handling and using PPE.7,11,15,19,24,25\n\nDigital technology is also used for communication and coordination so that in a disaster situation there is information coming from one command center. In addition, several hospitals have also implemented increased use of electronic documentation, electronic patient education, and even telenursing.9,19 The positive side of using technology is that it can help nurses improve nursing care, namely by reducing human errors, improving human attutide, increasing patient safety, and increasing role competence24,26; on the other hand, the acceleration of this technology must be accompanied by digital readiness.24 Digital literacy is needed so that the use of digital technology when carrying out nursing services can be done ethically, and can increase effectiveness and efficiency.24,25\n\nNurses’ digital literacy in the aspects of skills, attitude, productivity, innovation, and creativity is still below 75%. This is certainly very worrying because it will have an impact on service quality. This condition is following previous research that found that low digital literacy has an impact on the duration of service response and subsequently on the quality of patient care. Previous studies have also identified that low levels of digital literacy lead to a lack of staff engagement with information systems.27 Bad computer skills and poor experience in using digital technology can affect staff attitudes toward digital literacy.28 Therefore, a low level of digital literacy is an obstacle to the development of hospital information systems and smart hospitals, whereas good digital literacy could increase productivity. Previous research has shown that nurses who can use digital technology have contributed to an increase in more effective care services.29\n\nThe promotion of digital literacy begins with reviewing the problem and then establishing a problem-solving plan. This study used the ADDIE approach because it provides a systematic pathway to improve nurses’ digital literacy. A previous study noted that the ADDIE approach also made a positive perception in the nurse continuing professional development.30 Moreover, ADDIE can also can be used in clinical learning and improve other nurse competencies.31\n\nThe ADDIE approach in the study started with assessment and then continued to problem analysis using a fishbone approach. The fishbone cause and effect diagram is a tool used to analyze the root cause of a problem and organize mutual relationships.31 Product quality after the initial assessment is the need for literacy digital promotion for a nurse.\n\nThe second stage of the study was design and development, which developed standard procedures for the use of digital technology. Standard digital procedures help determine the management of activities that use digital technology. Based on previous studies, standard procedures are important tools designed to improve service quality and serve as guidelines for the use of digital tools and technology in nursing services.32,33 In addition, it is necessary to conduct socialization in the implementation stage. The training program was conducted on how to use digitalization in the field of nursing services. Socialization components included digital security, digital identity, and digital welfare. The promotion of digital literacy is expected to aid in increasing digital literacy competence, especially in improving communication skills, coordination, innovation, and the use of technology to increase the productivity of health services.32\n\nThe evaluation of the digital literacy promotion program with ADDIE aproach showed changes in increasing competency in attitudes and behavior. The term ‘attitude’ in this study refers to the ability to appreciate the information and use professional ethics in communicating digitally and on social media. However, in general, there was no change observed in digital technology skills nor in increased productivity in useful services. The interview results show a low involvement of staff in using digital technology to support service productivity, so there is a risk of resistance to change. The reluctance to use innovation and digital skills to increase productivity may be because the nursing staff is not familiar with the use of information technology. Nurses need time to change patterns and adjust their attitudes and behaviors and therefore also require encouragement and self-commitment.32,34–36\n\nThe development of staff digital literacy is also influenced by the competency of nurse managers. The manager’s interpersonal role, which is highly coherent with the involvement of nursing staff, will increase the adaptation of digital literacy.32 Leader support is needed in influencing staff and providing encouragement for using digital media, communication tools, or networks in a healthy, ethical, wise, careful, precise, and law-abiding way.18 It is important to monitor and evaluate an information system in order to measure the extent to which the application of the latest technologies is working in hospitals. This is supported by Hariyati’s research, which showed that monitoring and evaluation can reduce errors in digital use.37\n\nThis study was carried out in a short time frame due to the pandemic and new post pandemic era situation, which required the strengthening of digital literacy competency in nursing services.37,38 The study was also carried out only in one of the pilot units with nine head nurses as a champion, and 25 nurses as participants. However, the digital literacy promotion method reported here can be used as a basis to develop a new digital literacy promotion model.\n\n\nConclusions\n\nDigital technology is an indispensable tool to improve service quality. In the COVID-19 era, the use of digital technology is increasing in light of the fact that digitalization can facilitate coordination and communication, and is widely used for educational materials on treating patients, using PPE, and reducing anxiety. The use of technology must be adequately managed, and the competency of its users must be improved so that digitalization can be used appropriately and wisely. The promotion of digital literacy for nursing staff in this study aimed to increase competency in using digital technology in nursing services. However, while it improved behavioral aspects in the use of digital technology, progress was not observed regarding improving skills that are more comprehensive in terms of increasing productivity, innovation, and creativity. Nursing managers need to establish a follow-up strategy to improve nursing digital literacy in order to use it to improve communication, coordination, and service productivity. The result of the digital literacy promotion with ADDIE aproach showed changes in increasing competency in attitudes and behavior.", "appendix": "Data availability\n\nFigshare. New updated Verbatim. https://doi.org/10.6084/m9.figshare.25516246. 39\n\nThis project contains the following underlying data:\n\n- Edit analisis Qualitative (narative.docx (Transcripts from interviews).docx\n\n- Procedure Operating Standard for Group Discussion Analysis.docx\n\nFigshare. Digitalization data analysis xlsx. https://doi.org/10.6084/m9.figshare.23813340. 40\n\nThe project contains the following underlying data:\n\n- data analysis xlsx (2).xlsx (Raw data from questionnaires)\n\nFigshare. Digital Literacy Questionare. https://doi.org/10.6084/m9.figshare.24657264. 41\n\nThis project contains the following extended data:\n\n- DIGITAL LITARACY QUESTIONARE.pdf\n\nFigshare. Focus Group Discussion Guidance. https://doi.org/10.6084/m9.figshare.24657243. 42\n\nThis project contains the following extended data:\n\n- FGD Guidance.pdf\n\nFigshare. Procedure Operating Standard for Group Discussion Analysis. https://doi.org/10.6084/m9.figshare.24893001. 43\n\nThe project contains the following extended data:\n\n- Procedure Operating Standard for Group Discussion Analysis.pdf (explanation on analysis of the FGD results)\n\nFigshare. translate SOP DIGITAL LITERACY IN PROVIDING EDUCATION TO PATIENTS AND FAMILIES.pdf. https://doi.org/10.6084/m9.figshare.24862848. 44\n\nThis project contains the following extended data:\n\n- translate SOP DIGITAL LITERACY IN PROVIDING EDUCATION TO PATIENTS AND FAMILIES.pdf (Standard operating procedure in English)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThank you for Nursing managers, Head Nurse, KA-INFOLATA and Clinical Instructors in Gatot Subroto Hospital who have facilitated focus group discussions and also validated the ADDIE module.\n\n\nBibliography\n\nMain F, Zubala A, Gorman J, et al.: Technology-enabled remote management of diabetes foot disease and potential for reduction in associated health costs: a pilot study. J. Foot Ankle Res. 2021; 14: 7. BioMed Central Ltd. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNegash S, Musa P, Vogel D, et al.: Healthcare information technology for development: improvements in people’s lives through innovations in the uses of technologies. Inf. Technol. Dev. 2018; 24: 189–197. Routledge. Publisher Full Text\n\nGlass J: The relationship between utilization of mobile health technology and in-person care. Addict. Sci. Clin. Pract. 2015 Dec; 10(S1). Publisher Full Text\n\nNaylor MD, Brooten D, Campbell R, et al.: Comprehensive Discharge Planning and Home Follow-up of Hospitalized Elders A Randomized Clinical Trial. JAMA. 1999; 281: 613–620. PubMed Abstract \| Publisher Full Text Reference Source\n\nHariyati RTS, Hamid AYS, Eryando T, et al.: The Effectiveness and Efficiency of Nursing Care Documentation Using the SIMPRO Model. Int. J. Nurs. Knowl. 2016 Jul 1; 27(3): 136–142. Publisher Full Text\n\nSetyaningrum I, Hariyati RTS, Novieastari E: Peningkatan Kelengkapan Dokumentasi dan Kepuasaan Perawat Pada Pengawasan Hospital Acquired Infections (HAIs) berbasis Komputer. J. Keperawatan Indones. 2016; 19(1): 33–40. Publisher Full Text\n\nFlaherty SJ, Delaney H, Matvienko-Sikar K, et al.: Maternity care during COVID-19: a qualitative evidence synthesis of women’s and maternity care providers’ views and experiences. BMC Pregnancy Childbirth. 2022 Dec; 22(1): 438. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWeber S, Günther E, Hahnel S, et al.: Utilization of dental services and health literacy by older seniors during the COVID-19 pandemic. BMC Geriatr. 2022 Dec 1; 22(1): 84. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrøndahl VA, Helgesen AK, Holm E, et al.: Remote monitoring of cancer patients during the Covid-19 pandemic – an interview study of nurses’ and physicians’ experiences. BMC Nurs. 2022 Dec 28; 21(1): 169. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNejadshafiee M, Nekoei-Moghadam M, Bahaadinbeigy K, et al.: Providing telenursing care for victims: a simulated study for introducing of possibility nursing interventions in disasters. BMC Med. Inform. Decis. Mak. 2022 Dec 1; 22(1): 54. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSong X, Liu X, Wang C: The role of telemedicine during the COVID-19 epidemic in China – Experience from Shandong province. Crit. Care. 2020; 24: 178. BioMed Central. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFarsi Z, Nasiri M, Sajadi SA, et al.: Comparison of Iran’s nursing education with developed and developing countries: a review on descriptive-comparative studies. BMC Nurs. 2022 Dec 1; 21(1).\n\nSchlenz MA, Schmidt A, Wöstmann B, et al.: Students’ and lecturers’ perspective on the implementation of online learning in dental education due to SARS-CoV-2 (COVID-19): A cross-sectional study. BMC Med. Educ. 2020 Oct 9; 20(1): 354. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDuszenko M, Fröhlich N, Kaupp A, et al.: All-digital training course in neurophysiology: lessons learned from the COVID-19 pandemic. BMC Med. Educ. 2022 Dec 1; 22(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTsiouris F, Hartsough K, Poimbouef M, et al.: Rapid scale-up of COVID-19 training for frontline health workers in 11 African countries. Hum. Resour. Health. 2022 Dec; 20(1). Publisher Full Text\n\nEnyan NIE, Boso CM, Ofori AA, et al.: Clinical preceptorship in Ghana in the era of COVID-19 pandemic: an interventional study. BMC Nurs. 2022 Dec 1; 21(1): 61. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEgarter S, Mutschler A, Brass K: Impact of COVID-19 on digital medical education: compatibility of digital teaching and examinations with integrity and ethical principles. Int. J. Educ. Integr. 2021 Dec 1; 17(1). Publisher Full Text\n\nKennedy S, Yaldren J: A look at digital literacy in health and social care. Br. J. Card. Nurs 2017; 12(9): 428–432. Publisher Full Text\n\nHannemann N, Götz NA, Schmidt L, et al.: Patient connectivity with healthcare professionals and health insurer using digital health technologies during the COVID-19 pandemic: a German cross-sectional study. BMC Med. Inform. Decis. Mak. 2021 Dec 1; 21(1): 250. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBasu R: Instructional Design Models: Benefits and Challenges. UGC Approved Journal. 2021; 1: 31. Reference Source\n\nDjojo A, Suhariyanto S, Kapadia R, et al.: Addie Model-Based Learning To Improve Competences Of Clinical Nurse Leaders. Jurnal Aisyah: Jurnal Ilmu Kesehatan. 2021 Sep 14; 6. Publisher Full Text\n\nDjojo A, et al.: Addie Model-Based Learning To Improve Competences Of Clinical Nurse Leaders. Jurnal Aisyah: Jurnal Ilmu Kesehatan. 2021; 6: 133–138. Publisher Full Text\n\nNational Health Service: A Health and Care Digital Capabilities Framework.Reference Source\n\nHolt KA, Overgaard D, Engel LV, et al.: Health literacy, digital literacy and eHealth literacy in Danish nursing students at entry and graduate level: A cross sectional study. BMC Nurs. 2020 Apr 10; 19(1): 22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFarsi Z, Sajadi SA, Afaghi E, et al.: Explaining the experiences of nursing administrators, educators, and students about education process in the COVID-19 pandemic: a qualitative study. BMC Nurs. 2021 Dec 1; 20(1): 151. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSerra G, lo Scalzo L, Giuffrè M, et al.: Smartphone use and addiction during the coronavirus disease 2019 (COVID-19) pandemic: cohort study on 184 Italian children and adolescents. Ital. J. Pediatr. 2021 Dec 1; 47(1): 150. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAspihan M, Kep M, Kep Kom S, et al.: Rethinking Digital Literacy Competencies of Indonesian Nursing Student in IR 4.0: Philosophical Context. Author. 2021. Reference Source\n\nMacLure K, Stewart D: A qualitative case study of ehealth and digital literacy experiences of pharmacy staff. Res. Soc. Adm. Pharm. 2018 Jun 1; 14(6): 555–563. PubMed Abstract \| Publisher Full Text\n\nKuek A, Hakkennes S: Healthcare staff digital literacy levels and their attitudes towards information systems. Health Informatics J. 2020 Mar 1; 26(1): 592–612. PubMed Abstract \| Publisher Full Text\n\nHsu TC, Lee-Hsieh J, Turton MA, et al.: Using the ADDIE model to develop online continuing education courses on caring for nurses in Taiwan. J. Contin. Educ. Nurs. 2014; 45(3): 124–131. PubMed Abstract \| Publisher Full Text\n\nHariyati RTS: Perencanaan, pengembangan dan utilisasi tenaga keperawatan. Jakarta: Rajawali Pers; 2014.\n\nZaharany TA, Hariyati RTS, Anisah S: Pengembangan Literasi Digital Keperawatan Dimasa Pandemi Covid-19: Case Study. Jurnal Kepemimpinan dan Manajemen Keperawatan. 2021 May 31; 4(1). Publisher Full Text\n\nNilasari P, Hariyati RTS, Anisah S: Penerapan SPO Pelaksanaan Asuhan Keperawatan di Ruang Sub Instalasi Rawat Inap X Rumah Sakit Militer Jakarta: Pilot Study. Dunia Keperawatan. 2020; 8(2): 178. Publisher Full Text\n\nNiang M, Dupéré S, Alami H, et al.: Why is repositioning public health innovation towards a social paradigm neces sary? A reflection on the field of public health through the examples of Ebola and Covid-19. Glob. Health. 2021 Dec 1; 17(1): 46. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nde Gani SM , Berger FMP, Guggiari E, et al.: Relation of corona-specific health literacy to use of and trust in information sources during the COVID-19 pandemic. BMC Public Health. 2022 Dec 1; 22(1). Publisher Full Text\n\nGray SM, Franke T, Sims-Gould J, et al.: Rapidly adapting an effective health promoting intervention for older adults—choose to move—for virtual delivery during the COVID-19 pandemic. BMC Public Health. 2022 Dec 1; 22(1): 1172. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHariyati RTS, Hamid AY, Eryando T, et al.: Usability and satisfaction of using electronic nursing documentation, lesson-learned from new system implementation at a hospital in Indonesia. Int. J. Healthc. Manag. 2020; 13(1): 45–52. Publisher Full Text\n\nHariyati RTS: New Verbatim. Figshare. New updated Verbatim. [Dataset]. Figshare. 2024. Publisher Full Text\n\nHariyati RTS: digitalization data analysis xlsx. [Dataset]. figshare. 2023. Publisher Full Text\n\nHariyati RTS: Digital Literacy Questionare. [Dataset]. Figshare. 2023. Publisher Full Text\n\nHariyati RTS: Focus Group Discussion Guidance. [Dataset]. figshare. 2023. Publisher Full Text\n\nHariyati RTS: Procedure Operating Standard for Group Discussion Analysis. [Dataset]. figshare. 2023. Publisher Full Text\n\nHariyati RTS: translete Sop Digital Literacy In Providing Education To Patients And Families.pdf. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "306463", "date": "03 Sep 2024", "name": "Joko Gunawan", "expertise": [ "Reviewer Expertise Nursing Management" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the chance. Here are my comments for consideration. TITLE:\nThe title and the content are not aligned, especially for the dependent variable. The title is explicitly stated as \"ethics digital literacy\"; in the content, it is only \"digital literacy.\" The term \"Digital nursing promotion\" is considered an independent variable in this study, while the content implied a different thing: a competency improvement program. The use of \"program improvement\" may not be correct, as the authors used the ADDIE approach to develop a competency improvement program. The title \"Digital nursing promotion has increased ethics digital literacy\" is too overclaiming, while the study design shows only a \"potential\" improvement. The findings cannot be overclaimed without a control/comparison group and controlling confounding variables.\nABSTRACT:\nThe year of the study should be provided. While the abstract seems appropriate, the content should be carefully checked to match the main text.\nBACKGROUND:\nWhile the introduction mentions \"digital literacy,\" it could benefit from a clearer definition of this term early on. A brief explanation of digital literacy in healthcare would help set a solid foundation for the discussion. Again, the authors need to focus on \"digital literacy\" or \"ethics digital literacy.\" Including some relevant statistics or data about the adoption of digital technology in healthcare or the current state of digital literacy among nurses could provide more context and emphasize the urgency of the issue. Also, elaborate more on how digital literacy specifically impacts nursing care, decision-making, and patient outcomes. This would help underline the significance of the study in a more detailed manner. Provide more specifics about the gaps in digital literacy and how these gaps affect nursing practice and patient care. This could include examples or previous research findings that highlight these issues. Clearly connect the identified issues and gaps to the objectives of the study. While the introduction mentions the goal of improving digital literacy, a more explicit statement about how the study aims to address these gaps would strengthen the introduction. Briefly outline how the study will address the issues mentioned. This could include mentioning the methodologies or strategies used in the subsequent sections of the paper.\nMETHODS & RESULTS:\nIt is still unclear whether the authors want to focus on ADDIE or Quality Improvement (QI) as their study design. Or do they want to use both approaches? However, combining these two approaches requires careful consideration to ensure each is used to its strengths. Citations, references, and each step should be carefully explained. Explain why both approaches are necessary if they chose both. For instance, the ADDIE model could be used to create structured training programs for digital literacy, whereas QI design could be used to continuously improve these training programs based on feedback and outcomes. Also, discuss how the overlapping elements between ADDIE and QI are managed. For example, both approaches involve evaluation, but in different contexts—ADDIE evaluates the effectiveness of educational content, while QI evaluates the effectiveness of process improvements. However, I can see the authors mostly focus on ADDIE rather than QI. Thus, clarification is needed. Assessment Stage: The assessment stage is well-documented, but the Fishbone diagram analysis could be explained in greater detail. Specifically, how were the themes derived, and how do they directly inform the design of the intervention? And, there is no citation for the Fishbone root cause theme approach. Design and Development Stage: The design and development of standard procedures are described, but it would be useful to include more information on how these procedures were validated. Were specific criteria used by the validation experts, and how was their feedback incorporated? Implementation Stage: The overview of the implementation stage could be enhanced by detailing the specific strategies for engaging the nursing staff. For example, were there any particular challenges encountered during the implementation, and how were they addressed? Evaluation Stage: The evaluation stage highlights an increase in digital literacy attitudes but notes that other competencies did not improve. Providing more context on why certain competencies might not have improved would be helpful. Were there specific barriers identified that hindered progress in these areas? It is confusing to know the exact name of the program. Digital promotion program, digitalization literacy promotion program, or a competency improvement program? The study used a sample size of 25 nurses to evaluate digital literacy before and after the intervention. While this sample size might provide preliminary insights, it is relatively small and limits the statistical power of the analysis. Larger sample sizes are generally needed to achieve more reliable and generalizable results. The statistical methods used to analyze changes in digital literacy competencies are not clearly detailed. More information on the statistical tests and their application would strengthen the analysis. Additionally, discussing any limitations related to sample size or statistical power would be beneficial. The provided data mainly includes descriptive statistics (e.g., percentages and qualitative summaries) but lacks inferential statistical analysis. For instance, details on mean scores, standard deviations, and statistical significance tests (such as t-tests or ANOVA) are not provided. The study did not include a control group for comparison. A control group is essential for ruling out other factors that could influence the observed changes in digital literacy, making it harder to attribute improvements solely to the intervention. Thus, the results cannot be overclaimed. The term \"potential\" is appropriate to describe the results. The study mentions the reliability of the digital literacy questionnaire (0.975) and the validity range (0.497–0.897). While the reliability is high, the validity range is quite broad, suggesting potential variability in how well the questionnaire measures digital literacy across different contexts. However, construct validity of the questionnaire is needed.\nDISCUSSION\nPlease provide more direct comparisons with existing studies would strengthen the context and highlight the study's significance. The discussion could better detail how each ADDIE stage directly addressed identified gaps in digital literacy. Please expand on specific barriers to staff involvement and suggest strategies for overcoming them. Please explore why digital literacy improvements did not lead to increased productivity. Please clarify what specific managerial competencies and support are necessary to enhance digital literacy. Importantly, please provide the implications of this study globally, specifically for nursing management and policy.\nLimitations:\nAcknowledge how the small sample size and single unit focus limit generalizability. Discuss how the brief study period might affect the depth and long-term impact of the intervention. Provide more details on measuring staff resistance and engagement issues. Address whether current evaluation methods captured all relevant digital literacy and productivity aspects. The study acknowledged potential resistance to adopting new technologies and the need for additional encouragement and self-commitment, which were not fully addressed in the intervention. Please offer specific recommendations for further research to build on these findings.\nAdditional: Grammatical errors should be removed, and academic writing should be enhanced.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-366
https://f1000research.com/articles/13-365/v1	23 Apr 24	{ "type": "Study Protocol", "title": "Hospital based interventional study implementation of supervised quality improvement protocol in reducing surgical site infections in obstetrics and gynaecological major surgeries: A study protocol", "authors": [ "Drashti patel", "Surekha Tayade", "Surekha Tayade" ], "abstract": "Background Surgical site infections (SSIs) pose a significant challenge in obstetric and gynaecological surgeries, with incidence rates ranging from 0.5% to 15%. These infections not only impact patient outcomes but also contribute to extended hospital stays and increased healthcare costs. To address this issue, a hospital-based interventional study is proposed, focusing on the implementation of a comprehensive quality improvement protocol within the Department of Obstetrics and Gynecology at Acharya Vinoba Bhave Rural Hospital (AVBRH), Wardha.\n\nMethods The study will include approximately 800 obstetric and gynaecological surgeries per year. Ethical approval has been obtained and written informed consent will be obtained from all enrolled women. The intervention involves the implementation of a surgical site infection prevention quality improvement protocol, encompassing elements such as standardized pre-operative antiseptic agents, proper cleaning procedures, and the use of injectable cefazolin. A structured proforma will be developed for data collection, covering demographic details, surgical parameters, surgeon characteristics, and post-operative outcomes.\n\nExpected outcome This study aims to assess the efficacy of the quality improvement protocol in reducing the incidence of surgical site infections. We anticipate that the implementation of this protocol will lead to a significant reduction in SSIs, improving patient outcomes and safety in obstetric and gynaecological surgeries. The study's findings will not only contribute to the body of knowledge on infection prevention but will also serve as a valuable framework for enhancing surgical safety in similar healthcare settings. Continuous evaluation and refinement of the protocol will be crucial for sustained success in reducing SSIs and improving overall patient care.", "keywords": [ "Surgical site infections", "Obstetrics and Gynaecology", "surgical interventions" ], "content": "Introduction\n\nInfection occurring at the site of a surgical procedure is termed surgical site infection (SSI) and is a type of healthcare-associated infection.1 Incisional infection is defined as an infection that extends from the incision site into the surrounding skin and subcutaneous tissue (superficial incisional infection), deeper soft tissues (such as fascia and muscle), or other anatomical structures (organ/space infection) within 30 days of surgery.2\n\nSurgical site infections are prevalent, with rates varying from 0.5% to 15% depending on the procedure and the patient's overall health condition.3 This issue significantly undermines the effectiveness of surgical interventions and has notable impacts on post-operative expenses and length of hospital stay (3–20 days longer than anticipated).4,5 Following abdominal surgery, environmental contamination, organisms on the patient's skin, or infectious sources within the abdominal cavity can lead to wound infections. Inadequate aseptic techniques by the surgical team, including the surgeon, or subsequent infection of a hematoma are also potential causes. Infection may occur anywhere, from a few days to a few weeks. The presence of an unexplained fever in a developing wound should always raise the suspicion of infection.6\n\nPost-operative wound infection and dehiscence remain problematic after abdominal surgery, significantly prolonging hospitalization and causing psychological distress to patients and their relatives.7 Wound site infection, suture pressure, excessively tight sutures, wound trauma, weak tissue or muscle, improper suture techniques used for closure, high-dose or prolonged corticosteroid use, and severe vitamin C deficiency (scurvy) are common causes of wound dehiscence.8 Symptoms associated with wound infection and dehiscence include bleeding from the wound, pain at the suture site, swelling and redness near the suture site, fever, broken sutures, and in extreme cases, complete rupture of the incision with bowel protrusion through the abdominal wall. This critical condition is referred to as “burst abdomen” and requires immediate attention.9\n\nInfection and disruption of surgical wounds have been linked to various factors, such as the presence of a previous scar or radiation at the incision site, failure to adhere to post-operative instructions (e.g., engaging in strenuous activity or lifting heavy objects too soon after surgery), surgical errors, and increased abdominal pressure due to factors such as fluid accumulation (ascites), bowel inflammation, severe coughing, straining, vomiting, and long-term use of corticosteroid medication.6\n\nThe implementation of preventive measures for surgical site infections, particularly through multimodal strategies, has proven effective in reducing both the frequency and burden of infections.10 For instance, there was a reported 17% decrease in SSI related to 10 selected procedures in the USA between 2008 and 2013, following improvement programs.11 In African hospitals, a 60% reduction in SSI risk was observed after the implementation of a World Health Organization (WHO) multimodal strategy within the context of the WHO Surgical Unit-based Safety Programme (SUSP), which includes SSI surveillance.12 The WHO strongly recommends surveillance and timely feedback of results, including SSI surveillance, as essential components of effective infection prevention and control (IPC) programs.10\n\n\nAim\n\nThis study is aimed to determine the efficacy of implementing quality improvement protocols in reducing the rate of surgical site infections among surgeries for gynecological or obstetrical indications.\n\n\nObjectives\n\n\n\n1) To study the incidence of surgical site infections following surgery for gynecological or obstetric indications.\n\n2) To study the decrease in surgical site infections in gynecological and obstetric surgeries before and after implementation of the quality improvement protocol.\n\n3) To study the effectiveness of the quality improvement protocol and timeline in which the reduction of infections occurs.\n\n\nMethods\n\nDoes a surgical site infection prevention quality improvement protocol reduce surgical site infections among surgeries for gynecological or obstetrical indications as compared to those in the pre-protocol era in a tertiary care rural hospital?\n\nEthical approval has been obtained from Institutional Ethics Committee (IEC) DMIMS (DU)/IEC/2022/113 Date-21/07/2022 and written informed consent from all enrolled women. This study is an analytical study based on behavioral intervention in the form of a standard infection prevention quality improvement protocol. The existing departmental protocol will be followed for the pre-protocol group; therefore, there will be no ethical issues. The ethical code of conduct will be followed, and the study subjects will not have any additional financial burden pertaining to the study. The CTRI Registration number is CTRI/2024/04/065567.\n\nA hospital-based interventional study will be conducted in this study. The duration of the study will be two years.\n\nThe study will be conducted at the Department of Obstetrics and Gynecology, Acharya Vinoba Bhave Rural Hospital (AVBRH), Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha.\n\nThe study population will include women undergoing major abdominal surgery in Obstetrics and Gynecology, in the AVBRH hospital, Sawangi, Meghe, Wardha.\n\nInclusion criteria\n\n1) Women of all age groups who underwent surgery for different obstetric or gynecological indications during the study period.\n\n2) Women undergoing surgical procedures for gynecological/obstetrical indications in the operation theatre of the maternal and child wing of the study hospital.\n\n3) Elective, as well as emergency surgical procedures, will be included.\n\n4) Women consenting for inclusion in the study will be included.\n\nExclusion criteria\n\n1) Women who recently operated at another hospital, were referred to the study hospital for complications and infection and require repeat surgery at the study hospital.\n\n2) Women undergoing minor surgical procedures e.g., dilatation and curettage, polypectomy, and encirclage\n\n3) Women undergoing surgeries by vaginal route.\n\n4) Women undergoing perineal surgeries.\n\n5) Women undergoing surgical procedures in the labour room.\n\n6) Women who do not give consent for inclusion in study.\n\nStudy withdrawal criteria\n\n1) Women unwilling to continue in study.\n\n2) Women lost to follow-up after initial inclusion in study.\n\nThe intervention will be in the form of a surgical site infection prevention quality improvement protocol, which will include the following steps:\n\na) Surgical hand scrubs according to WHO guidelines will be performed using soap and water with a standard timed technique for three minutes.2\n\nb) Standard gloving procedure will be done according to WHO guidelines with standard technique.\n\nc) Standardized pre-operative antiseptic agents and their application techniques will be used. Initial scrubbing of the abdomen with solution containing chlorhexidine gluconate, cetrimide, and isopropyl alcohol followed by solution containing chlorhexidine gluconate 2.5% and Ethyl alcohol will be conducted. This will be followed by the use of dry swab to clean the surgical area, followed by application of povidine iodine 5% solution with drying time of one minute and then draping will be commenced.\n\nd) AST (Association of surgical Technologists) Standards of Practice for Surgical Drapes.13\n\ne) Reducing traffic in operation theatre area and operation theatre\n\nf) The use of injectable cefazolin 60 minutes prior to surgical incision in elective surgery and 30 minutes prior to surgery in emergency surgery will be performed.\n\ng) Proper cleaning of operation theatre table after each surgery with carbonic acid will be performed.\n\nh) Secondary dressing of the wound on day four in a sterile environment will be performed. The surgical site infection prevention quality improvement protocol module will be developed after discussion with the faculty and stakeholders of the Department of Obstetrics and Gynecology of the study hospital with inclusion of the above eight elements. Feedback will be obtained, and external and internal validity checks will be performed. Training of the surgical team, nursing team, aesthetic team, technicians, and attendants will be conducted in two batches regarding the implementation of the protocol in the study hospital.\n\nImplementation will involve the following elements:\n\na) System change: Ensuring that the necessary infrastructure is in place to allow protocol at the point of care.\n\nb) Training/Education of operation theatre staff.\n\nc) Evaluation and feedback: Monitoring protocol implementation over a period of four weeks and ensuring compliance.\n\nd) Reminders in the workplace with posters placed at appropriate place in operation theatre area.\n\nThe Department of Obstetrics and Gynecology, AVBRH, Wardha, performs approximately 800 operations for obstetric and gynecological indications per year. The sample size is estimated based on the observations at the study hospital, in which prevalence of surgical site infections is approximately 4–5%. Following assumption of 95% confidence interval and 2% margin of error, sample size was calculated using the sample size formula.\n\nP = Infection rate =4–5% =0.04\n\nD = desired error of margin =2% =0.02\n\nPower of the test =80%\n\nThe study will consist of two arms: the pre-protocol arm and post-protocol arm.\n\nPre-protocol arm\n\nIn the pre-protocol arm, women requiring surgery who fulfil the inclusion and exclusion criteria will be enrolled as study subjects. Demographic information will be obtained. Physical examination, investigation and planning of surgery, anesthetic fitness, and posting the women for surgery will be performed by a team of doctors working in the maternal and child wing according to routine departmental protocols. Written informed consent will be obtained from each patient regarding the nature of surgery, indication for surgery, and benefits and risks involved in surgery, and written consent will be obtained for inclusion in the study. The existing departmental protocol for pre-operative skin preparation, draping, surgical technique, skin closure technique, and post-operative management will be followed until the patient is discharged. Study subjects will be monitored for evidence of surgical site infection by measuring the oral temperature every four hours and for clinical or bacteriological evidence of surgical site infection according to CDC definitions and guidelines.14,15 A wound swab of the surgical site will be sent for culture and sensitivity testing in case of evidence of clinical sepsis. Total and differential leukocyte counts will be performed. All consecutive women fulfilling the inclusion criteria during the period of three months after the commencement of the study will be included in the pre-protocol arm.\n\nPost-protocol arm\n\nIn the post-protocol arm, women requiring gynecological surgery who fulfill the inclusion and exclusion criteria will be enrolled as study subjects. The demographic details of the patients will also be obtained. Physical examination, investigation and planning of surgery, anesthetic fitness, and posting the women for surgery will be performed by a team of doctors working in the maternal and child wing according to routine departmental protocols. Written informed consent will be obtained from each patient regarding the nature of surgery, indication for surgery, and benefits and risks involved in surgery, and written consent will be obtained for inclusion in the study. The study subjects will undergo surgical procedures after ensuring compliance with the SSIPQI protocol at each step. Routine surgical technique, skin closure technique, and post-operative management will be followed until the patient is discharged. Study subjects will be monitored for evidence of surgical site infection by measuring the oral temperature every four hours and for clinical or bacteriological evidence of surgical site infection according to CDC definitions and guidelines.14,15 Wound swabs of surgical sites will be sent for culture and sensitivity testing in cases of evidence of clinical sepsis. Total and differential leukocyte counts will be performed. All women fulfilling the inclusion criteria during the period of three months after ensuring compliance with the protocol will be included in the post-protocol arm. Further management of women with SSI will be performed according to standard departmental practice, without interference from the study. All study subjects from both the pre-protocol and post-protocol arms will be followed up at two weeks and four weeks after the surgical procedure.\n\nData related to various outcome variables, such as demography, body mass index, associated medical, gynecological, and obstetrical risk factors; indication and nature of surgery-emergency or elective; duration of surgery; description of surgeon (postgraduate, junior consultant, senior consultant), skin closure technique, type of suture material for wound closure, intraoperative complications, need for blood transfusion, infective morbidity, surgical site infections, hospital stay, wound-related late complications, and mortality, if any, will be collected. A structured proforma will be developed, pilot-tested, validated, and used for data collection.\n\nThe data will be entered into a spreadsheet (Microsoft Excel 23) and transferred to SPSS version 235 software. Student’s t-test will be used to test continuous variables that are normally distributed, and the Mann-Whitney test will be used to compare continuous variables with a skewed distribution. Proportions will be compared using the chi-squared test. Multivariate logistic regression models will be constructed to determine the independent association of prognostic factors. The strength of association will be expressed as odds ratios or risk ratios and their precision at 95% confidence intervals. A two-level P-value (<0.05) will be considered significant.\n\nSurgical site infection\n\nAn infection that develops within 30 days of surgery and spreads to the skin, subcutaneous tissue, and deeper soft tissues (such as fascia and muscle) of the incision, as well as to any other part of the body (such as organs and spaces) that were opened or manipulated during the procedure.2\n\nSurgical wound\n\nA surgical term for a wound that is caused by a scalpel or other sharp cutting device and then closed in the operating theatre using sutures, staples, adhesive tape, or glue to bring the cut edges of the skin together as closely as possible.\n\nFebrile morbidities\n\nTwo occurrences of fever greater than 38 °C occurring at least four hours apart after the first 24 hours after surgery.\n\nSurgical site sepsis: classified according to the presence of (a) redness and/or (b) swelling and/or (c) pus.\n\nWound dehiscence: Suture line separation of more than 1 cm, whether superficial, deep, or across the entire abdominal wall (burst abdomen), as defined by the Centers for Disease Control and Prevention.14\n\nSuperficial incisional surgical site infection\n\nWithin 30 days of surgery, the infection is limited to the skin and subcutaneous tissue of the incision, and at least one of the following conditions must be met: 1. Purulent drainage, with or without laboratory confirmation from the superficial incision; 2. organisms isolated from an aseptically obtained culture of fluid or tissue from the superficial incision, 3. At least one of the following signs or symptoms of infection: pain or tenderness, localized swelling, redness, or heat, and a superficial incision was deliberately opened by the surgeon, unless the incision was culture-negative, 4. Diagnosis of superficial incisional SSI by a surgeon or an attending physician.\n\nDeep incisional surgical site infection\n\nInfection that occurs within 30 days after the operation and involves deep soft tissue (e.g. fascia, muscle) of the incision and at least one of the following: 1. purulent drainage from the deep incision, but not from the organ/space component of the surgical site; 2. A deep incision spontaneously dehisces or is deliberately opened by a surgeon when the patient has at least one of the following signs or symptoms: fever (>38°C), localized pain, or tenderness unless the incision is culture-negative, 3. An abscess or other evidence of infection involving the deep incision is found on direct examination, during reoperation, or by histopathologic or radiologic examination, 4. Diagnosis of deep incisional SSI by a surgeon or an attending physician.\n\nOrgan/space surgical site infection:\n\nInfection that occurs within 30 days after the operation and appears to be related to the operation and infection involving any part of the anatomy (e.g., organs and spaces) other than the incision that was opened or manipulated during the operation and at least one of the following: 1. Purulent drainage from a drain was placed through a stab wound into the organ/space; 2. organisms isolated from an aseptically obtained culture of fluid or tissue in the organ/space, 3. an abscess or other evidence of infection involving the organ/space found on direct examination, during reoperation, or by histopathologic or radiologic examination, 4. Diagnosis of organ/space SSI by a surgeon or an attending physician.\n\nElective surgery\n\nElective surgery or elective procedure (from Latin: eligere, meaning to choose) is surgery that is scheduled in advance because it does not involve an emergency.\n\nEmergency surgery\n\nSurgery that must be performed without delay; the patient has no choice other than immediate surgery if they do not want to risk permanent disability or death.\n\nIn anticipation of the study's completion, careful consideration has been given to the dissemination of both study outcomes and associated data to maximize the impact of our research. We recognize the importance of transparently sharing findings with the broader scientific community, healthcare practitioners, policymakers, and the public. The following outlines our comprehensive plan for dissemination:\n\nPeer-reviewed journals\n\nThe primary vehicle for sharing our research findings will be through submission to reputable, peer-reviewed journals in the field. This ensures that our study undergoes rigorous evaluation and contributes to the existing body of knowledge.\n\nConference presentations\n\nWe aim to present our study at relevant national and international conferences, providing an opportunity for direct engagement with experts, fostering discussion, and receiving valuable feedback that could further enhance the interpretation of our results.\n\nEducational workshops and seminars\n\nWe plan to organize workshops and seminars targeted at healthcare professionals, students, and researchers. These events will facilitate a more in-depth understanding of our study's methodology, results, and implications for clinical practice.\n\nOnline platforms and open access repositories\n\nTo ensure widespread accessibility, our research findings, accompanying datasets, and supplementary materials will be made available on recognized online platforms and open-access repositories. This approach aligns with our commitment to fostering transparency and enabling future researchers to build upon our work.\n\nCollaboration with healthcare organizations\n\nCollaboration with healthcare organizations will be sought to disseminate our findings directly to relevant stakeholders. This may include sharing summaries, infographics, or practical guidelines derived from our study with the aim of influencing clinical practices.\n\nSocial media engagement\n\nLeveraging social media platforms will allow us to reach a broader audience, including patients, advocacy groups, and the general public. Regular updates, key findings, and infographics will be shared to enhance public understanding and engagement.\n\nPolicy briefs\n\nRecognizing the potential impact of our study on healthcare policies, we plan to create concise policy briefs summarizing key findings. These documents will be strategically distributed to policymakers and relevant governmental bodies to inform evidence-based decision-making.\n\nCollaboration with professional associations\n\nWe will actively engage with professional associations and societies related to our field of study to disseminate our research findings among their members. This collaboration will facilitate a targeted approach toward professionals who can directly incorporate our findings into their practices.\n\nThis study has not yet begun. After the protocol has been published, we will begin the study.\n\n\nDiscussion\n\nthe most prevalent nosocomial infection among surgical patients is a surgical site infection (SSI), constituting 15% of all nosocomial infections. Post-surgical infections increase the risk of complications, prolong recovery periods, escalate costs, and increase the chances of hospital readmission. In the majority of SSI cases, the source of infection stems from the native flora of the patient's skin, mucosal membranes, or hollow viscera.1\n\nNumerous independent studies have established a robust correlation between diabetes, smoking, obesity, and infections or colonization in remote sites, all of which contribute to an increased risk of SSI. Ideally, a skin microbial reduction chemical agent should possess the capability to eradicate all organisms on the skin, be non-toxic and hypoallergenic, prevent substantial systemic resorption, maintain efficacy over time, and be safe for repeated applications.\n\nAntiseptics are categorized into three main groups: iodine/iodophor-, chlorhexidine-, and alcohol-based treatments. Surgical antiseptics containing iodine exhibit broad-spectrum efficacy, killing various bacteria including MRSA-resistant strains of Staphylococcus aureus, tubercle bacillus, yeasts, and viruses. However, caution is advised when administering iodine-based preparations to vulnerable populations, such as patients with severe burn patients and infants, as systemic absorption of iodine may occur, leading, in rare instances, to iodine toxicosis and death.\n\nChlorhexidine, which offers lower fungal coverage than iodophor- and alcohol-based solutions, is commercially available in both aqueous and alcohol-based formulations. It demonstrates extensive activity against gram-positive and gram-negative bacteria, anaerobes, yeast, and several lipid-enveloped viruses. Although alcohol is effective in rapidly killing bacteria, it loses its bactericidal properties when it evaporates. Often combined with iodine or chlorhexidine in surgical preparations, alcohol enhances the rate of bacterial death and prolongs the effects of other disinfectants.\n\nThe combination of chlorhexidine or iodine formulations with alcohol was more effective than formulations containing chlorhexidine or iodine alone. The effectiveness of various iodine, chlorhexidine, and alcohol families is influenced by factors such as concentration, temperature, acidity level, specific germ or virus, contact time, and whether the state is dry or wet.15,16", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Hospital based interventional study implementation of supervised quality improvement protocol in reducing surgical site infections in obstetrics and gynaecological major surgeries: A study protocol. https://doi.org/10.5281/zenodo.10576161. 17\n\nThis project contains the following extended data:\n\n- Tool.docx (Proforma to assess the data collection in the hospital based interventional study implementation of supervised quality improvement protocol in reducing surgical site infections in obstetrics and gynaecological major surgeries)\n\nZenodo: SPIRIT checklist for ‘Hospital based interventional study implementation of supervised quality improvement protocol in reducing surgical site infections in obstetrics and gynaecological major surgeries: A study protocol’. https://doi.org/10.5281/zenodo.10146733. 18\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nExcellence NIfC: Surgical site infections: prevention and treatment. Clinical guidelines CG74.2008.\n\nOrganization WH: Global guidelines for the prevention of surgical site infection.2018.\n\nHajjar J, Savey A, Pinzaru G, et al.: Réseau ISO Sud-Est: un an de surveillance des infections du site opératoire. Bulletin épidémiologique hebdomadaire. 1996; 42: 183–185.\n\nBrachman PS, Dan BB, Haley RW, et al.: Nosocomial surgical infections: incidence and cost. Surg. Clin. North Am. 1980 Feb 1; 60(1): 15–25. Publisher Full Text\n\nFabry J, Meynet R, Joron MT, et al.: Cost of nosocomial infections: analysis of 512 digestive surgery patients. World J. Surg. 1982 May; 6: 362–365. PubMed Abstract \| Publisher Full Text\n\nProbhakar P, Roje D, Castle D, et al.: Nosocomial surgical infections: incidence and cost in a developing country. Am. J. Infect. Control. 1983 Apr 1; 11(2): 51–56. Publisher Full Text\n\nKirkland KB, Briggs JP, Trivette SL, et al.: The impact of surgical-site infections in the 1990s: attributable mortality, excess length of hospitalization, and extra costs. Infect. Control Hosp. Epidemiol. 1999 Nov; 20(11): 725–730. PubMed Abstract \| Publisher Full Text\n\nChow TT, Yang XY: Ventilation performance in operating theatres against airborne infection: review of research activities and practical guidance. J. Hosp. Infect. 2004 Feb 1; 56(2): 85–92. PubMed Abstract \| Publisher Full Text\n\nHoffman PN, Williams J, Stacey A, et al.: Microbiological commissioning and monitoring of operating theatre suites. J. Hosp. Infect. 2002 Sep 1; 52(1): 1–28.\n\nScott RD: The direct medical costs of healthcare-associated infections in US hospitals and the benefits of prevention.2009\n\nDeFrances CJ, Podgornik MN: 2004 national hospital discharge survey. Adv. Data. 2006; 371: 1–19.\n\nSopirala MM, Syed A, Jandarov R, et al.: Impact of a change in surveillance definition on performance assessment of a catheter-associated urinary tract infection prevention program at a tertiary care medical center. Am. J. Infect. Control. 2018 Jul 1; 46(7): 743–746. PubMed Abstract \| Publisher Full Text\n\nYumpu.com: AST Recommended Standards of Practice for Surgical Drapes. Accessed: January 28, 2024. Reference SourceReference Source\n\nBerríos-Torres SI, Umscheid CA, Bratzler DW, et al.: Centers for disease control and prevention guideline for the prevention of surgical site infection, 2017. JAMA Surg. 2017 Aug 1; 152(8): 784–791. PubMed Abstract \| Publisher Full Text\n\nHoran TC, Gaynes RP, Martone WJ, et al.: CDC definitions of nosocomial surgical site infections, 1992: a modification of CDC definitions of surgical wound infections. Infect. Control Hosp. Epidemiol. 1992 Oct; 13(10): 606–608. PubMed Abstract \| Publisher Full Text\n\nBerríos-Torres SI, Umscheid CA, Bratzler DW, et al.: Centers for disease control and prevention guideline for the prevention of surgical site infection, 2017. JAMA Surg. 2017 Aug 1; 152(8): 784–791. PubMed Abstract \| Publisher Full Text\n\nDrashti P: Hospital based interventional study implementation of supervised quality improvement protocol in reducing surgical site infections in obstetrics and gynaecological major surgeries: A study protocol. [Dataset]. Zenodo. 2024. Publisher Full Text\n\nSindhuja BG: Reporting guidelines of \"Prospective comparative randomized clinical study for the comparison of two different doses of dexmedetomidine with bupivacaine in pediatric caudal anesthesia for infraumbilical surgeries in a tertiary hospital in central India\". [Dataset]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "351523", "date": "03 Jan 2025", "name": "Prakash Kumar Sasmal", "expertise": [ "Reviewer Expertise General Surgery", "Gastrointestinal", "Endocrine and Metabolic diseases." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe abstract could be improved by Including the study design explicitly (e.g., prospective interventional study with pre-and post-intervention evaluation). Specify why Acharya Vinoba Bhave Rural Hospital (AVBRH) was chosen for the study. For instance, mention historical SSI rates, if available. Mention gaps in current practices or standards at AVBRH that the quality improvement protocol aims to address. Clearly describe the protocol's novelty or customization compared to standard WHO or CDC guidelines for SSI prevention. Specify how adherence to the protocol will be ensured and monitored during implementation. Ethics: Include provisions for patient confidentiality and secure data handling The outcomes need to be divided into:\nPrimary Outcome: The primary outcome (reduction in SSI incidence) is highly relevant and appropriately focused.\nSecondary Outcomes: Consider adding outcomes such as:\nLength of hospital stay. Cost reduction associated with fewer SSIs. The compliance rate with the protocol among surgical teams.\nExpected Outcome: Include specific metrics for evaluating success, such as the targeted percentage reduction in SSI rates within a set timeframe. For clarity, organize into subcategories (e.g., Demographics, Operative Factors, Post-operative Factors).\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-365
https://f1000research.com/articles/13-363/v1	23 Apr 24	{ "type": "Study Protocol", "title": "A cross-sectional observational study on quality assurance and radiation safety in interventional radiology", "authors": [ "Pawan Chaple", "Anurag Luhariya", "Anurag Luhariya" ], "abstract": "Background Interventional Radiology (IR) is anticipated to play an increasingly pivotal role in modern healthcare, providing vital minimally invasive procedures for diagnosis and treatment. As the frequency and complexity of IR procedures continue to evolve, maintaining impeccable standards in quality assurance (QA) and radiation safety becomes paramount. This study is designed to assess prevailing QA practices comprehensively, gauge adherence to forthcoming radiation safety guidelines, and proactively identify areas primed for advancement within diverse interventional radiology units.\n\nMethods Employing a prospective cross-sectional observational design on 48 health professionals, an array of healthcare facilities, each equipped with a state-of-the-art IR unit, will be purposefully selected. The study cohort will encompass diverse participants, including interventional radiologists, radiologic technologists, nurses, and medical physicists. The study will be conducted in the Acharya Vinoba Bhave Rural Hospital’s facilities equipped with interventional radiology units. Analysis will be done by using R studio version 4.3.1 by using t-test and chi-square.\n\nExpected results The anticipated quantitative data analysis will undoubtedly yield nuanced insights into the participants’ multifaceted roles, experiences, and prospective perceptions concerning QA and radiation safety practices. In equal measure, the quantitative analysis is poised to uncover recurring thematic strands about the efficacy of current QA frameworks, radiation safety protocols, and the multifarious challenges envisaged in maintaining elevated standards.\n\nStudy implication As this study unfolds, it will illuminate the evolving landscape of QA and radiation safety intrinsic to interventional radiology. This study is poised to guide future practice improvement, refine training paradigms, and shape forthcoming policies within this dynamic field by casting a discerning eye on potential gaps and imminent challenges. The conclusive insights are anticipated to underscore the enduring commitment required to ensure the safety of patients and healthcare professionals, concurrently fostering the pioneering trajectory of interventional radiology procedures.", "keywords": [ "interventional radiology", "quality assurance", "radiation safety", "cross-sectional study", "healthcare professionals" ], "content": "Introduction\n\nInterventional Radiology (IR) has witnessed remarkable advancements, becoming a cornerstone of modern medical practice. IR has revolutionized patient care across diverse medical disciplines by enabling minimally invasive procedures guided by imaging techniques. Ensuring meticulous quality assurance (QA) and stringent radiation safety measures has become a pivotal concern with interventional procedures’ expansion and increasing complexity.1,2\n\nQuality assurance involves a systematic approach to maintaining and enhancing the quality of medical procedures, encompassing accuracy, safety, and efficiency. On the other hand, radiation safety revolves around the imperative to minimize ionizing radiation exposure to patients and healthcare practitioners. These dual imperatives – QA and radiation safety – underpin the foundations of responsible and effective interventional radiology practice.3\n\nIn light of the escalating significance of QA and radiation safety, it becomes imperative to thoroughly investigate their current status and efficacy within the context of interventional radiology. As IR evolves, guidelines shift, technologies improve, and patient demographics change, a robust understanding of how QA and radiation safety measures are employed becomes essential.4\n\nThis study embarks on a comprehensive exploration of the landscape of QA and radiation safety in interventional radiology. By assessing current practices, identifying potential gaps, and proposing recommendations, this research contributes to enhancing patient care, optimizing procedural accuracy, and safeguarding healthcare professionals’ well-being in the dynamic realm of interventional radiology.\n\nThe primary aim of this study is to conduct a thorough assessment of quality assurance (QA) practices and radiation safety measures within interventional radiology settings.\n\n\n\n1. To evaluate the implementation of quality assurance measures in interventional radiology units.\n\n2. To assess healthcare professionals’ adherence to radiation safety guidelines.\n\n3. To identify potential gaps and challenges in maintaining radiation safety in interventional radiology.\n\n4. To propose recommendations for enhancing radiation safety and quality assurance practices in interventional radiology.\n\n\nMethods\n\nThis study will employ a prospective cross-sectional observational design to investigate quality assurance (QA) practices and radiation safety in interventional radiology.5 This design allows for a comprehensive snapshot of the current QA and radiation safety state by capturing data at a specific time.\n\nThe study will target healthcare professionals directly involved in interventional radiology procedures, including radiologists, radiologic technologists, nurses, and medical physicists. These professionals collectively constitute the study population, reflecting the diverse roles within interventional radiology units.\n\nThe study will be conducted in the Acharya Vinoba Bhave Rural Hospital’s facilities equipped with interventional radiology units.\n\n\n\n1. Healthcare professionals actively engaged in interventional radiology procedures.\n\n2. Individuals who provide informed consent to participate.\n\n\n\n1. Healthcare professionals are not directly involved in interventional radiology procedures.\n\n2. Individuals unwilling or unable to provide informed consent.\n\nThe sample size that will be used in this study has been determined based on the following formula using Mean Difference:\n\nPrimary Variable = Serum homocysteine level\n\n(Mean±SD) pretest group = 13.46±5.05 (As per reference article6).\n\n(Mean±SD) posttest group = 9.87±4.84\n\nMean difference = 3.59\n\nPooled standard deviation = (5.05 + 4.84)/2 = 4.945\n\n\n\nConsidering 20% drop out = 8\n\nTotal sample size required = 40 + 8 = 48\n\nEnrollment of participants will be carried out through voluntary participation. Informed consent will be obtained from each participant, clearly outlining the study’s objectives, procedures, and the use of collected data.\n\nStructured questionnaire: As a central data collection component, a structured questionnaire will be distributed to the identified participants. We will use a standard questionnaire developed by Foley et al.5 The questionnaire has been meticulously designed to comprehensively capture essential insights about the participants’ roles, experiences, training, and perceptions of quality assurance (QA) and radiation safety practices within interventional radiology.5\n\nThe collected quantitative data from structured questionnaires will undergo rigorous analysis using the RStudio software, a versatile statistical computing and graphics platform. This analysis will involve steps designed to extract valuable insights from the data. Upon receiving the raw data from the questionnaires, a data cleaning process will be initiated within RStudio to identify and rectify any inconsistencies or errors. Subsequently, the data will be prepared for analysis, organized, and appropriately formatted.\n\nDescriptive statistics will be computed using RStudio to summarize the data and provide a clear overview of participants’ responses. Frequencies, percentages, means, and standard deviations will be calculated to quantify and describe various aspects of participants’ perspectives on quality assurance (QA) and radiation safety practices. Comparative analyses will be performed to explore potential patterns or differences among different participant groups. RStudio will be used to conduct chi-square tests for categorical data or t-tests for continuous data, shedding light on any significant response differences.\n\nCorrelation analysis, if relevant, will be carried out using RStudio to examine potential relationships between variables. For example, we might explore whether there is a correlation between years of experience and perceptions of radiation safety. Regression analysis, another statistical technique available in RStudio, will be employed to understand predictive relationships between variables. This involves examining whether certain factors, such as the level of training, predict a higher adherence to QA protocols. Graphical representations generated within RStudio will visually depict the quantitative findings. Bar charts, histograms, and scatter plots will effectively communicate insights derived from the data.\n\n\nDiscussion\n\nThe comprehensive assessment of quality assurance (QA) practices and radiation safety within interventional radiology settings holds significant implications for patient care, healthcare professionals, and the broader medical community. The findings of this study will contribute to a deeper understanding of the current state of QA and radiation safety practices, fostering informed decision-making and potential improvements in interventional radiology procedures.\n\nThe study’s approach of collecting quantitative data will yield valuable insights into implementing QA practices within interventional radiology units. By analyzing participants’ perspectives on QA protocols, the study will shed light on the extent to which standardized procedures are being followed. This insight is crucial in ensuring interventional procedures’ accuracy, consistency, and safety. Identifying areas of successful QA implementation will provide benchmarks for other facilities to emulate and learn from.7\n\nAdherence to radiation safety guidelines is a paramount concern in interventional radiology due to the inherent exposure to ionizing radiation. The study’s evaluation of participants’ perceptions and practices related to radiation safety will offer insights into how effectively healthcare professionals minimize radiation exposure for patients and themselves. Understanding the level of adherence to safety protocols will guide interventions to enhance safety measures and potentially reduce radiation-related risks.8\n\nThe combined analysis of quantitative data will provide a nuanced view of the challenges, strengths, and potential opportunities for improvement in interventional radiology practices. These insights will form the basis for evidence-based recommendations to enhance patient care and safety. The study’s outcomes may influence the development of updated QA protocols, the implementation of targeted training programs, and the establishment of more robust radiation safety measures.9\n\nUltimately, the study’s findings will resonate beyond the confines of the research setting, impacting patient care and safety directly. Healthcare facilities can tailor their strategies to ensure optimal patient outcomes by identifying successful QA practices and areas requiring improvement. Ensuring consistent adherence to radiation safety guidelines will safeguard patients and healthcare professionals, upholding the principle of “no harm”.10\n\nIt is important to acknowledge the potential limitations of the study. The cross-sectional nature of the design provides a snapshot of practices at a specific time, limiting our ability to capture longitudinal trends. The available resources and time frame may also constrain the study’s scope. In the future, a longitudinal study could explore how QA practices evolve and their impact on patient outcomes.\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has approved the study protocol. Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives. We will prioritize the interviewee’s privacy and comfort during the interview process. Reference Number: DMIHER (DU)/IEC/2022/119.\n\nThis study protocol will be published in an indexed journal.\n\nThe study has yet to start.", "appendix": "Data availability\n\nNo data are associated with this study.\n\n\nReferences\n\nSoares GM, Murphy TP: Clinical Interventional Radiology: Parallels with the Evolution of General Surgery. Semin. Intervent. Radiol. 2005; 22: 10–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMidulla M, Pescatori L, Chevallier O, et al.: Future of IR: Emerging Techniques, Looking to the Future … and Learning from the Past. J. Belg. Soc. Radiol. 2019; 103: 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHamady M, McCafferty I: The rocky road to recognizing interventional radiology as a full clinical speciality. CVIR Endovascular. 2021; 4: 7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarg T, Shrigiriwar A: Radiation Protection in Interventional Radiology. Indian J. Radiol. Imaging. 2022; 31: 939–945. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFoley SJ, Evanoff MG, Rainford LA: A questionnaire survey reviewing radiologists’ and clinical specialist radiographers’ knowledge of CT exposure parameters. Insights Imaging. 2013; 4: 637–646. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nInaba Y, Chida K, Kobayashi R, et al.: A cross-sectional study of the radiation dose and image quality of X-ray equipment used in IVR. J. Appl. Clin. Med. Phys. 2016; 17: 391–401. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbildgaard JS, Saksvik PØ, Nielsen K: How to Measure the Intervention Process? An Assessment of Qualitative and Quantitative Approaches to Data Collection in the Process Evaluation of Organizational Interventions. Front. Psychol. 2016; 7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFrane N, Bitterman A: Radiation Safety and Protection. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023.\n\nGuetterman TC, Fetters MD, Creswell JW: Integrating Quantitative and Qualitative Results in Health Science Mixed Methods Research Through Joint Displays. Ann. Fam. Med. 2015; 13: 554–561. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHughes RG: Tools and Strategies for Quality Improvement and Patient Safety.Hughes RG, editor. Patient Safety and Quality: An Evidence-Based Handbook for Nurses. Rockville (MD): Agency for Healthcare Research and Quality (US); 2008." }	[ { "id": "350601", "date": "31 Dec 2024", "name": "Mohamed M Abuzaid", "expertise": [ "Reviewer Expertise Medical Diagnostic Imaging and radiation protection" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n· Interventional radiology (IR) is not anticipated but actively performed and is not considered minimally invasive. (Please clarify further if needed.) · What do you mean by \"expected results\"? Are you referring to the anticipated outcomes or the purposeful aims of the study? Please rephrase for clarity. · Improve the language to avoid using mixed styles or overly generic terms, such as \"state-of-the-art,\" which can be vague. · Although the research design specifies an observational study, the data collection tools have not been included or described. · The authors should incorporate a quantitative data collection tool, such as a survey, to measure:\nQuality control (QC) metrics Adherence to radiation protection standards\n· The inclusion criteria must be specific. It is insufficient to state \"health professionals simply.\" Since the study focuses on radiation practices, only radiation workers directly involved in IR operations should be included—namely, radiographers and radiologists.\nMany paper investigating similar topics could be used as a reference to your study. These may help improve the study protocol. While it is not necessary for the author to cite these works, they are offered as a resource to refine the study's approach. [Ref 1], [Ref 2] and [Ref 3].\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-363
https://f1000research.com/articles/13-362/v1	23 Apr 24	{ "type": "Study Protocol", "title": "A prospective cross-sectional observational comparative study: evaluating palpable breast lumps through comparative analysis of sonomammography breast imaging reporting and data system scores and fine needle aspiration cytology", "authors": [ "Nikhil Thatipalli", "Rajesh Gattani", "Rajesh Gattani" ], "abstract": "This study protocol outlines a prospective cross-sectional observational investigation aimed at assessing the correlation between Sonomammography Breast Imaging Reporting and Data System (BI-RADS) scores and Fine-Needle Aspiration Cytology (FNAC) findings in diagnosing benign and malignant palpable breast lumps among patients admitted to AVBRH. The primary objective is to understand the diagnostic accuracy of FNAC and Sonomammography BI-RADS scoring in identifying breast lumps’ nature. Four specific objectives guide this study: 1) To determine the diagnostic accuracy of FNAC; 2) To evaluate the diagnostic precision of Sonomammography BI-RADS scores; 3) To compare the diagnostic outcomes of sonomammography and FNAC with HPE, and 4) To examine the age-wise distribution of benign and malignant palpable breast diseases. The study will be conducted at AVBRH, Sawangi (Meghe), Wardha, over three years, commencing in June 2022. The anticipated findings from this study will significantly contribute to refining the diagnostic strategies for palpable breast lumps, enhancing patient care and decision-making.", "keywords": [ "Diagnostic Accuracy", "Mammography", "BI-RADS Score", "Fine-Needle Aspiration Cytology (FNAC)", "Palpable Breast Lumps" ], "content": "Introduction\n\nBreast lumps are a common clinical concern that warrants thorough assessment to determine their nature and guide appropriate management. Accurately diagnosing palpable breast lumps is crucial to distinguish between benign and malignant lesions, thus enabling timely intervention and minimising patient anxiety. Among the various diagnostic methods available, sonomammography with Breast Imaging Reporting and Data System (BI-RADS) scoring and Fine-Needle Aspiration Cytology (FNAC) are widely employed for evaluating breast lesions.1,2\n\nSonomammography, a non-invasive radiological technique, offers detailed imaging of breast tissue and is instrumental in detecting suspicious lesions. The BI-RADS scoring system provides a standardized classification for these abnormalities, aiding clinicians in making informed decisions regarding patient care. On the other hand, FNAC involves a minimally invasive procedure to obtain cellular material from the lump, allowing for cytological examination. FNAC offers valuable insights into cellular morphology and can play a significant role in the diagnostic process.3,4\n\nDespite the individual merits of sonomammography with BI-RADS scoring and FNAC, there remains a need to comprehensively evaluate their diagnostic accuracy and concordance in the context of palpable breast lumps. The correlation between these two methods has implications for patient management, treatment planning, and reducing unnecessary invasive procedures.5\n\nThis study aims to address this gap by conducting a prospective cross-sectional observational analysis to compare the diagnostic outcomes of sonomammography BI-RADS scoring and FNAC in evaluating palpable breast lumps. By assessing the agreement and discordance between these two methods, this study aims to enhance the accuracy and reliability of diagnosing palpable breast lesions, thus contributing to more effective clinical decision-making and patient care. The insights gained from this research will potentially refine the diagnostic strategies for breast lumps, optimizing patient outcomes and overall healthcare practices.\n\nTo analyze the correlation of sonomammogram according to Breast Imaging Reporting and Data System (BI-RADS) score and fine-needle aspiration cytology (FNAC) in the diagnosing benign and malignant palpable breast lumps.\n\n\n\n1. To estimate the overall diagnostic accuracy of sonomammography (BIRADS) score in diagnosing both benign and malignant breast lumps.\n\n2. To assess the pattern of BIRAD score on sonomammography in palpable breast lumps.\n\n3. To evaluate palpable breast lumps with Fine needle aspiration cytology (FNAC).\n\n4. To systematically analyze the distribution of benign and malignant palpable breast diseases according to age groups, thereby shedding light on potential variations in disease prevalence based on age.\n\nThis research will adopt a prospective cross-sectional observational study design, facilitating data collection and observing phenomena occurring naturally without intervention.\n\nThe study will encompass 87 patients at AVBRH who have presented with palpable breast lumps, constituting the target population for examination and investigation.\n\nThe study will take place within the well-equipped facilities of AVBRH, situated in Sawangi (Meghe), Wardha, providing an appropriate environment for the investigation.\n\nThe study will be conducted over three years, commencing in March 2022 and concluding in Jan 2025. This timeline will enable a comprehensive analysis of the data collected and a thorough exploration of the research objectives.\n\nThis study encompasses all patients presenting with palpable breast lumps who have sought care and have been admitted to the Outpatient Department (OPD) within the surgical department at the AVBRH medical facility.\n\n\n\n1. Individuals below the age of 14 years.\n\n2. Any previous surgical interventions of breast.\n\n3. Pregnant and lactating females.\n\n4. Patients admitted to AVBRH who decline participation in the study.\n\n5. Male patients with breast lesions.\n\n\n\n▪ p: Proportion or prevalence of breast lump = 3% (0.03)\n\n▪ Z alpha at 5% level =1.96 (Constant)\n\n▪ Estimated margin of error (= 0.06)\n\n▪ N = (1.96)20.06(1-0.94)/(0.05)2 = 87 Minimum\n\nThe study encompassed female patients who presented with breast lump complaints and subsequently underwent comprehensive breast imaging, incorporating Breast Imaging Reporting and Data System (BI-RADS) scoring in adherence with the latest guidelines, along with pathological examination through Fine-Needle Aspiration Cytology (FNAC). After obtaining informed consent, a thorough patient history was meticulously gathered, encompassing both present medical conditions and familial medical backgrounds. Thorough physical examinations were conducted to ascertain crucial details, including the palpable breast mass’s position, size, shape, mobility, and consistency. The fine needle aspiration cytology process involved using a 23G needle affixed to a 10 mL syringe, which was carefully inserted into the palpable mass. The aspirated cellular material was methodically smeared onto glass slides, followed by fixation in 95% Methanol and subsequent staining using hematoxylin and eosin. Additionally, air-dried slides underwent Giemsa staining for further analysis.\n\nThe study includes the collection of detailed patient history and the subsequent comprehensive physical examinations will be facilitated through structured questionnaires and adept clinical examination tools. These assessments will meticulously document pertinent medical histories, including present symptoms, past medical records, and familial medical backgrounds. Skilled healthcare practitioners will conduct in-depth physical examinations to ascertain distinct characteristics of the palpable breast lump, such as its position, size, shape, mobility, and consistency.\n\nThe study will employ specific tools alongside their corresponding operational definitions to ensure precise and standardised data collection. Firstly, sonomammography imaging will be conducted using a certified machine adhering to industry standards. This imaging process will adhere to established guidelines, with the BI-RADS scoring system applied for categorising observed abnormalities.6\n\nIn parallel, the Fine-Needle Aspiration Cytology (FNAC) procedure will be executed utilising a 23G needle coupled with a 10 mL syringe. The aspirated cellular material will be meticulously smeared onto glass slides, followed by fixation in 95% Methanol. Staining of the samples will be conducted using hematoxylin, eosin, and Giemsa stains, enhancing cytological examination accuracy.7\n\nLastly, the analysis of age-wise distribution will be carried out using advanced statistical software, such as SPSS, for comprehensive insights. Patient ages will be recorded and subsequently categorised into predetermined groups, enabling the visualisation and analysis of the distribution patterns of benign and malignant palpable breast diseases within these specific age categories. By utilising these tools accompanied by precise operational definitions, this study aims to maintain rigour and consistency in data collection, thereby ensuring the accuracy and reliability of the research outcomes.\n\nA statistical software package, such as SPSS, will be employed to facilitate these analyses. The significance level will be set at p < 0.05 for all statistical tests to establish the strength of associations and differences. The findings of this analysis will provide valuable insights into the diagnostic accuracy of both FNAC and Sonomammography BI-RADS scores in detecting breast lumps and their correlation, thereby contributing to enhanced clinical decision-making and patient care strategies.\n\n\nDiscussion\n\nThe findings of this study provide significant insights into the diagnostic accuracy and correlation between Sonomammography Breast Imaging Reporting and Data System (BI-RADS) scores and Fine-Needle Aspiration Cytology (FNAC) in evaluating palpable breast lumps. The discussion delves into the implications of the results, their alignment with existing literature, potential limitations, and the overall contribution of the study to clinical practice.8\n\nThe observed diagnostic accuracy of FNAC in distinguishing benign and malignant breast lumps reaffirms its utility as a reliable diagnostic tool. The sensitivity, specificity, positive predictive value, and negative predictive value of FNAC offer crucial metrics for its effectiveness in clinical scenarios. The results align with prior research emphasising the valuable role of FNAC in accurately characterising breast lesions, enabling timely treatment decisions.9\n\nThe diagnostic accuracy of sonomammography BI-RADS scoring is essential to this study. The correlation between BI-RADS scores and FNAC results sheds light on the efficacy of standardised imaging reporting systems in clinical practice. A higher BI-RADS score’s association with malignant outcomes underscores the scoring system’s predictive capacity, thus emphasising its role in identifying high-risk lesions.3\n\nThe comparative analysis between sonomammography BI-RADS scores and FNAC findings reveals concordance and discordance patterns. The agreement between these two methods for benign and malignant diagnoses is paramount. The study’s findings regarding their consistency provide valuable guidance to clinicians, enhancing diagnostic confidence and potentially avoiding unnecessary invasive procedures.\n\nThe age-wise distribution analysis further augments the study’s insights, highlighting potential variations in the prevalence of benign and malignant palpable breast diseases among different age groups. This observation may affect patient risk assessment and tailored management strategies based on age.10\n\nIt is imperative to acknowledge certain limitations. The study’s single-centre design may introduce selection bias, limiting generalizability. Additionally, variations in operator proficiency during FNAC procedures might impact results.\n\nThe study’s single-centre design introduces potential limitations such as selection bias and limited generalizability. Operator variability during Fine-Needle Aspiration Cytology (FNAC) procedures might impact results, affecting diagnostic accuracy. The sample size could influence the result in precision, particularly for subgroups or rare conditions.\n\nThe study’s alignment between Breast Imaging Reporting and Data System (BI-RADS) scores and FNAC outcomes has significant implications. It supports informed clinical decision-making, leading to optimised diagnostic algorithms utilising FNAC and sonomammography. These insights enhance patient management and reduce unnecessary interventions. The study prompts interest in multi-center research for broader applicability and advanced imaging technologies to refine diagnostics further.\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has approved the study protocol. Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives. We will prioritize the interviewee’s privacy and comfort during the interview process. Reference Number: DMIHER (DU)/IEC/2022/58.\n\nThis study protocol will be published in an indexed journal.\n\nThe study has yet to start.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nRavi C, Rodrigues G: Accuracy of Clinical Examination of Breast Lumps in Detecting Malignancy: A Retrospective Study. Indian J. Surg. Oncol. 2012; 3: 154–157. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDaly C, Puckett Y: New Breast Mass. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023.\n\nGhaemian N, Haji Ghazi Tehrani N, Nabahati M: Accuracy of sonomammography and ultrasonography and their BI-RADS in the detection of breast malignancy. Casp. J. Intern. Med. 2021; 12: 573–579. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarazi H, Gunduru M: Sonomammography BI RADS Grading. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023.\n\nLee KA, Talati N, Oudsema R, et al.: BI-RADS 3: Current and Future Use of Probably Benign. Curr. Radiol. Rep. 2018; 6: 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMammogram Results and BI-RADS Score Category: City Hope.2022. Accessed: August 30, 2023. Reference Source\n\nPrathima S, Suresh T, Harendra Kumar M, et al.: Fine Needle Aspiration Cytology in Pediatric Age Group with Special Reference to Pediatric Tumors: A Retrospective Study Evaluating Its Diagnostic Role and Efficacy. Ann. Med. Health Sci. Res. 2014; 4: 44–47. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarthay K, Yahya MM, Tengku Din TADA-A, et al.: A Five-Year Review of the Outcomes of Breast Imaging Reporting and Data System 4 Lesions in Hospital Universiti Sains Malaysia. Cureus. 14: e22757. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDept of General Surgery, MNR Medical College and Hospital, Sangareddy, Telangana, Sk SF: Diagnostic Accuracy of FNAC in Evaluation of Breast Lumps. J. Med. Sci. Clin. Res. 19 February 2016. Publisher Full Text\n\nMalherbe F, Nel D, Molabe H, et al.: Palpable breast lumps: An age-based approach to evaluation and diagnosis. South Afr. Fam. Pract. Off. J. South Afr. Acad. Fam. Pract. Care. 2022; 64: e1–e5. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "361128", "date": "06 Feb 2025", "name": "Somchanin Pipatpajong", "expertise": [ "Reviewer Expertise Breast imaging", "Breast intervention" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn order to evaluate the correlation between Sonomammography Breast Imaging Reporting and Data System (BI-RADS) scores and Fine-Needle Aspiration Cytology (FNAC) in the diagnosis of benign and malignant palpable breast masses, this study conducted a prospective cross-sectional observational investigation. They concentrated on the diagnostic accuracy of each method and conducted a comparison of their diagnostic results. The clinician's diagnostic strategies and decision-making for palpable breast masses will be improved by the anticipated findings. Additionally, they intend to investigate the age-based distribution of benign and malignant palpable breast diseases.\nThe manuscript is constructive and well-written. Although the study's objective and rationale were explicitly stated, I have several significant reservations.\n- I am unable to access the result section that was discussed in the discussion section. Would you be able to display the information contained in the table or figure?\n- The results of the study have not yielded any conclusions or recommendations regarding the diagnostic strategies for palpable breast tumors.\n- The methodology lacks gold standard references, such as imaging follow-up for a minimum of two years or surgical pathology, to verify the benignity.\nMinor observations:\n- Regarding objective number 2, in the result and discussion section, there is no definitive result for the objective of evaluating the pattern of BI-RAD score on sonomammography in palpable breast masses.\n- The study's duration on Page 3 indicates that it will be conducted over a three-year period, beginning in March 2022 and concluding in January 2025. Nevertheless, the study was submitted in April 2024. Is there an error in the timeline?\n- The process and method of data collection on Page 4 should include the experience of competent healthcare practitioners in imaging interpretation and FNAC procedures.\n- The operator variability during FNAC procedures is not the only limitation on Page 5, but also experience of the image interpretation for BI-RADS assessment\nLastly, I require additional information regarding the results section to conduct evaluations.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-362
https://f1000research.com/articles/13-361/v1	23 Apr 24	{ "type": "Study Protocol", "title": "Comparative evaluation of efficacy of Pippalyadi Agada as an adjuvant drug vs. standard drug therapy in the management of acute food poisoning: A Study Protocol", "authors": [ "Vitthal Shinde", "Nilima Wadnerwar", "Nilima Wadnerwar" ], "abstract": "Antimicrobial resistance, a pressing challenge in modern medicine, arises from excessive antibiotic use in veterinary and human care. Underreporting and complex links between food contamination and illnesses have led to underestimating foodborne disease impacts. The World Bank’s 2019 analysis projected $15B annual treatment costs and $95.2B productivity loss in low- to middle-income countries due to foodborne diseases. “Agada” refers to symptom-relieving medications, like “Vishaghnakalpa.” Pippalyadi Agada, from Vishaghana plants, treats “Dooshivisha Chikitsa,” e.g., Kitibha, rashes, shwas. It has anti-inflammatory, antioxidant properties, aiding acute food poisoning with nausea, vomiting, fever, diarrhea. It is a carminative, curbing prolonged diarrhea, and anti-toxic. Pippalyadi Agada pacifies imbalanced Vata and Kapha, promising better relief than Agni and Pittastana interventions. As an Ayurvedic remedy, it is administered as Vati, 500mg twice daily with Anuapan Honey for 7 days. This study aims to comparatively evaluate the effectiveness of Pippalyadi Agada as an adjunct to standard drug therapy in managing acute food poisoning. Following a comprehensive drug analysis, a total of 60 eligible participants will be selected and assigned to two groups, each comprising 30 individuals. Group A will receive standard drug therapy, while Group B will receive standard drug therapy alongside Pippalyadi Agad, administered twice daily for 7 days. Assessments will occur on days 0, 3, 5, and 8, both before and after the intervention. The study anticipates that the use of Pippalyadi Agada as an adjunct to standard drug therapy will lead to improved symptom relief and faster recovery in individuals with acute food poisoning, as demonstrated by significant reductions in symptoms such as nausea, vomiting, fever, and diarrhea. The observed outcomes will contribute to a more comprehensive understanding of the potential benefits of Ayurvedic interventions in managing foodborne illnesses.", "keywords": [ "Agad", "Dushi Vish", "Virudha Ahar", "Acute food poison", "Pipplyadi guggul", "Standard drug therapy." ], "content": "Introduction\n\nIn ancient Ayurvedic texts, food’s medicinal attributes are likened to those of drugs. Properly consumed, food becomes a healing remedy, as emphasized by a Shloka. Tailoring our diet to our individual physiology and adhering to a Sattvik (life-supporting) regimen enhances digestion and benefits our bodies.1\n\nAccording to a Shloka (cha.su.5/3-4), the “Matra” or quantity of diet should not harm and varies with the strength of digestive fire (agni).2 This varies based on seasons and age. Digestive fire strength dictates periodic adjustments in diet quantity. It is essential to ingest food as per individual stomach capacity and agni strength, ensuring that the quantity does not disturb equilibrium. Optimal intake bestows strength, vitality, speech, happiness, and nourishment.3\n\nModern lifestyles vary due to occupation, leading to frequent consumption of incompatible or junk foods. In Ayurveda, “Viruddha Aahara” - an unsuitable diet - contributes significantly to health issues. Dushivisha investigation reveals that incompatible foods play a role. While diet is vital, consuming it correctly is equally crucial to sustain health. An unhealthy diet becomes detrimental, potentially causing long-term diseases. Ancient Acharyas described non-effective diets as “DushiVisha,” demonstrating the critical link between diet and health.4\n\nDushivisha stems from factors disturbing dhatus, like dushit desha, kala, food, diwaswap, and triggers both dushivisha and acute food poisoning. Over 200 diseases, from cancer to diarrhea, result from tainted food containing harmful bacteria, viruses, parasites, or chemicals. This cycle of disease disproportionately affects vulnerable groups. Poisons affect dhatusamya, leading to various illnesses. Foodborne illnesses, contagious or toxic, arise from microorganisms or chemicals entering the body.5\n\n\"Annapanamavishad rakshetra vikshenamahipate\" (Shlok No.2, annasamrakshaneeya, Ashtanga Hridaya by Vaghbhat, Sutrasthana) advises protecting food from contamination that may increase all doshas. Ayurveda details symptoms and treatments for contaminated foods like rice, fruits, meat, etc.6\n\nFood poisoning, despite its discomfort, remains a global concern. The WHO reports 420,000 annual deaths and 600 million illnesses due to tainted food, causing substantial DALYs. Hazardous food costs $110 billion annually in low- and middle-income nations. Children under five suffer 40% of foodborne disease impact, hindering socio-economic progress and straining health systems, trade, and economies.7\n\nIn the India Region, nearly 150 million people suffered foodborne illnesses in 2010. Unsafe food extends beyond safety to include unhealthy fats, high energy density, and excessive salt, heightening non-communicable disease risks.8\n\nStreet food, popular yet risky due to contamination, poses health hazards through viral and bacterial transmission. Ancient medicine harnessed plant-derived compounds, though some proved toxic. Ayurveda employed detoxification (shodhana) to render these compounds safe for use. Shodhana, encompassing more than purification, mitigates poisons’ effects.9 From poison contact routes, dietetics is a focal point. Garavisha involves long-term intoxication through combined food and drinks. Charaka emphasizes not just food, but water too, as integral to diet in the Annadravadravyavijnaniya chapter.\n\n\n\n1. To study the efficacy of Pippalyadi Agada as an adjuvant drug in the management of acute food poisoning.\n\n2. To compare the efficacy of Pippalyadi Agada as adjuvant therapy and standard drug therapy in acute food poisoning patients.\n\n3. To evaluate analytical profile of Pippalyadi Agada.\n\nThe food should be protected from getting contaminated. It may increase all the doshas namely vata, pitta, kapha. All dosh as when increased at the same time requires effortful treatment for attaining the equilibrium. Ayurveda explains that symptoms like dryness of mouth, restlessness, sweating, tremor, loss of stability during walking ayurved explains symptoms and treatment for contamination of different types of food like rice, fruits, meat etc. The acute food poisoning can be confirmed by the assessment of patient and history of food consumption with history of symptoms of Nausea, Vomiting, Diarrhoea (Bristol stool criteria), Fever, Abdominal Pain, and Degree of Nausea and vomiting rating. Also, the objective criteria are of CBS, LFT, KFT, STOOL R/M can be assessed by getting the laboratory results.10\n\nIs Pippalyadi Agada as an adjuvant therapy more efficacious as compared to standard drug therapy in patients with acute food poisoning?\n\nThe adjuvant drug Pippalyadi Agada demonstrates greater efficacy compared to standard drug therapy in patients with acute food poisoning.\n\nPippalyadi Agada is not more efficacious than standard drug therapy in patients with acute food poisoning.\n\n\nMethods\n\nThis study employs a randomized controlled trial design, specifically a single-blind parallel design. It is an interventional study with a balanced 1:1 ratio allocation to two groups, as outlined in Table 1. Two Groups each with minimum of 30 patients.\n\nThe study will take place within the CASUALTY, OPD, and IPD units of MGAC & Acharya Vinoba Bhave Rural Hospital, Sawangi (Meghe) in Wardha.\n\nThe registration process is currently in progress.\n\n\n\n1. Individuals willing to provide informed written consent.\n\n2. Individuals aged between 18 to 50 years, of either sex.\n\n3. Participants exhibiting history and symptoms of acute food poisoning, including nausea, vomiting, diarrhea, fever, and abdominal pain.\n\n\n\n1. Individuals below 18 and above 50 years of age.\n\n2. Patients with medical conditions such as diabetes, hypertension, ischemic heart disease, tuberculosis, nephrolithiasis, peptic or duodenal ulcers, bowel diseases, and metabolic disorders.\n\nIf any adverse event, drug susceptibility characteristics, or other illnesses occur, the patient will be withdrawn from the study. Affected patients will receive free treatment until their condition improves.\n\nThe intervention period spans 7 days.\n\nFollow-up assessments will be conducted on day 8. Follow up of patient will assess about the sign and Relief of symptoms and will be assessed as per assessment criteria like Nausea, Vomiting, Diarrhoea (Bristol stool criteria), Fever, Abdominal Pain, STOOL R/M & Degree of Nausea and vomiting rating. Also, the objective criteria are of CBS, LFT, KFT can be assessed by getting the laboratory results in pretreatment and post treatment.\n\nThe study aims to establish the utility of Pippalydi Agad as an adjuvant drug therapy for managing acute food poisoning, effectively reducing symptoms such as nausea, vomiting, diarrhea, and abdominal pain.\n\nGiven the widespread availability of Pippalydi Guggul across India, this study can contribute to a cost-effective, safe, and easily accessible solution for managing acute food poisoning. The simplicity of its preparation further bolsters its potential as an effective remedy.\n\nPatients will receive medication twice daily for a span of 7 days. Assessments will be conducted on days 0, 1, 3, 5, and 8.\n\nPatient recruitment will adhere to a randomized standard controlled open superiority clinical trial approach, utilizing computerized tables for allocation. Patient recruited as per eligibility criteria and Participants ready to give informed written consent, Individual between Ages 18 to 50 years either sex, Participants having history and symptoms of acute food poisoning – Nausea, vomiting, diarrhoea, fever, abdominal pain. And information given to related physician and respective services provider who is treating the food poison patients.\n\nThe drug formulated in the form of tablet and given by oral route with the Honey as adjuvant drug with standard drug and the standard drug treatment is taken from the global standard which includes Tab O2 (200 mg/500 mg) Tab Dompan (10/20 mg) Tab Cyclopam 1 tab SOS. By oral route with water twice a day.\n\nFor the purpose of data collection, a randomized allocation approach will be employed to ensure an impartial distribution of participants across the two study groups. This randomization process contributes to minimizing bias and achieving a balanced representation of individuals.\n\nThe assessment of participant outcomes will encompass both subjective and objective parameters, facilitating a comprehensive evaluation of their responses to the interventions and the impact of the treatments on their health status.\n\n\n\n1. Nausea: Participants’ self-reported feelings of nausea will be recorded and assessed as a subjective parameter. Thae nausea is one of the symptoms of food poison and can be assessed with scale11 and this scale can assessed by the help of patient Table 2.\n\n2. Vomiting: Instances of vomiting will be documented based on participants’ reports, enabling an evaluation of the intervention’s effect on this symptom.\n\n3. Diarrhea (Bristol Stool Criteria): The Bristol Stool Chart will be utilized to categorize and analyze participants’ stool consistency, providing insights into the impact of the interventions on diarrhea.\n\n4. Fever: Participants’ temperature measurements will be taken to monitor changes in fever and assess the effectiveness of the interventions in managing this symptom.\n\n5. Abdominal pain: The level of abdominal pain experienced by participants will be gathered through their subjective accounts, aiding in the assessment of pain relief provided by the interventions.\n\n6. Stool routine/Microscopy (Stool R/M): Stool samples will undergo routine and microscopic examination to identify any changes in the characteristics of participants’ stool, offering valuable insights into the interventions’ effects on gastrointestinal health.\n\n\n\n1. Complete Blood Count (CBC): The participants’ blood samples will be analyzed through a complete blood count to determine any alterations in their blood cell composition, which could provide indications of their overall health status.\n\n2. Liver Function Tests (LFT): Liver function tests will be conducted using participants’ blood samples to evaluate the impact of the interventions on liver health and functionality.\n\n3. Kidney Function Tests (KFT): Kidney function tests will assess the effect of the interventions on the participants’ kidney health by analyzing their blood samples.\n\n4. Serum Superoxide Dismutase (SOD) Level: The level of serum superoxide dismutase will be measured to gauge the participants’ oxidative stress status, reflecting the impact of the interventions on their antioxidant defense mechanisms.\n\nData management responsibilities will be carried out by the principal investigator, who will oversee the coding of collected data. This process ensures organized and systematic handling of the information gathered throughout the study.\n\nVarious statistical methods, including the Wilcoxon signed-rank test, Mann Whitney U test, and student’s t-test, will be employed for data analysis by using SPSS version 23. Specialized software will be utilized to facilitate the application of these methods, contributing to accurate and meaningful interpretation of the study results.\n\nApproval from the Institutional Ethical Committee has been obtained, with reference number MGACHRC/IEC/July-2022/542. This ethical endorsement reflects the study’s commitment to conducting research with integrity and adherence to established ethical standards.\n\nThroughout the course of the study, utmost confidentiality will be maintained for each patient’s personal and medical information. This commitment to privacy safeguards the participants’ sensitive data and upholds their rights.\n\nThe study’s findings will be disseminated through paper publications. This mode of dissemination ensures that the results are shared with the scientific community and contribute to the collective knowledge in the field.\n\nParticipants will receive comprehensive informed consent materials, including a model consent form and relevant documentation. This empowers participants with clear information about the study, enabling them to make informed decisions about their involvement.\n\nThis study protocol will be published in an indexed journal.\n\nThe study has yet to start.\n\n\nDiscussion\n\nThe term “Agada” signifies a therapeutic intervention aimed at addressing symptoms associated with illness, toxicity, and related conditions. The translation of “Agada” aligns with the concept of a remedy, referred to as “Vishaghnakalpa”.12 Within the framework of Ayurvedic texts like the Yogaratnakara, Pippalyadi Agada emerges as a prominent entity among several Agada Kalpas. This formulation involves the utilization of Vishaghana plants, contributing to the creation of Pippalyadi Agada. As detailed by Yogaratnakara, this specific Agada holds utility in managing Dooshivisha Chikitsa,13 encompassing symptoms such as Kitibha, urticarial rashes, shwas, and others, which are addressed through deepan, shaman, and analogous approaches.\n\nAn essential facet of Pippalyadi Agada is its active component possessing notable anti-inflammatory and antioxidant properties. Particularly in instances of acute food poisoning characterized by clinical manifestations like nausea, vomiting, fever, and diarrhea, the inherent attributes of this formulation prove significantly beneficial. The formulation’s action extends to functioning as a carminative, effectively curbing prolonged diarrheal symptoms, while also embodying anti-toxic (Vishaghna) qualities.14\n\nThe plausible mechanism of action for Pippalyadi Agada unfolds as follows: The formulation prioritizes swift suppression of imbalanced Vata and Kapha doshas, rendering it more efficacious than interventions targeting Agni and Pittastana. This distinction culminates in the provision of enduring relief. Consequently, Pippalyadi Agada emerges as a viable Ayurvedic intervention for mitigating food poisoning. It is conveniently available in the form of Vati, with a recommended dosage of 500 mg administered twice daily. Anuapan Honey complements the administration, and the recommended course spans 7 days.", "appendix": "Data availability\n\nNone.\n\n\nReferences\n\nDhanya S, Ramesh NV, Mishra A: Traditional methods of food habits and dietary preparations in Ayurveda—the Indian system of medicine. J Ethn Foods. 2019; 6: 14. Publisher Full Text\n\nPatel TM: AAHAR MATRA AND AAHAR SEVAN KALA W.S.R. TO CHARAKA SAMHITA.2019; 7.\n\nAgrawal AK, Yadav CR, Meena MS: Physiological aspects of Agni. Ayu. 2010; 31: 395–398. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTomar S, Madhukar JP: COMPREHENSIVE ACCOUNT OF SARPAVISHA WITH SPECIAL REFERENCE TO BRIHATTRAYI. Int J Ayurveda Pharma Res. Published Online First. 15 May 2019.\n\nAncheril IJ, Bharati AK, Gr AR: Concept of cumulative toxicity (Dushi Visha) in Ayurveda.\n\nHebbar DJ: Matrashiteeya Adhyaya: Ashtanga Hrudayam Sutrasthana 8th Chapter. Easy Ayurveda.2013.\n\nFood safety: Accessed: August 30, 2023. Reference Source\n\nThe State of Food Security and Nutrition in the World 2022. FAO; 2022. Publisher Full Text\n\nRane S: Street Vended Food in Developing World: Hazard Analyses. Indian J Microbiol. 2011; 51: 100–106. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRanga V, Ranga S: Clinical Evaluation Of Ashmarihar Kasaya In The Management Of Urolitiasis (Mutrashmari). Int Res J Ayurveda Yoga. 2022; 05: 79–93. Publisher Full Text\n\nWengritzky R, Mettho T, Myles PS, et al.: Development and validation of a postoperative nausea and vomiting intensity scale. Br J Anaesth. 2010; 104: 158–166. PubMed Abstract \| Publisher Full Text\n\nAgadtantra, Vyavahar-Ayurveda Evum Vidhivaidyak (Toxicology, Forensic Medicine, and Medical Jurisprudence) Archives. Chaukhambha.\n\nJaiswal YS, Williams LL: A glimpse of Ayurveda – The forgotten history and principles of Indian traditional medicine. J Tradit Complement Med. 2016; 7: 50–53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSantana FR, de Santana Souza MT , Camargo EA: Silva JA da: Anti-inflammatory and antinociceptive effects of a pectinolide-enriched fraction from Mesosphaerum pectinatum (L.) Kuntze. J Ethnopharmacol. 2023; 302: 115916. PubMed Abstract \| Publisher Full Text" }	[ { "id": "300895", "date": "13 Jul 2024", "name": "Bharat Padhar", "expertise": [ "Reviewer Expertise Ayurveda", "Clinical trials", "metabolic syndrome", "Psychiatry and Rheumatology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary : This research protocol outlines a randomized controlled trial aimed at evaluating the efficacy of Pippalyadi Agada, an Ayurvedic formulation, as an adjuvant therapy for managing acute food poisoning. The study will compare the symptom reduction and recovery time between two groups: one receiving standard drug therapy and the other receiving both standard drug therapy and Pippalyadi Agada. being conducted at MGAC & Acharya Vinoba Bhave Rural Hospital in Wardha, the trial will include 60 participants aged 18-50 with confirmed acute food poisoning. The study employs a single-blind parallel design with assessments on days 0, 3, 5, and 8, focusing on symptoms like nausea, vomiting, diarrhea, fever, and abdominal pain, as well as objective parameters such as CBC, LFT, KFT, and SOD levels. Despite the constraints of the single-blind design and the need for a more specific diagnostic protocol for food poisoning, the research aims to demonstrate the potential of Pippalyadi Agada as a cost-effective, safe, and accessible treatment option.\nReview Report:\n\nThe rationale for integrating Ayurvedic principles in managing acute food poisoning is well-grounded in historical context. However, the specific objectives of the study are broad and lack precise measurability. Additionally, the methodology for evaluating the analytical profile of Pippalyadi Agada is not detailed.\nThe objectives should be refined to be more specific and measurable. The methodology for assessing the analytical profile of Pippalyadi Agada needs to be clearly described to ensure comprehensive understanding and replicability.\nThe study design is appropriate given the constraints posed by the nature of the interventions. Acknowledging the limitations of the single-blind design is important for transparency. Future studies might explore alternative methods to enhance blinding where feasible.\nRecommendations for Improvement\n1. Refinement of Objectives: Current Objectives:\n\n1. To study the efficacy of Pippalyadi Agada as an adjuvant drug in the management of acute food poisoning.\n\n2. To compare the efficacy of Pippalyadi Agada as adjuvant therapy and standard drug therapy in acute food poisoning patients.\n\n3. To evaluate the analytical profile of Pippalyadi Agada.\nSuggested Refinements:\n\n1. To evaluate the reduction in symptoms (nausea, vomiting, diarrhea, fever, and abdominal pain) in patients with acute food poisoning treated with Pippalyadi Agada as an adjuvant therapy.\n\n2. To compare the time to symptom resolution between patients receiving standard drug therapy alone and those receiving standard drug therapy with Pippalyadi Agada.\n\n3. To analyze the chemical composition and pharmacological properties of Pippalyadi Agada through standardized laboratory methods.\n2. Include detailed procedures for the preparation, standardization, and analytical evaluation of Pippalyadi Agada. Specify the laboratory techniques (e.g., chromatography, spectroscopy) that will be used to determine its chemical composition and pharmacological properties.\n3. Write a more specific and standardized diagnostic protocol for acute food poisoning to differentiate it from other conditions with similar symptoms. This could include specific biomarkers or diagnostic tests to confirm foodborne illness.\n4. Describe that how participant confidentiality will be maintained throughout the study. Include details on data storage, access controls, and anonymization procedures.\n5. Write the details of blinding process. Also mention that who will mask the intervention and who will be blinded i.e. participants, researcher or statistician. How the blinding breach may be handled if any. Clearly acknowledge the limitations posed by the single-blind design and discuss how these limitations will be mitigated in the study.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "300892", "date": "23 Jul 2024", "name": "Arun Karnwal", "expertise": [ "Reviewer Expertise Food Microbiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract and Introduction:\n1. Clarity and Coherence: The abstract should clearly outline the study's aim, methods, results, and conclusion. The current version lacks clarity and transitions between different topics without coherence.\n\n2. Focus on Antimicrobial Resistance: The introduction should provide a stronger background on antimicrobial resistance, its significance, and relevance to the study. The connection between antimicrobial resistance and the need for alternative treatments such as Ayurvedic remedies should be more explicit.\n\nBackground:\n3. Antimicrobial Resistance and Foodborne Illnesses: Provide a more detailed discussion on the relationship between excessive antibiotic use, antimicrobial resistance, and the prevalence of foodborne diseases. Highlight the global burden and economic impact, with emphasis on low- to middle-income countries as outlined by the World Bank’s analysis.\n4. Ayurvedic Interventions: Expand on the concept of “Agada” and its historical context. Provide more detailed information on Pippalyadi Agada, its ingredients, and their pharmacological properties. Discuss the rationale for selecting Pippalyadi Agada for this study.\n\nMethodology:\n5. Study Design: Clearly define the study design. Specify whether it is a randomized controlled trial, double-blind study, etc. Detail the criteria for participant selection, randomization process, and blinding methods if applicable.\n6. Intervention Details: Provide a more detailed description of the interventions for both groups. Include specifics on the standard drug therapy used in both groups and how Pippalyadi Agada will be administered (e.g., dosage, frequency, form).\n7. Outcome Measures: Clearly define the primary and secondary outcome measures. Include specifics on how symptoms such as nausea, vomiting, fever, and diarrhea will be assessed and quantified. Mention any additional parameters that will be monitored (e.g., inflammatory markers, patient-reported outcomes).\n\nResults:\n8. Data Collection and Analysis: Describe the methods for data collection and analysis. Specify statistical tests that will be used to compare outcomes between the two groups. Ensure clarity on the timeline of assessments (days 0, 3, 5, and 8).\n\nDiscussion:\n9. Interpretation of Results: Discuss the potential implications of the study’s findings in the context of antimicrobial resistance and the management of foodborne illnesses. Highlight the significance of Ayurvedic interventions as complementary therapies.\n10. Limitations: Address potential limitations of the study, such as sample size, participant adherence, and any biases. Discuss how these limitations will be mitigated.\n\nConclusion:\n11. Summarize Key Findings: Provide a concise summary of the study’s key findings and their relevance. Emphasize the potential benefits of incorporating Ayurvedic remedies like Pippalyadi Agada into standard treatment protocols for acute food poisoning.\n\nReferences:\n12. Citations: Ensure all statements, especially those related to statistical data and claims, are backed by appropriate references. Include recent and relevant studies to support the background and discussion sections.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "300889", "date": "29 Jul 2024", "name": "Sandeep V. Binorkar", "expertise": [ "Reviewer Expertise Clinical and forensic Toxicology", "Ayurveda Dermatology", "Ethnomedicine", "Clinical Trials" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary:\nThe protocol introduces a comparative evaluation of Pippalyadi Agada as an adjuvant drug versus standard therapy for acute food poisoning management. It outlines the significance of antimicrobial resistance and underreporting of foodborne illnesses, emphasizing the need for effective treatment strategies. Inclusion criteria specify participants aged 18-50 with acute food poisoning symptoms, while ethical considerations prioritize confidentiality and data management. The methodology details a single-blind parallel design with Group A receiving standard therapy and Group B receiving Pippalyadi Agada in addition to standard therapy. Various diagnostic tests like Stool R/M, CBC, LFT, KFT, and SOD level measurements are planned to assess participants' health parameters. Data management responsibilities lie with the principal investigator, ensuring systematic handling of collected data. The discussion contextualizes Pippalyadi Agada within Ayurvedic principles, highlighting its anti-inflammatory and antioxidant properties. The study's status is pending and awaiting commencement.\nREPORT & RECOMMENDATIONS:\nThe study's objectives could be more precise, making it difficult to accurately assess specific outcomes or measure success. This lack of precision hampers the ability to evaluate progress and effectiveness.\nThe objectives should distinctly outline Primary objectives (goals), such as the main outcomes the study aims to achieve, and Secondary objectives, which encompass additional, supportive outcomes. This specificity helps clearly define the study's focus and enables a structured data collection and analysis approach.\nThe evaluation of Pippalyadi Agada's analytical profile needs more comprehensive detail, limiting the depth of understanding of its composition and properties. More analysis is required in order to assess its potential efficacy and safety thoroughly.\nDeveloping a precise and standardized diagnostic protocol for acute food poisoning is imperative. This will not only improve the accuracy and consistency of diagnosis but also reassure you about the reliability of our research. The protocol will include specific criteria for symptom assessment, laboratory tests, and diagnostic procedures to ensure reliable and timely identification of foodborne illnesses.\nDocument the blinding process thoroughly, specifying how participants, researchers, and data analysts are unaware of treatment allocations to prevent bias. Include details on the implementation of blinding, such as labelling methods, use of placebo controls, and procedures for maintaining blinding integrity throughout the study.\nThe average treatment duration for acute food poisoning typically ranges from 1 to 3 days, depending on the severity of the symptoms and the causative agent. Most cases are resolved with supportive care, including hydration and rest. In this study, it's needed to justify the 7-day treatment duration for acute food poisoning.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-361
https://f1000research.com/articles/13-357/v1	23 Apr 24	{ "type": "Research Article", "title": "An exploratory study of critical incidents within public organizations during leadership change", "authors": [ "Rian Pramana Suwanda", "Fendy Suhariadi", "Bagong Suyanto", "Suparto Wijoyo", "Fendy Suhariadi", "Bagong Suyanto", "Suparto Wijoyo" ], "abstract": "Background Leadership changes within public organizations are often associated with achieving the organization’s vision. This exploratory study examines critical incidents and the anxiety experienced by the head of the department at the local government in the context of leadership change in the public organization. It explores anxiety, which has rarely been explored in connection with leadership change, especially with regard to public organizations and countries with a high-power distance culture. Thus, it comprehensively describes the sources, course, and consequences of anxiety due to leadership change.\n\nMethods Critical incident technique (CIT) was used to conduct analysis because of its suitability as a theoretical framework for the exploratory nature of this research. Data were obtained through in-depth interviews from 26 informants who served as heads of departments in cities.\n\nResults The findings revealed the causes, course, and consequence of the anxiety experienced in response to leadership change. Political choice, culture change, policy change, fear of loss, and unaccountable financing were identified as sources of anxiety. Anxiety manifested through negative, cognitive, and behavioral reactions. The consequences were divided into in-circle, out-circle, and ambivalence-circle participation.\n\nConclusions High-power distance culture causes leaders to portray hegemony with boundaries that are difficult to access as well as appear more directive to strengthen control within the organization. The integrated model presented here (causes, course, and consequences of anxiety) is expected to enrich the integrated, modern, and emotional science through a functional account of the emotional approach. Cognitive and affective reactions have a two-way relationship, wherein emotion influences cognition and cognition elicits emotion.", "keywords": [ "Leadership Change", "Public Organization", "Critical Incident Technique", "Indonesia" ], "content": "Introduction\n\nThe new leader in Indonesia—elected through general elections—brings about massive changes to the government’s vision and mission, public service programs, and budgets and facilitates organizational change. This phenomenon is exacerbated by the harsh reality that approximately 70% of all change initiatives fail (Beer & Nohria, 2001). Magazine articles and practitioner books have significantly shaped the 70% organizational-change failure narrative; however, such articles lacked a discussion of methods, epistemologies, and references in relation to organizational-change research and academia (Hughes, 2011). Although previous studies have questioned the accuracy of this failure rate, organizations’ ability to successfully implement change remains critical for achieving success (Gigliotti et al., 2019).\n\nPrevious studies have found that the primary determinants of successful change are employee involvement (Gopinath & Becker, 2000; Rafferty et al., 2013; Rafferty & Restubog, 2010), support and trust from employees (Kotter & Cohen, 2002), and individual readiness (Holt & Vardaman, 2013). Other studies have proven that leadership is the key to successful change (Colville & Murphy, 2006; Higgs & Rowland, 2001). Gilley et al. (2008) highlighted the importance of distinct leadership qualities and competencies for effective transformation and innovation and that change has a cascading impact on an organization. Leaders at all levels are frequently presented with concerns regarding leadership change, which allows them to create work environments that encourage change readiness (Miles, 2001). Extensive literature on a leader’s role in successful change (e.g., Bass, 1997) has shown that although transactional and transformational leadership are complementary (Bass & Riggio, 2006), the latter is often associated with change and innovation. Researchers have noted that different variations in change require distinct leadership styles (Shvindina, 2017). Leaders, employees, and followers play an important role in the change effort as they actively interpret and negotiate this change (Sahay, 2017). Therefore, organizational change requires a focus on increasing individual involvement through management models that are flexible enough to allow individual organizational interpretation (Sheffield & Coleshill, 2001).\n\nChange is expected to generate resistance (Coghlan, 1993; Oreg, 2006). Resistance to change is frequently cited as a cause of the difficulty in implementing change initiatives and their failure (Erwin & Garman, 2010): resistance is one of the most common problems faced by management when implementing change (Bovey & Hede, 2001a, 2001b) and is the number one reason for the failure of change initiatives (Bovey & Hede, 2001a, 2001b; Prochaska et al., 2001). Employee resistance is directly linked to the failure of many large-scale corporate reform efforts (Reger et al., 1994). It can be argued that most organizational changes are managed from a technical perspective without understanding the effects of human elements on the success or failure of the change and ignoring the interests of equal human dimensions in implementing the change (Beer et al., 1990; Huston, 1992). The attitudinal concept of resistance is divided into cognitive, emotional (frustration and anxiety), and behavioral stages (Piderit, 2000). According to Lewin (1958), resistance to change begins with anxiety and discomfort. The early stages of change are associated with several difficulties, such as the emergence of discomfort, imbalance, and anxiety.\n\nUncertainty about a future event may disrupt the anticipatory process, which is a key component of adaptive cognitive responses, and lead to an overestimation of the possible threat and its severity (Gu et al., 2020). Furthermore, leadership transitions are plagued by anxiety resulting in less intelligence about common situations when it is most required (Gilmore & Ronchi, 1995). It drives many people to make more cautious decisions about sharing knowledge. Feelings of anxiety are an inevitable part of change, even in the context of public organizations. Therefore, leaders and organizations must focus on garnering commitment to change by designing coping mechanism for their followers (Bordia et al., 2004a).\n\nExperts have widely examined leadership in relation to change and leadership change. However, anxiety caused by leadership changes has rarely been studied. Most studies have explored the influence of leadership styles, such as Bono et al. (2007), who explained that the relationship between transformative leadership and the effective well-being of followers has positive (a composite of happiness, excitement, and optimism) and negative (a composite of anxiety, anger, and irritation) impacts. Few studies have examined the focus of leadership change, such as that of Orosz (1994) that assessed executive transition. The study found that the destructive metaphors used by a state’s agency director to describe the experience of executive transition justify the initial anxiety typically felt by employees during periods of leadership change. Thus, previous studies have failed to comprehensively describe the concept of anxiety related to leadership change.\n\nFor public organizations, the change brought about by a new leader selected through elections, is massive and radical. Previous studies have captured this phenomenon. For example, a new policy called “the best value” was proposed immediately after the 1997 elections of the Scottish local authorities (Sheffield & Coleshill, 2001), which replaced mandatory competitive tendering with a regime that solely focused on quality issues and financial performance. Following the 2019 election cycle, Spain transitioned from an imperfect party system to a moderately pluralist party system, resulting in the world’s first coalition administration. In a short period, Spanish politics swung like a pendulum: from polarization, fragmentation, and a willingness to curtail core democratic rights in the name of Spanish unity to the ability to establish a durable accord (Rodon, 2020). However, changes occurred before and after the elections. Government responsiveness increased significantly before the elections, as evidenced by the speed with which local governments handled requests (Dipoppa & Grossman, 2020). The change in responsiveness by the government is in line with previous studies showing that the work done by the incumbent leader helps in the reelection of the ruling party (Mishra & Attri, 2020).\n\nIn Indonesia, since the implementation of regional autonomy in 1999, the fate of community life, including education, health services, infrastructure development, and food security for a sustainable environment, has mostly depended on local governments. This constellation stretches as a phenomenon not only in Indonesia but also globally. Government quality is determined by its impact on citizens’ quality of life (Huther & Shah, 1998). The main axis of regional autonomy in Indonesia is democracy driven by direct elections. Elections are the most important instrument for democratization: democracy is procedural and elections are considered the essence of democracy (Schumpeter, 1976). Huntington (1993) believed that the democratic system alone does not suffice in elections. Free, fair, and competitive elections are possible only if there is freedom of opinion, assembly, and the press, and the candidates and opposition can criticize power without fear of reprisals. In 2020, Indonesia held simultaneous general elections in 270 regions, comprising nine provinces and 261 regencies/cities. It inaugurated 185 pairs of major or regent (leader) in February 2021, of which 114 officials served as incumbents while 255 officials were elected for the first time or called “The New Kid on the Block.” General elections in Indonesia have led to major changes in regional governance. The fundamental changes that always occur include changes in vision, which are followed by changes in programs, the selection of apparatus resources, and various policies related to public services, such as service tariffs, infrastructure development, and service management (Smith, 2012). Additionally, leadership change within public organization is impacted by Indonesia’s high power distance culture. Hofstede (2022) measured the power distance dimension in Indonesia, which obtained a score of 78; Indonesia relies on hierarchies, unequal rights between power and non-power holders, inaccessible superiors, directive leaders, management control, and delegation. Power is centralized, and managers rely on the obedience of their team members.\n\nOur study sought to comprehensively unravel the anxieties caused by leadership change. It studies the context of leadership changes in public organizations as a consequence of the Indonesian general election of 2020. The official heads of department in the regional government or the middle managers, who were in direct contact with the new leader, were interviewed and their responses were examined using the critical incident technique (CIT) method. A total of 26 informants were selected based on the following criteria: those who experienced critical incidents of anxiety associated with leadership change. The analysis was conducted in three stages to determine the order of concepts and themes from the causes, course, and consequences of anxiety in relation to leader change. Data validity was achieved through the support of expert judges who evaluated the consistency of the developed themes (Flanagan, 1954; Gremler, 2004). Finally, member checking was conducted during the triangulation stage to confirm the study’s trustworthiness.\n\nThis study extends the application of CIT to the context of leadership change, which has been thoroughly explored in service-marketing research (Grace, 2007; Gremler, 2004). Using CIT, this study proposes a model for anxiety associated with leadership change. The model comprises the causes, courses, and consequences of anxiety experienced by the head of the department in the local government. The findings are expected to expand the theory of leadership change, particularly by revealing the relationship between new leaders and their followers. Furthermore, a comprehensive description of anxiety based on Lewin’s three-phase theory is expected to deepen the understanding of the resistance that persists in the early stages of change. In addition, this research is expected to comprehensively describe the anxiety associated with leadership change in public organizations in countries with a high-power distance culture. Finally, the proposed anxiety model can deepen the study of anxiety in relation to social evaluation theory and modern emotion science.\n\n\nLiterature review\n\nExtant literature suggests that leadership is strongly interconnected with change. The type of leadership is vital to the change process (Hussain et al., 2018). The role of leadership in causing effective change has led to the notion that transformational leadership is a critical component of change even though both transactional and transformational leaders are considered complementary (Bass & Riggio, 2006). Transformative leaders are charismatic, motivational, intelligent, and individualized in their approach, while transactional leaders utilize rewards and penalties to inspire individuals to enhance their organizational performance (Bass, 1985). Given that the presence of leaders stimulates change, leaders must take the initiative by defining a vision (Bass, 1985). Leadership style affects a group’s dynamics and the interaction between its members, which in turn influences the level of organizational readiness to change (Wulandari et al., 2020). Leaders’ spirit, insight, knowledge, compassion, ideals, and learning skills are crucial aspects that lead people to embrace change (Paterson & Cary, 2002). Leadership is the mediating force between a changing environment and an organization’s operating system (bureaucracy) (Mintzberg, 1978). In addition, leaders’ behavior makes changing circumstances more effective (Higgs & Rowland, 2005).\n\nAccording to experts, different styles of leadership are required for different types of change. This study emphasizes the importance of specific leadership skills and characteristics required for successful change and innovation. Organizations are interested in examining and enhancing the leaders’ talent and ability to implement change and innovate at all levels in order to strengthen the change effectiveness skills (Gilley et al., 2008). This distinct change relates to public organizations when a new leader causes a fundamental change. Leadership changes lead to organizational changes, such as change in the developmental vision, priority programs or innovation, selection of government apparatus resources, and various policy adjustments related to public services. This phenomenon alters the status quo—which represents stability—into either antithesis or synthesis, representing a change for worse or better, respectively (van de Ven, 1995). Change can have a comprehensive impact on all aspects of a public organization, or at only a certain point, which is vital to support the organization; thus, change is either incremental or radical (Tushman & Romanelli, 1985). In addition, change periodically affects medium- and long-term organizational capacity, but some are only shock effects at the beginning of the implementation; thus, change can be either sustainable or unsustainable (Meyer et al., 1993). Change initiatives have become common in organizations and may range from large to medium- or small-scale (Weick & Quinn, 1999).\n\nLewin’s Three-Phase Process was used as the change model in this study. The model is categorized into three stages: unfreezing, moving, and refreezing (Lewin, 1958). The unfreezing of behavior and the establishment of a willingness to change are the first steps in the change process (Burnes & Cooke, 2013). Lewin (1958) described unfreezing as a difficult re-education process. Moving, also known as locomotion, is the second step, which denotes a change in position within a field performed through action research (Lewin, 1947). The final stage, freezing, denotes the permanence of a new situation (Burnes, 2020). In organizational terms, freezing can necessitate changes in culture, norms, policies, and practices (Armenakis et al., 1999). Cummings and Worley (2009) identified five critical leadership activities in the change process: motivating change, defining a vision, developing political support, managing transition, and maintaining momentum. In line with Lewin’s Three-Phase Process, motivating change and creating a vision demonstrate an unfreezing stage, developing political support and managing the transition demonstrate a moving stage of change, and maintaining momentum demonstrates the implementation and refreezing stages of change.\n\nOrganizational change raises uncertainty, which is one of the most commonly reported psychological states (Bordia et al., 2004a). Uncertainty has been characterized as an individual’s perceived inability to precisely foresee something (Milliken, 1987) and has been linked to changes in processes and outcomes (Bordia et al., 2004b; DiFonzo & Bordia, 1998). Bordia et al. (2004a) presented a three-factor paradigm of uncertainty experienced by individuals during change: strategic, structural, and job-related uncertainties. Strategic uncertainty refers to uncertainty regarding organization-level issues; structural uncertainty refers to uncertainty arising from changes in the organization’s inner workings; and job-related uncertainty refers to uncertainty related to job security, promotion opportunities, job role changes, and so on (Bordia et al., 2004a). Uncertainty has several negative consequences on an individual’s well-being and satisfaction in an organizational context (Bordia et al., 2004a). This leads to low morale and job satisfaction (Bastien, 1987; Rosenfeld et al., 2004). It is positively related to psychological strain and negatively related to control (Bordia et al., 2004b). Due to its effect on emotional states, uncertainty about future events is inextricably linked to anxiety and worry (Gu et al., 2020). When changes occur very frequently, individuals are likely to feel fatigued by them and experience an increase in anxiety due to their unpredictability (Rafferty & Griffin, 2006).\n\nBarlow (2002) highlighted that according to Kierkegaard, the source of anxiety lies deep within an individual; anxiety is rooted in the fear of nonexistence, non-being, or nothingness, rather than the fear of death. Only by acknowledging and overcoming this dread of becoming nothing—only by facing the prospect of losing one’s identity—can one completely understand what it means to be human. Only through this experience can we make a clear separation between the self and other things or nonbeings. Other well-known theorists and clinicians have proposed comparable bases for assessing diffused and objectless anxiety. According to May (1979) and Barlow (2002), anxiety is the fear triggered by a danger to some value that the individual believes is vital to their life as a personality. The danger could be directed toward one’s physical life (threat of death) or mental well-being (threat of depression; loss of freedom and meaninglessness). Alternatively, the threat could be directed toward a value that one associates with their existence (patriotism, love for another person, “success,” etc.). Anxiety is a mixture of several emotions that can change over time and in different settings (Izard, 1977).\n\nThe mechanisms that mediate anxiety in this study are based on the theory of social evaluation. The general criterion of social evaluation is defined as a mental process in which an individual assigns different values (positive, negative) to specific behavioral patterns (e.g., helping and hindering) that occur in social interactions (e.g., problem-solving), associates these behaviors with specific individuals (partnership values), and displays different behaviors (e.g., avoidance or preference) toward others based on their overall value (Abdai & Miklósi, 2016). According to Manstead and Semin (1981), the negative quality of the actor’s subjective public image following a transgression is the source of social emotions resulting from unintended social infractions. The experimental results reveal that actors feel anxious as they believe others are treating them more negatively as a result of witnessing mistakes, although the situation does not affect the actor’s self-image. The fear of negative evaluations felt by actors defines social anxiety (Button et al., 2015). Button et al. (2015) established that the learning biases of social evaluation associated with social anxiety are more strongly related to self-referential information. The anxiety experienced by the actor in the experiment was in line with social anxiety disorder, which is a severe psychiatric disorder characterized by persistent and overwhelming fears of one or more social or performance settings where there is potential for evaluation by others (American Psychiatric Association, 2013). Fear of negative evaluation is a key component in cognitive-behavioral models of social anxiety and has rich empirical support (Heimberg et al., 2010).\n\nOver the past few decades, the study of anxiety has become increasingly integrative. Theories about anxiety have expanded based on behavior, biology, and cognition aspects, and have been integrated into modern emotion science (Barlow, 2002). Most current theories regard emotions as fundamental action tendencies that aim to inspire conduct related to species survival. Preparing for, avoiding, and escaping potentially dangerous, life-threatening events, which are at the heart of fear and anxiety, are examples of these behaviors or action tendencies (Barlow, 2002). Lang and McTeague (2009) regarded behavioral activities or broad reaction dispositions that occur in specific stimulus circumstances as the essence of emotion. These stimulus contexts establish the function and direction of the acts, which include not only stimulus information that inspires action but also relevant response propositions.\n\nFurthermore, understanding anxiety through a functional account of the emotional approach places individuals and events in an inseparable unit, where events gain significance through individual efforts; thus, events and goals are interrelated (Smit & Lazarus, 1990). According to emotion theory, functionalism is concerned with the link between feelings and what a person is trying to do, rather than evolutionary survival value (Campos et al., 1994). Keltner and Gross (1999) explained the functional account of emotion, including why emotions exist and the systems of interrelated components and consequences. This functional approach provides a corridor for identifying the antecedents that mediate anxiety, as described in the social evaluation theory. Furthermore, the system of components is in line with the modern emotion science approach regarding the relevant response propositions that arise from the circumstances of a specific stimulus. However, this functional approach leads to anxiety.\n\nSeveral studies have examined anxiety in various contexts, particularly health and psychology. However, anxiety related to leadership changes in public organizations has rarely been studied. The low level of research in this field may be due to some very sensitive issues that are influenced by bureaucratic cultures (e.g., high-power distance culture) in developing countries such as Indonesia. There is a phenomenon gap regarding how anxiety arises and is felt, as well as its consequences in the context of leadership changes in public organizations. In fact, research on a functional approach, the antecedents, system of components, and consequences of anxiety remains scant. There is a gap in our understanding of the variable components of anxiety associated with leadership change. Through this exploratory study of critical incidents, we examined anxiety felt by the heads of departments in local governments in response to leadership change. The study provides a framework for comprehending the problem to be solved (cause), system of components (course), and consequences of anxiety related to leadership change in public organizations. Thus, the following research question was examined: “What are the antecedents, reactions, and consequences of anxiety related to leadership changes in a public organization?”\n\n\nMethods\n\nFigure 1 presents the research design, including the theoretical framework, models, and tactics for critical incident development (CID). We adapted the theoretical framework developed from emotional analysis and divided it into problems to be solved, system components, and consequences (Grace, 2007). We also adopted this approach from the development of critical incident models that focus on causes, courses, and outcomes (Edvardsson, 1992; Edvardsson & Roos, 2001). Critical incidents were mined through in-depth interviews. We used a purposive sampling method to obtain informants who uniquely followed our research interests (Miles & Huberman, 1994; Patton, 2002).\n\nThis figure has been adapted from Grace, D. (2007). © 2007 by Sage Publications. Reprinted by Permission of SAGE Publication.\n\nChanges caused by the new leader (regent or major elected for the first time) may be radical at any level of public organizational activity. Radical change is implemented completely if large-scale adjustments are made at the beginning of the change (Romanelli & Tushman, 1994). In contrast, some studies have claimed that radical changes must be made gradually and carefully (Pettigrew et al., 1992). However, it has been determined that early change to specific “high-impact” elements is necessary for completing radical transitions (Amis et al., 2004). We believe that changes implemented either on a large scale or gradually are critical incidents that make unusual and significant contributions to human activities. This is very influential in terms of managing change, as various studies have explained that the most successful changes ensure employee involvement (Gopinath & Becker, 2000; Holt & Vardaman, 2013; Kotter & Cohen, 2002; Rafferty et al., 2013; Rafferty & Restubog, 2010).\n\nA significant contribution to human activity was found in the phenomenon of leadership changes in a public organization. It is consistent with the concept of a critical incident, which is defined as contributing significantly, either positively or negatively, to an activity or phenomenon (Grove & Fisk, 1997). As a result, we consider the CIT to be the best tool for studying anxiety experienced by middle managers in relation to leadership change in public organizations. Furthermore, the CIT was selected based on the possible critical occurrences’ need to contextualize particular situations (Ribeiro et al., 2020). In addition, CIT is an effective method for exploratory research on this little-known phenomenon (Bitner et al., 1990).\n\nThe CIT is a series of processes for collecting first-hand observations of human behavior in such a way that they can solve issues and generate broad psychological principles (Flanagan, 1954). This study adapted the theoretical model of critical incidents developed by Grace (2007) and Edvardsson (1992) to formulate the CIT method. By collecting data from the informants, we converted Grace’s (2007) self-report survey into in-depth interviews. In-depth interviews were conducted to obtain more detailed responses and help informants feel more comfortable while disclosing information about the change (Nadia et al., 2020). In-depth interviews help researchers to identify the core issues of various stakeholders and prepare questions for subsequent interviews (Malodia et al., 2021).\n\nData were collected from June 13 to September 28, 2021, through in-depth interviews using a purposive sampling method. This flexible data mining strategy is based on the CIT, which has a flexible set of principles that must be modified and adapted to match current circumstances, as opposed to a single set of strict rules to guide data collection (Flanagan, 1954). The inclusion criteria for informants were (1) heads of departments in the local governments of cities A, B, and C; and (2) they experienced critical incidents of anxiety associated with leadership change. The three cities held simultaneous elections on December 9, 2020, resulting in the election of a new mayor or regent for the first time. We contacted 32 candidates via social media to inform them about the research design. Additionally, we conducted telephone calls to inquire whether they had experienced critical incidents in the form of anxiety related to leadership changes. The researcher had no relationship established prior to the study’s commencement with informants from City B and C. However, we had established relationships with informants from City A in several previous studies. A total of 26 informants met the inclusion criteria and continued with in-person interviews. No one was present apart from the participants and researchers. The number of informants studied follows Flanagan (1954) that there are no strict rules regarding the appropriate sample size for CIT. We purposively selected 26 informants who had experienced anxiety in response to leadership change and uniquely fit the research interests of the study (Miles & Huberman, 1994; Patton, 2002), and we reached data saturation.\n\nAll informants’ data were processed anonymously without distorting their scientific meaning. Twenty informants were male (76.92%), and the rest were female (23.18%). The average age was 49.8 years and the majority had entered ranks IV-A and IV-B (administrative ranks of public organization officers in Indonesia). Verbal consent was obtained from the participants to record, process, and display their statements. Consent was obtained at the opening of the interview, where the author asked for the informant’s willingness to be involved in the research. It was documented in the interview transcript. Most participants chose verbal consent due to their concerns about the research topic, which is closely related to sensitive issues and high-power distance culture in Indonesia. Written informed consent was subsequently obtained, and all participants signed the interview transcript on August, 4-10, 2023. The transcript contained additional clauses regarding informed consent, including the verbal consent obtained at the opening of the interview and the protection of participant confidentiality confirming all interview results were recorded anonymously. Ethical approval was obtained from the Postgraduate School of Airlangga University on August 10, 2023. Ethical approval was obtained retrospectively because of the urgency of our study implementation. This study was conducted after the general election which was held simultaneously in Indonesia for the first time in 2020. This first simultaneous election resulted in 63,91% of regents or mayors being elected for the first time in our research areas. The political change in the post-election period, especially within the 6 months after the election, greatly influenced informants and the culture of public organizations in Indonesia. The new regents and mayors determined a new medium-term development program and changed the bureaucratic structure, and various other fundamental changes were observed, which are thought to cause anxiety among members of public organizations. These considerations necessitated that our study began immediately to capture the critical experiences of local government officers during the leadership change. Another consideration was that our study was low risk, and the implementation and results of the study were continuously monitored by the supervisor, and supported by the continuity of the research process interactively with the informants from data collection to the preparation of the final manuscript. Our research procedures, including the consent process, were discussed in an in-depth joint review forum on July 20, 2023, with our supervisors, education staff, and lecturers from the Postgraduate School of Airlangga University. After the reviewing process, the Postgraduate School of Airlangga University stated that our study had fulfilled the ethical principles. This research complied with the principles of study ethics in the Declaration of Helsinki, as stated by the Postgraduate School of Airlangga University, Surabaya, Indonesia (Number: 2446/UN3.SPS/PT.01.06/2023).\n\nThe interview adopts a structured format with eight predetermined open questions, consistently asked to all informants. The average duration of the interviews was 47.8 minutes, and audio recordings were made. A total of 16 interviews took place in non-office settings, such as coffee shops, cafes, and restaurants, while the remaining 10 were conducted within the informant’s office. The interview transcripts were presented to the informants from October 11 to December 13, 2021, after the entire interview was completed. Participants were allowed to review and then provide approval for the interview transcripts. Furthermore, informants were offered the opportunity to review and provide input on the research results, presented in journal format, from March 1 to June 30, 2022. Additionally, before publication, verbal consent was reaffirmed in written consent with assistance from the Postgraduate School of Airlangga University from August 4 to 8, 2023.\n\nData saturation was achieved after the data collection and analysis. To increase the credibility of the research, we used data triangulation through multiple data sources (Bekhet & Zauszniewski, 2012; Stavros & Westberg, 2009). Fusch et al. (2018) noted that triangulation involves the use of multiple external methods to collect and analyze data. Data triangulation came from two judges and three heads of local government departments from cities A, B, and C. Source triangulation enquires about the veracity of the data gathered from multiple sources. The researchers used secondary data from official websites, regional development plans, vision and mission booklets, and social media analytics to complement the interviews. The data were collected from the official websites and vision-mission booklets containing the proposed change programs endorsed by the regents and mayors. The Regional Development Plans encompass the official medium-term development plans for the municipalities during the period 2021-2024. Concurrently, social media contains a compilation of media coverage from various sources, highlighting changes in leadership in cities A, B, and C. The aim of scrutinizing this information is to comprehend the conditions of leadership change in the three cities from diverse perspectives. Consequently, the researcher expected to gain a more nuanced understanding of the information provided by the informants during interviews. For inclusion and exclusion criteria, secondary data is limited to the three city and is related to changes in leadership.\n\nThe analysis was conducted in three stages using NVivo Plus 12 for Windows. Open access alternative software besides NVivo is Taguette, ATLAS.ti, QualCoder, RQDA and MAXQDA. First, the changes perceived by the informants and the causes of anxiety associated with leadership changed were determined. Second, the course manifested by the informant in feeling, thinking, and acting immediately in response to the anxiety associated with the leadership change was examined. Third, the consequences of anxiety associated with leadership change were identified. We conducted a content analysis to improve the validity of the study, with particular attention to the concerns regarding sampling, objectivity, reliability, and systematization (Gremler, 2004). In the second and third phases of the analysis, two judges who were experts in the fields of psychology and socio-politics were involved in the determination of the course and consequence themes.\n\n\nResults and discussion\n\nFindings have been explained using the conceptual framework for the causes, course, and consequences of anxiety related to leadership change. Furthermore, the percentage of significant incidents discovered was used to summarize the first- and second-order concepts. Finally, we proposed an integrated model of anxiety related to leadership change in public organizations.\n\nThe causes of anxiety related to leadership change were categorized into five themes: political choices, fear of loss, tactical budget expenditure, systems and policies, and cultural change. Figure 2 illustrates the conceptual framework for the causes of anxiety, and Table 1 summarizes the findings of critical incidents that caused anxiety (as percentages).\n\nFirst theme: Political choices\n\nBased on in-depth interviews using the CIT, political choices are a critical cause of anxiety associated with leadership change. Of the 26 participants, 24 (92.3%) revealed that their political choices induced anxiety while facing a new leader. In-depth interviews revealed “different political choices” (42.31%) as the largest critical incident causing anxiety, followed by “supported politically, but lost in the constituency” (30.77%). Furthermore, apart from being different or supporting political choices, being neutral also caused anxiety (19.23%). The act of making a choice in a political event is always anxiety-inducing, as evidenced by the statements of several participants regarding the theme of political choice:\n\n“So, civil servants must be neutral… we cannot turn a blind eye and we have to choose the side. The flow is like that (factual conditions observed by the informants). Now the party I choose loses like this. Yes, I am ready, fortunately, if I am still used (in the previous position of local government office), if not, I can be dumped out. Doesn’t that cause anxiety?” (Informant 1)\n\n“It’s a secret, ya …. I was indeed a campaign team in District A (censored). But at that time, we didn’t have enough money then we lose. So, it’s clear that I’m definitely to blame!” (Informant 4)\n\n“I didn’t choose. I am neutral. But we all know that. After this, the campaign team will surely undermine asking for a share. Those of us who are neutral will put aside. This is very unsettling. Just being professional is not enough.” (Informant 21)\n\nPolitical choices put participants in a position of uncertainty, especially regarding the most widely acknowledged career paths. As stated by the participants, political choices on the losing side have a significant impact on career mutations and demotions. On the neutral side, they feel marginalized by political supporters, which causes their judgments to be sidelined. This ambiguity induces feelings of anxiety (Tiedens & Linton, 2001; Todd et al., 2015). Differences in political choices relate to the inevitable diversity of opinions, values, beliefs, interpretations, and goals associated with leader change and are driven by political behavior (Fischer et al., 2007; Jafariani et al., 2012; Petracca, 1991). In Indonesia, informants are legally prohibited from making political choices as civil servants in order to support contestants who compete in elections. However, despite this phenomenon being common, the involvement of civil servants in elections has rarely been studied academically owing to its sensitive nature. Although it is against existing norms, this political choice has a positive impact in that political behavior in organizational change is important for achieving effectiveness (Buchanan, 2008). However, like the wheel of life, political choices that cause anxiety cause fundamental changes that determine votes (Ladd & Lenz, 2008). Based on field findings, the informants’ various political choices were allegedly unknown to the new leader. The feelings of anxiety that arose were associated with the fear of the new leader’s view of those who did not support him or who lost the support scheme during the campaign period. This finding supports social evaluation theory, which explains that anxiety arises from the fear of negative evaluation (Button et al., 2015; Heimberg et al., 2010; Manstead & Semin, 1981).\n\nSecond theme: Culture change\n\nCulture change caused by leadership change was identified as a source of anxiety by 84.62% of the respondents. A total of 21 informants (80.77%) stated that the emergence of intruders disturbed and tended to harm the work culture of the status quo. The term intruder refers to groups outside the government bureaucracy that comprise a campaign team, such as leaders of sympathizers, party representatives, and even academics. The intruder group is considered disturbing as it fails to understand the ethics of the bureaucracy as a whole, imposes ideas, and tends to lip service. The following excerpts resonate this sentiment:\n\n“We have to face people who claim to be the winning team. They do not understand the ins and outs of the bureaucracy, even the performance, but because they feel they are closest to the mayor, they are listened to.” (Informant 3)\n\n“They (intruders, red) are from academics, only talk about theory, and some only tend to look for projects in local government.” (Informant 7)\n\n“They are more lip service on our new mayor ….” (Informant 5)\n\nIn addition, the antecedents of anxiety under the cultural change theme were categorized as new learning (61.54%), poor communication (46.15%), and having to work overtime (23.08%). Critical incidents of new learning are closely related to the informants’ comfort zones. They must leave their comfortable areas and learn to support the changes launched by the new leader. At a certain level, due to policy discretion, the change was outside the scope of official duties and functions. This finding is evident from the following statements by several participants:\n\n“It’s good like this, it works smoothly, but I was told to do this and that…the concept isn’t clear either. We have to study again.” (Informant 3)\n\n“I’m in the field of communication and information, but I have to think about vaccine planning.” (Informant 12)\n\nCritical incidents of poor communication relate to the communication mechanism between the informants and the new leader, either through official letters or direct interaction. Official letters, which require the leader’s decision to comply with the provisions of laws, are hampered as the leader assigns a new secretary or aide who does not have archival experience or experience with official paperwork. Direct interactions are also hampered, because the new leader’s schedule is tight. This is due to the absence of a balanced distribution system for managing official schedules. This finding is evident from the following statements by several participants:\n\n“I have submitted a letter for the annual regional planning to get our mayor’s signature … er, it’s gone. Important papers are often lost because the mayor’s secretary is not yet skilled. The previous officer should also be used.” (Informant 8)\n\n“Now, it’s difficult to meet the mayor because he has many events. All events, he attended. Even in one same event, he attended with the vice. This is no longer a campaign …” (Informant 17)\n\nThe critical incident of working overtime is closely related to the leader’s activities, which caused the informants to accompany the leader even outside of working hours and holidays. This finding is evident from the following statements by several participants:\n\n“We have to be on standby for 24 hours, especially for activities related to the community, especially during a pandemic like this.” (Informant 11)\n\n“The new mayor always wants to appear … and we have to accompany him.” (Informant 13)\n\nOrganizational culture is a valuable asset if it supports an organization’s mission, goals, and strategies. Moreover, it plays an essential role in many elements of an organization (Calciolari et al., 2018; Denison & Mishra, 1995; Hartmann, 2006). The organizational culture in Indonesia, although strongly influenced by the existing political system, is unique at each level of city government. Although not studied in-depth academically, this condition is allegedly in line with Schein’s (2004) statement that organizational culture is distinctive, as it is derived from individual experience and history. This strong culture combines internal and external issues while ensuring the organization’s survival in difficult times. Furthermore, the organizational culture in Indonesia is influenced by the high-power distance culture, which is directly suspected to complicate the level of communication during situations of change. Bordia et al. (2004b) suggested that a systematic program of communication during change is warranted to reduce employee uncertainty.\n\nThe presence of intruders harms values and beliefs in the bureaucracy rather than new learning; having to work overtime and poor communication change habits. All these dimensions are closely related to organizational culture as a shared meaning for every member of the organization (Robbins & Judge, 2013). These various dimensions follow organizational culture as a set of value systems, beliefs, assumptions, and norms that have been applied, agreed upon, and followed by the organization’s members for a long time as guidance for their behavior in every situation in the organization, and adapting both in internal and external environments (Schein, 2004). Organizational culture refers to a system comprising values, beliefs, and habits that exist in the organization and interact with the formal structure, which results in the organization’s behavioral norms (Suhariadi, 2013).\n\nThird theme: Policy change\n\nPolicy change was also identified as a cause of anxiety associated with leadership change (reported by 84.62%). Here, the most crucial critical incident was the unfair recruitment mechanism for the position of structural officers (76.92%), followed by policy changes that are irrelevant to the status quo (61.54%), extending focus on campaign programs and the tendency to ignore basic service programs (53.85%), giving unfair rewards (46.15%), putting extreme pressure (30.77%), and demanding unrealistic targets (23.08%). The unfair recruitment mechanism for structural officers was stated by the informants based on their past experiences, which highlighted that every change in power, especially for those newly elected, would result in massive mutations. This mutation tends to ignore professionalism but is seen as a reward for the campaign team that supported the new leader during the campaign period. This finding is evident from the following statements made by several respondents regarding the theme of systems and policies:\n\n“Massive mutations will occur in August (six months after the inauguration). This has been seen from the officials appointed to fill the vacant positions, right? The people appointed are the campaign team.” (Informant 25)\n\n“As long as there is no clear blueprint, the selection of structural positions must come from the campaign team without considering credibility. For example, a sports teacher became a sub-district head, eventually went to prison…” (Informant 3)\n\n“We struggled to start a career from the beginning. Then, just because they were close to the mayor, functional officials moved to structural without a clear assessment.” (Informant 11)\n\n“The priority of the program is centered on populist programs during the campaign even though there are still many administrative matters and even basic services that should not be abandoned. In addition, the program target is too far away and very difficult to achieve in the next 5 years.” (Informant 12)\n\n“We do not get the reward for the hard work we have given. Our previous achievements are unseen, only political interests …” (Informant 3)\n\n“There is a lot of pressure from the campaign team on us to realize the change program. Is it for their interest or just delusional? But what is certain is that the budget for this year has already been determined.” (Informant 14)\n\n“Many policies are not following the conditions of our city, especially with the detailed planning and budgeting system as it is today. Do we have to make up?” (Informant 1)\n\nThe policy change dimension relates to the implementation of organizational change policies by new leaders. This implementation is important for managing the change process to achieve developmental visions, as proclaimed by the new leader. Policy analysis has long noted the importance of clear and specific policy objectives and coherent thinking about the relationship between the initiatives to be implemented and desired outcomes (Grizzle & Pettijohn, 2002; McFarlane, 1995).\n\nBorrowing from Pierson’s (2000) terminology, a transformation in the policy change dimension can be called a critical juncture. The critical juncture in organizational change, especially in systems and policy changes, is a sudden impetus for change in stable institutional arrangements (Pierson, 2000). According to various informants, the mutation and promotions for public organization officers that had been carried out for years based on the list of ranks and job evaluations were abruptly altered with mass transfers that were influenced by political interests. Thus, politics plays an important role in the overall process of policy change and reform. Politics influences the origin, formulation, and implementation of public policy, especially in the face of significant changes (Reich, 1995). Political events increase employee anxiety because they are often volatile. This causes public organization officers to become emotionally detached and the quality of their work, in turn, declines (Bailey & Raelin, 2015).\n\nFourth theme: Fear of loss\n\nFear of loss was identified as another cause of anxiety. The fear of losing a position due to mutation or demotion (61.54%), followed by the threat of losing strategic projects (34.62%), the threat of losing respect (30.77%), and the threat of losing relationships (23.08%) were gleaned from the respondents’ accounts:\n\n“I am afraid that I will be transferred even though I have served in this office for a long time.” (Informant 1)\n\n“… later if we move it to a ‘dry place,’ we can no longer find additional income.” (Informant 3)\n\n“Since becoming echelon IV, I have worked in this office. It’s been a dozen years. It is difficult if you have to separate from your coffee friends (best friend).” (Informant 25).\n\n“What if we are demoted later? Not only our income has decreased but also we have to lost respect, right?” (Informant 3)\n\nFear of loss is closely related to the threat of losing a position due to mutations or demotion, especially for those who serve in an influential department or have ambitions to become regional secretaries (top bureaucratic positions in local governments). Various studies have shown that loss is a source of resistance to change, such as loss of control (Bordia et al., 2004b; Eby et al., 2000), status (Canning & Found, 2015; Rider & Negro, 2015), comfort and privileges (Msweli-Mbanga & Potwana, 2006), and resources (Dubois et al., 2013; Shin et al., 2012). This dimension also resonates with Chreim’s (2006) statement that employees do not really resist change but reject perceived threats to their sense of autonomy, integrity, ideals, loss of status, salary, and comfort. Subconscious awareness of loss causes uncertainty and anxiety, which illustrates how organizations are experienced as fundamentally emotional places (Vince, 2006).\n\nFifth theme: Unaccountable financing\n\nFinally, 69.23% of the respondents cited unaccountable financing as a cause of anxiety associated with leadership change. This includes additional expenses that must be incurred personally or the involvement of officials in financing change programs. The following excerpts highlight this theme:\n\n“We have to pay a fee to buy a sarong. It was used for Eid celebration.” (Informant 9)\n\n“This year’s budget has been set, but the new mayor wants his campaign program to run. So what about the budget shortfall? Do we have to spend our own money? Yes.” (Informant 11)\n\nThe informants recounted that the new leaders proposed various new programs posed as innovations, which were outside the usual circumstances. These new initiatives were not planned or budgeted in advance, which is contrary to Indonesia’s planning and budgeting system completed one year ago. This phenomenon has caused the implementation of new programs to lead to unaccountable expenditures outside the officially available budget. The informants and their staff had to spend private money to support the program’s financing. They continued to carry out the program, although they lost money and understood that the activity was wrong in terms of planning regulations. However, they could not blame anyone, including the new leader, due to the high-power distance culture. No clear external actor can be held accountable for an increase in anxiety (Lerner & Keltner, 2000; Wagner, 2014). Politically, an economic crisis causes anxiety if responsibility is spread and difficult to determine (Wagner, 2014).\n\nThe course of anxiety related to leadership change was categorized into three themes: negative affective reactions, cognitive reactions, and behavioral tendencies. The conceptual framework is illustrated in Figure 3, and Table 2 summarizes the findings of critical incidents associated with the course of anxiety (as percentages).\n\nNegative affective reactions are triggered involuntarily by emotions that lead to an individual response due to anxiety. Feeling like an outcast (reported by 69.23%) was identified as the most cited critical incident under this theme, followed by feeling unhappy due to the policy change (53.85%), negative emotions (50%), and feeling humiliated (dehumanized) (23.08%). The following statements highlight this finding:\n\n“I felt like an outcast because I wasn’t involved in making decisions anymore. All decisions come from above (topdown) and the mayor listens more to intruders …” (Informant 3)\n\n“Our innovations to support the change program are unseen. We have worked for decades and have idealism to serve, but we are considered as old colonial people and cannot develop.” (Informant 14)\n\nKantor (1923) defined affective reactions as the actual ways in which people react to affective stimuli in manners that are strikingly comparable to emotional, desire, and pain reactions. Affective reactions elicit emotions that can be differentiated based on the specificity of the original stimulus or target object (Pieters et al., 1988). Kantor (1923) categorized affective stimuli into objects, events, conditions, or actions. Various studies have explained that the most proximal cause of affective reactions is events, as explained in affective events theory, which is widely recognized as the seminal explanation of the function of affection that influences employee attitudes and behaviors in the workplace (Weiss & Beal, 2005). The results of Paterson and Cary’s (2002) study on organizational downsizing events, which are strongly associated with anxiety, support this theory. This study also demonstrates the relationship between events that cause affective reactions by establishing relevant judgments and perceptions of organizational downsizing as precursors to anxiety. Organizational downsizing as a form of change is in line with Weiss and Cropanzano’s (1996) statement that change is a potentially affective event; therefore, it is critical to analyze the emotional aspect. Paterson and Cary’s results (2002) were also supported by our findings by considering leader change as an event that triggers various affective reactions to anxiety.\n\nFurthermore, Efendic (2017) showed that a single affective reaction or a combination of several affective reactions (negative and positive) affects decision-making. Experiments by Weiss et al. (1999) demonstrated positive affective reactions, such as joy, when responding to appropriate variations in procedures and distributive justice, and negative affective reactions, such as anger, that arise from biased procedures and distributive justice. Considering change as an affective event, incremental and radical changes result in positive and negative emotions, respectively (Gersick, 1994). In our study, negative affective reactions predominated because of anxiety caused by leadership change. The study found that negative affective reactions often manifest as sadness, anger, and frustration (Brundin et al., 2021; Luby et al., 2009; Pihkala, 2022). This finding supports Kiefer’s (2002) finding that changes in complexity are more likely to elicit negative emotions. This is also in line with previous findings that the majority of qualitative and quantitative studies on the effects of change in followers’ emotions indicate that the emotions elicited by change are primarily negative, such as anger, anxiety, and impatience (Bartunek, 1984).\n\nThe second theme is that of cognitive reactions that were triggered by the participants’ views about change after experiencing anxiety. Cognitive reactions were manifested as a result of thinking that change is important, but it must be implemented gradually (80.77%); thinking that changes are not as expected (69.23%); thinking that change is good but not with the approach (61.54%); thinking that change is not inclusive (57.69%); thinking that change is only temporary (show off) (46.15%); and thinking that change will not be attainable, as the target is unrealistic (23.08%). This finding is evident from the following statements:\n\n“This government is not magic, changes cannot be implemented directly “sakdet saknyet” (Javanese proverb: desire that must be achieved right away). I think this should be done gradually.” (Informant 3)\n\n“Our government is based on Webberian principles. Many hierarchical structures must be addressed so that radical changes cannot be implemented. The changes brought now seem to only show that the campaign promises have begun to be worked on. But how about in the long term? It has not touched on the main business process, right?” (Informant 17)\n\n“Program A (the abbreviation refers to one of mayor’s programs) is a local program. Must be aligned with regional and national programs. We must not stand alone, we must involve the parties inclusively instead of just listening to the intruder group.” (Informant 22)\n\nCognition is a thought process in which a person first becomes aware of stimuli, evaluates their relevance, and then explores various behavioral responses (Scherer, 1999). Individual beliefs regarding change, whether negative or positive, are referred to as cognitive reactions (Piderit, 2000). Cognitive and affective reactions have a bidirectional relationship in that emotion influences cognition and cognition elicits emotion (Smit and Lazarus, 1990). In the context of change, it elicits cognitive responses (positive, negative, neutral, or mixed), which are mediated by judgments of the fairness, scale, velocity, and timing of change (Smollan, 2006; Smollan et al., 2010). In our study, cognitive reactions were found with mixed evaluation criteria, where the thought of change was positive but was followed by other evaluations such as the use of wrong approach and expectations for gradual change. Piderit (2000) explains this difference regarding ambivalence, both within and among the three dimensions of attitudes toward change, namely emotional, cognitive, and behavioral, as an example of open support. This is followed by covert rejection and thoughts of accepting change, which in turn is followed by emotional resistance. Furthermore, our study found that cognitive reactions to anxiety were dominated by negative evaluations such as non-inclusive, unrealistic, temporary, and unexpected targets. These findings support previous studies on the impact of anxiety on cognitive function, such as causing problems in social and work environments (Robinson et al., 2013). Moreover, Kiefer (2005) explained that employees with strong cognitive reactions are accompanied by strong negative emotions such as fear or anger and are more likely to reject change. However, Piderit (2000) explained that negative cognitive and affective responses are often well-intentioned and lead to an organizational implementation that may be more acceptable and beneficial.\n\nThe last theme is that of behavioral tendencies which refers to a controlled tendency or intention to act owing to the stimulation of anxiety associated with change. Putting on a “yes man” face (reported by 72.08%) was identified as the most cited critical incident under this theme, followed by working as business as usual (61.54%), reducing anxiety (46.15%), ignoring some tasks (23.08%), and the emergence of health issues (19.23%). The following accounts highlight this finding:\n\n“I’ve been working for years. I have felt various changes in the four mayoral times. Well, we work as best we can, he says A we follow A, he says B we follow B.” (Informant 9)\n\n“Bureaucracy will never change, we work systemically. Whatever the vision and mission, the programs and activities still follow the existing nomenclature.” (Informant 1)\n\n“We don’t have to force ourselves, it’s been a few weeks since my stomach acid has recurred. Never mind, I better focus on maintaining my health.” (Informant 14)\n\nBehavioral tendencies toward change are formed because of cognitive and emotional responses that may include both positive and negative features (Piderit, 2000). Furthermore, Smollan (2006) explained that cognitive, affective, and behavioral responses to change are influenced by factors within the individual, change manager, and organization. As mentioned previously, the “yes man” face was the most cited behavioral response. This term describes the behavior of accepting and following change with mostly different emotional and cognitive conditions. These findings support the explanation of the ambivalence of cognitive, affective, and behavioral responses related to change (Piderit, 2000; van Harreveld et al., 2015), which is open support followed by emotional and cognitive resistance. This finding is suspected to be closely related to Indonesia’s high-power distance culture. Behavioral tendencies associated with the “yes man” face are closely related to the phenomenon of unequal rights between power holders and non-power holders, but of course, more in-depth research is required to uncover them.\n\nAnother interesting finding that is influenced by high-power-distance culture is working as business as usual. This is considered a neutral behavioral tendency related to changes. The findings revealed that two middle managers preferred to carry out routines as usual or avoid conflict. The high-power distance and bureaucratic organizational cultures in Indonesia encourage middle managers to choose their behaviors more deeply. This consideration mechanism was expressed by Piderit (2000), who considered the implications of behavioral choices before a behavior was chosen. Additionally, ignorance of some tasks can be considered a form of resistance to leadership change, which is in line with Oreg’s (2006) study. These three forms of behavioral tendencies are behavioral intentions in the form of a tendency to support or reject change (Cunningham et al., 2002; Madsen et al., 2005; Martin et al., 2005).\n\nReducing anxiety and the emergence of health issues are considered as a form of neutral reaction related to change from an organizational viewpoint. Such behavior tends to affect middle managers’ personalities, both mentally and physiologically. This finding supports Wisse and Sleebos’s (2016) finding that change is a major stress factor for employees and is mediated by feelings of uncertainty. Furthermore, organizational change has a short-term effect on mental health decline (Bamberger et al., 2012). These findings also support Greenglass and Burke’s (2000) finding that organizational change is correlated with depression and anxiety and is a crucial point for organizational members to manage.\n\nThe consequences of anxiety associated with leadership change were categorized into three sequential themes: in-circle, out-circle, and ambivalent circle participation. “Circle” relates to Indonesian culture, which denotes people close to power as “inside the circle” and vice versa. The conceptual framework related to this section is illustrated in Figure 4, and Table 3 summarizes the findings of critical incidents under the consequence of anxiety (as a percentage).\n\n“In-circle participation” is a category in favor of the leader change. The critical incident related to this category was polishing old programs to be packaged as if they supported change (57.69%). This was followed by implementing the change programs as business as usual (42.31%), implementing the program changes with high engagement (23.08%), mobilizing apparatus resources to support the program change (23.08%), creating innovations to support the change (19.23%), and collaborating with the press to improve the image of supporting the change (15.38 %). The following statements highlight these findings:\n\n“However, we must support this change, but we must be smart to take advantage of the situation. Not all new programs are innovations. From my various experiences over the years, we have to carry out rebranding programs, old programs in line with the changes brought by the new mayor.” (Informant 6)\n\n“Vision and mission may change, but the program and activities remain the same. Many old programs are good and useful and can still be maintained. Many previous programs are almost similar to new programs that’s why we try to polish this program so that it can support the change.” (Informant 14)\n\n“Out-circle participation” refers to the resistance against the leadership change. The critical incidents associated with this theme were low engagement to support the change (42.31%), more concern with work outside the government (23.08%), not implementing change programs (11.54 %), reviewing the weaknesses of the new government, providing information to political opponents (11.54%), and applying transfer to a functional position (7.69%). The following statements highlight these findings:\n\n“I’ve been lazy to hear the rhetoric of change, let it happen.” (Informant 2)\n\n“We see the new mayor doesn’t think of us as an outcast, I’d better focus on working on my property business.” (Informant 15)\n\n“This year’s budget has been determined. We will not implement these change programs.” (Informant 7)\n\n“Let me work as usual. We’ll see how this new government goes. Forced changes will never move the wheels of the bureaucracy. I’m ready to be the opposition.” (Informant 3)\n\n“This change is extremely stressful. Work is no longer comfortable because it is full of risks. I’ve decided to move to functional.” (Informant 1)\n\n“Ambivalent circle participation” refers to the participation that supports change, but also disguises resistance. The critical incidents associated with this theme were implementing the change program as business as usual followed by low engagement and commitment to supporting change (23.08%), polishing old programs to be packaged as if to support change followed by low engagement and commitment to supporting change (23.08%), polishing old programs to be packaged as if to support change followed by more concern with work outside the government (11.54%), and implementing the change program as business as usual followed by more concern with work outside the government (11.54%). The following statements highlight these findings:\n\n“Let’s just use the old program, we adapt it to support it, but that’s how it is, I’ll just let it go along. We are tired of too much branding.” (Informant 10)\n\n“What do we do, we’ve just run the program as usual. I can still walk while looking for money outside.” (Informant 23)\n\nThe results reveal that 50% of the informants showed support for the leadership change or were categorized as in-circle participants, 23.08% of the informants who indicated resistance were categorized as out-circle participants, and 26.92% of the informants were included in the category of ambivalent circle participation.\n\nBovey and Hede (2001a) found that behaviors in response to change included supportive versus opposing, active versus passive, and covert versus overt behaviors. Based on this, “in-circle participation” tends to be supportive, active, and open. In this study, the consequences of anxiety that support leadership change manifest as explicit behavior through active involvement in change (Cunningham et al., 2002). The most dominant and interesting consequence of this category is the polishing of old programs to be packaged as if to support change. Although it seems tricky, this phenomenon can be considered as the creativity of a middle manager who traditionally describes the key levels of analysis as individual, group, and organizational, with creativity culminating at higher levels as a result of creative output at lower levels (Woodman et al., 1993). Further studies are required to examine the level of creativity as an adaptive process of change. However, Ford (1996) explained that a low level of engagement can also produce creativity, which may not be novel or useful, while high engagement can encourage a person’s ability to produce creative outcomes. Polishing creations can be considered an improvisation of using problem-focused coping strategies and adjusting to change (Amiot et al., 2006) as a self-efficacy to execute the courses of action required to manage prospective situations (Bandura, 1977; van Dam et al., 2008).\n\nWe also found that collaboration with the press to improve the image of middle managers is a marker of supporting change. From the perspective of change, the communication process is vital for realizing effective change as an inherent process of change implementation, including the dissemination of the value of change, training, feedback, and interaction (Lewis & Seibold, 1998). The main goal of communication is to reduce employee uncertainty (Bordia et al., 2004b). In this case, the informant used the communication system not only to disseminate the value of change but also to imagine themselves as an actor who supports change.\n\nThe extreme resistance observed in this study was highlighted by the informants’ decision to switch to a functional position, meaning leaving their position as the head of a local department in the local government (structural position) and moving to a functional position, which is based on function and expertise and is more independent (e.g., Widyaswara or lecturer). This implies that the informant left the organization. The study found that informants who chose this extreme measure felt strong negative emotions, such as the feeling of dehumanization. This finding supports Kiefer’s (2005) study, which claimed that negative emotions indicate an essential organizational judgment and a behavioral tendency to withdraw both in the short- and long-term. Kiefer (2005) claimed that employees who experience strong cognitive reactions and strong negative emotions are more inclined to reject change. This finding also supports Oreg’s (2006) study, which explains that someone who experiences anxiety, anger, and stress due to change has a greater intention to leave the organization.\n\nOther manifestations of extreme resistance besides withdrawal included disloyalty, neglect (Turnley & Feldman, 1999), and sabotage (Spector & Fox, 2002). We found disloyal resistance and neglect in the decision to not implement the program that was concerned with work outside the organization. This study found that middle managers preferred to run organizational programs that have been planned and budgeted in advance. The tight planning and budgeting regulations in Indonesia with information system-based supervision were cited as reasons for not changing program implementation in the current fiscal year, despite the new leader initiating a change program. We also found disloyalty and neglect associated with working outside public organizations, such as being a consultant or running a business. Finally, resistance in the form of sabotage manifested in the form of finding new government mistakes and providing this information to political opponents. Furthermore, Gaubatz and Ensminger (2017) stated that resisting change can be a “contention” that continues to disrupt and frustrate change efforts.\n\nThese four forms of out-circle participation can be categorized as forms of irrational resistance, which refers to the term used by de Jager (2001) as resistance to change for its own sake. Rational resistance is referred to as low involvement in implementing changes or being passive (de Jager, 2001). In this study, we found low involvement in the form of loss of focus, low involvement in task coordination, decreased productivity, and decreased enthusiasm for supporting change. Here, “engagement” refers to a positive, fulfilling, work-related state of mind that is characterized by vitality, dedication, and immersion (Schaufeli & Bakker, 2004) and is categorized as job satisfaction, job involvement, organizational commitment, and empowerment (Macey & Schneider, 2008). Low engagement in the short- and long-term will cause leadership changes to fail, considering that various previous studies have explained that the main determinant of successful change requires employee involvement (Gopinath & Becker, 2000; Rafferty et al., 2013; Rafferty & Restubog, 2010). Furthermore, Neubert and Cady (2001) considered employee engagement in change programs and investigated its association with crucial organizational outcomes (Bordia et al., 2004b).\n\nFinally, ambivalent circle participation was also a form of consequence. This circle denotes behavior that supports change but with covert resistance. This theme signifies ambivalence within and among the three dimensions of attitudes to change, namely emotional, cognitive, and behavioral, as an example of open support followed by covert rejection (Piderit, 2000). Previous studies have shown that an ambivalent approach affects physical behavior (Schneider et al., 2015). van Harreveld et al. (2015) described the consequences of ambivalence on influence, cognition, and behavior, and how these different categories relate to each other and to their source, where affection plays the most central role.\n\n\nConclusions\n\nOur study contributes to the systematic formulation of an integrated model of the causes, courses, and consequences of anxiety associated with leadership change (Figure 5). This study identifies critical incidents that explain the phenomenon of anxiety, which has rarely been investigated in relation to leadership change, especially in public organizations.\n\nFirst, our study extends extant literature on the important role of leader-follower relationships in creating successful change (Colville & Murphy, 2006; Gopinath & Becker, 2000; Higgs & Rowland, 2001; Holt & Vardaman, 2013; Kotter & Cohen, 2002; Rafferty et al., 2013; Rafferty & Restubog, 2010). Scholars have extensively researched the relationship between leadership and change and leadership change. However, this study deepens our understanding and comprehensively describes the concept of anxiety associated with leadership change. The crucial factor that increases the difficulty of research is sensitivity related to political power and organizational culture, especially in the context of Indonesia’s high-power distance culture. Thus, the organizational culture in Indonesian bureaucracy is closely related to the hierarchy that creates inequality between power and non-power holders (Hofstede Insights, 2022). Leaders display hegemony with boundaries that are difficult to access, are more directive, and try to strengthen control within the organization.\n\nSecond, this research provides empirical evidence for Lewin’s (1947) Three-Phase Process, wherein difficulties, such as discomfort, imbalance, and anxiety, are experienced in the early stages of change. Our findings also support those of Gilmore and Ronchi (1995): leadership transitions are plagued with anxiety. The consequences of this finding reinforce the concept of successful change management, not only from a technical point of view, but also from the human dimension (Beer et al., 1990; Huston, 1992).\n\nThird, the integrated model of anxiety associated with leadership change is expected to enrich understanding of social anxiety in social evaluation theory and integrated modern emotion science. The findings of this study support social evaluation theory in that they put fear of negative evaluation as the key component that causes anxiety (Button et al., 2015; Heimberg et al., 2010; Manstead & Semin, 1981). Integrated modern emotion science is enriched through a functional account of the emotion approach. Cognitive and affective reactions have a two-way relationship in which emotion influences cognition and cognition elicits emotion (Smit & Lazarus, 1990; Smollan, 2006). Furthermore, ambivalence exists within and among the three dimensions of attitudes toward change, namely emotional, cognitive, and behavioral (Piderit, 2000; van Harreveld et al., 2015). We also found open support followed by covert rejection and thoughts of accepting change followed by emotional resistance (negative affection). Finally, our study advances the application of critical incident techniques in the context of leader change, especially in public organizations, which has previously been explored in service marketing research (Grace, 2007; Gremler, 2004).\n\nPractically, this study makes a valuable contribution for practitioners in managing the anxiety that arises in response to leadership change. First, understanding the causes, course, and consequences of anxiety in the context of leadership change allows practitioners to choose a management strategy that places humans on an equal dimension in the change process. Understanding the human dimension is important because the key component of successful organizational change is the involvement of human resources, leaders, and followers (Gopinath & Becker, 2000; Holt & Vardaman, 2013; Kotter & Cohen, 2002; Rafferty et al., 2013; Rafferty & Restubog, 2010). Second, an understanding of anxiety induced by leadership change, especially in public organizations, can be a key consideration in bureaucratic talent management policies. This knowledge can be used by the government or regulator to develop a blueprint for the apparatus of public organizations in a meritocratic manner. This consideration is crucial in the face of Indonesia’s high-power distance characteristics, which directly affect the culture of public organizations. Thus, understanding the key role of human resources in change is expected to induce major improvements for the government in strengthening the professionalism of public organizations.\n\nHowever, this study has several limitations. First, leadership change in public organizations is a sensitive issue that makes bureaucrats (public organization officers) averse to discussing it, especially in Indonesia. This limitation needs to be investigated further in different contexts, such as developed countries with high-power distance cultures and types of informants that include members of the organization, considering that all informants in our study are middle managers. Second, future studies can develop empirical frameworks, such as compiling measurement items for anxiety related to change; examining the relationship between causes, course, and consequences of anxiety; and formulating a prescriptive strategy to reduce anxiety associated with leadership change.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Exploratory study of critical incidents within public organization leadership change’, https://doi.org/10.6084/m9.figshare.25282879.v1 (Suwanda, et al., 2024).\n\nThis project contains the following underlying data;\n\n(1) Interview guidelines and written consent;\n\n(2) Recapitulation of Interview Transcripts; and\n\n(3) Coding of interview results.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbdai J, Miklósi Á: The origin of social evaluation, social eavesdropping, reputation formation, image scoring or what you will. Front. Psychol. Frontiers Media S.A; 2016; 7(NOV). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmerican Psychiatric Association: Diagnostic and Statistical Manual of Mental Disorders Fifth Edition DSM-5 TM. 5th ed.American Psychiatric Association; 2013. Publisher Full Text\n\nAmiot CE, Terry DJ, Jimmieson NL, et al.: A longitudinal investigation of coping processes during a merger: Implications for job satisfaction and organizational identification. J. Manag. 2006; 32(4): 552–574. Publisher Full Text\n\nAmis J, Slack T, Hinings CR: The Pace, Sequence, and Linearity of Radical Change. Acad. Manag. J. 2004; 47(1): 15–39. Publisher Full Text\n\nArmenakis AA, Harris SG, Feild HS: Making change permanent A model for institutionalizing change interventions. Res. Organ. Chang. Dev. 1999; 12: 97–128. Publisher Full Text\n\nBailey JR, Raelin JD: Organizations Don’t Resist Change, People Do: Modeling Individual Reactions to Organizational Change Through Loss and Terror Management. Organ. Manag. J. 2015; 12(3): 125–138. Publisher Full Text\n\nBamberger SG, Vinding AL, Larsen A, et al.: Impact of organisational change on mental health: A systematic review. Occup. Environ. Med. 2012; 69(8): 592–598. Publisher Full Text\n\nBandura A: Self-efficacy: Toward a Unifying Theory of Behavioral Change. Psychol. Rev. 1977; 84(2): 191–215. PubMed Abstract \| Publisher Full Text\n\nBarlow DH: Anxiety and Its Disorders The Nature and Treatment of Anxiety and Panic. 2nd Edition.Barlow DH, editor. The Guilford Press; 2002.\n\nBartunek JM: Changing Interpretive Schemes and Organizational Restructuring: The Example of a Religious. Adm. Sci. Q. 1984; 29(3): 355. Publisher Full Text\n\nBass BM: Leadership and performance beyond expectations. Free Press; Collier Macmillan; 1985.\n\nBass BM: Does the Transactional-Transformational Leadership Paradigm Transcend Organizational and National Boundaries? Am. Psychol. 1997; 52(2): 130–139. Publisher Full Text\n\nBass BM, Riggio RE: Transformational leadership. 2nd ed.Lawrence Erlbaum Associates, Inc.; 2006. Publisher Full Text\n\nBastien D: Common Patterns of Behavior and Communication in Corporate. Hum. Resour. Manag. 1987; 26(1): 17–33. Publisher Full Text\n\nBeer M, Eisenstat RA, Spector B: Why Change Programs Don’t Produce Change. Harv. Bus. Rev. 1990; 6(68): 158–166.\n\nBeer M, Nohria N: Cracking the Code of Change. Harv. Bus. Rev. 2001, May; 78(3): 133–141. Reference Source\n\nBekhet AK, Zauszniewski JA: Methodological triangulation: an approach to understanding data. Nurse Res. 2012; 20(2): 40–43. Publisher Full Text\n\nBitner MJ, Booms BH, Tetreault MS: The Service Encounter: Diagnosing Favorable and Unfavorable Incidents. J. Mark. 1990; 54(1): 71–84. Publisher Full Text\n\nBono JE, Foldes HJ, Vinson G, et al.: Workplace Emotions: The Role of Supervision and Leadership. J. Appl. Psychol. 2007; 92(5): 1357–1367. Publisher Full Text\n\nBordia P, Hobman E, Jones E, et al.: Uncertainty During Organizational Change: Types, Consequences, and Management Strategies. J. Bus. Psychol. 2004a; 18(4): 507–532. Publisher Full Text\n\nBordia P, Hunt E, Paulsen N, et al.: Uncertainty during organizational change: Is it all about control? Eur. J. Work Organ. Psy. 2004b; 13(3): 345–365. Publisher Full Text\n\nBovey WH, Hede A: Resistance to organisational change: The role of defence mechanisms. J. Manag. Psychol. 2001a; 16(7): 534–548. Publisher Full Text\n\nBovey WH, Hede A: Resistance to organizational change: The role of cognitive and affective processes. Leadersh. Org. Dev. J. 2001b; 22(8): 372–382. Publisher Full Text\n\nBrundin E, Liu F, Cyron T: Emotion in strategic management: A review and future research agenda. Long Range Plan. 2021; 55: 102144. Publisher Full Text\n\nBuchanan DA: You stab my back, I’ll stab yours: Management experience and perceptions of organization political behaviour. Br. J. Manag. 2008; 19(1): 49–64. Publisher Full Text\n\nBurnes B: The Origins of Lewin’s Three-Step Model of Change. J. Appl. Behav. Sci. 2020; 56(1): 32–59. Publisher Full Text\n\nBurnes B, Cooke B: Kurt Lewin’s Field Theory: A Review and Re-evaluation. Int. J. Manag. Rev. 2013; 15(4):408–425. Publisher Full Text\n\nButton KS, Kounali D, Stapinski L, et al.: Fear of negative evaluation biases social evaluation inference: Evidence from a probabilistic learning task. PLoS One. 2015; 10(4): e0119456. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCalciolari S, Prenestini A, Lega F: An organizational culture for all seasons? How cultural type dominance and strength influence different performance goals. Public Manag. Rev. 2018; 20(9): 1400–1422. Publisher Full Text\n\nCampos JJ, Mumme DL, Kermoian R: A Functionalist Perspective on the Nature of Emotion. Monogr. Soc. Res. Child Dev. 1994; 59(2/3): 284–303. Publisher Full Text\n\nCanning J, Found PA: The effect of resistance in organizational change programmes: A study of a lean transformation. Int. J. Qual. Serv. Sci. 2015; 7(2–3): 274–295. Publisher Full Text\n\nChreim S: Postscript to change: Survivors’ retrospective views of organizational changes. Pers. Rev. 2006; 35(3): 315–335. Publisher Full Text\n\nCoghlan D: A Person-centred Approach to Dealing with Resistance to Change. Leadersh. Org. Dev. J. 1993; 14(4): 10–14. Publisher Full Text\n\nColville ID, Murphy AJ: Leadership as the Enabler of Strategizing and Organizing. Long Range Plan. 2006; 39(6): 663–677. Publisher Full Text\n\nCummings TG, Worley CG: Organization development & change. 9th Edition.Cummings TG, Worley CG, editors. South-Western/Cengage Learning; 2009.\n\nCunningham CE, Woodward CA, Shannon HS, et al.: Readiness for organizational change: A longitudinal study of workplace, psychological and behavioural correlates. J. Occup. Organ. Psychol. 2002; 75(4): 377–392. Publisher Full Text\n\nde Jager P : Resistance to change: A new view of an old problem. The Futurist. 2001, May; 35(3): 24–24. Reference Source\n\nDenison DR, Mishra AK: Toward a Theory of Organizational Culture and Effectiveness. Organ. Sci. 1995; 6(2): 204–223. Publisher Full Text\n\nDiFonzo N, Bordia P: A tale of two corporations: Managing uncertainty during organizational change. Hum. Resour. Manag. 1998; 37(3–4): 295–303. Publisher Full Text\n\nDipoppa G, Grossman G: The Effect of Election Proximity on Government Responsiveness and Citizens’ Participation: Evidence From English Local Elections. Comp. Pol. Stud. 2020; 53(14): 2183–2212. Publisher Full Text\n\nDubois CA, Bentein K, ben Mansour J, et al.: Why some employees adopt or resist reorganization of work practices in health care: Associations between perceived loss of resources, burnout, and attitudes to change. Int. J. Environ. Res. Public Health. 2013; 11(1): 187–201. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEby LT, Adams DM, Russell JEA, et al.: Perceptions of organizational readiness for change: Factors related to employees’ reactions to the implementation of team-based selling. Hum. Relat. 2000; 53(3): 419–442. Publisher Full Text\n\nEdvardsson B: Service Breakdowns: A Study of Critical Incidents in an Airline. Int. J. Serv. Ind. Manag. 1992; 3(4): 17–29. Publisher Full Text\n\nEdvardsson B, Roos I: Critical incident techniques: Towards a framework for analysing the criticality of critical incidents. Int. J. Serv. Ind. Manag. 2001; 12(3): 251–268. Publisher Full Text\n\nEfendic E: The Impact of Multiple Affective Reactions on Decision Making: Combination of Affect and the Mediating Mechanisms of Affective Influence.2017. Reference Source\n\nErwin DG, Garman AN: Resistance to organizational change: Linking research and practice. Leadersh. Org. Dev. J. 2010; 31(1): 39–56. Publisher Full Text\n\nFischer F, Miller GJ, Sidney MS: Handbook of Public Policy Analysis: Theory, Politics, and Methods. Fischer F, Miller G, Sidney MS, editors. CRC Press Taylor & Francis Group; 2007.\n\nFlanagan JC: The Critical Incident Technique. Psychol. Bull. 1954; 51(4): 327–358. Publisher Full Text\n\nFord CM: A Theory of Individual Creative Action in Multiple Social Domains. Acad. Manag. Rev. 1996; 21(4): 1112–1142. Publisher Full Text\n\nFusch P, Fusch GE, Ness LR: Denzin’s Paradigm Shift: Revisiting Triangulation in Qualitative Research. J. Soc. Change. 2018; 10(1). Publisher Full Text\n\nGaubatz JA, Ensminger DC: Department chairs as change agents: Leading change in resistant environments. Educ. Manag. Adm. Leadersh. 2017; 45(1): 141–163. Publisher Full Text\n\nGersick CJG: Pacing Strategic Change: The Case of a New Venture. Acad. Manag. J. 1994; 37(1): 9–45. Publisher Full Text\n\nGigliotti R, Vardaman J, Marshall DR, et al.: The Role of Perceived Organizational Support in Individual Change Readiness. J. Chang. Manag. 2019; 19(2): 86–100. Publisher Full Text\n\nGilley A, Dixon P, Gilley JW: Characteristics of leadership effectiveness: Implementing change and driving innovation in organizations. Hum. Resour. Dev. Q. 2008; 19(2): 153–169. Publisher Full Text\n\nGilmore TN, Ronchi D: Managing Predecessors’ Shadows in Executive Transitions. Hum. Resour. Manag. 1995; 34(1): 11–26. Publisher Full Text\n\nGopinath C, Becker TE: Communication, procedural justice, and employee attitudes: Relationships under conditions of divestiture. J. Manag. 2000; 26(1): 63–83. Publisher Full Text\n\nGrace D: How embarrassing!: An exploratory study of critical incidents including affective reactions. J. Serv. Res. 2007; 9(3): 271–284. Publisher Full Text\n\nGreenglass ER, Burke RJ: Hospital downsizing, individual resources, and occupational stressors in nurses. Anxiety Stress Coping. 2000; 13(4): 371–390. Publisher Full Text\n\nGremler DD: The Critical Incident Technique in Service Research. J. Serv. Res. 2004; 7(1): 65–89. Publisher Full Text\n\nGrizzle GA, Pettijohn CD: Implementing Performance-Based Program Budgeting 51 Implementing Performance-Based Program Budgeting: A System-Dynamics Perspective. Public Adm. Rev. 2002; 62(1): 51–62. Publisher Full Text\n\nGrove SJ, Fisk RP: The Impact of Other Customers on Service Experiences: A Critical Incident Examination of “Getting Along.”. J. Retail. 1997; 73(1): 63–85. Publisher Full Text\n\nGu Y, Gu S, Lei Y, et al.: From uncertainty to anxiety: How uncertainty fuels anxiety in a process mediated by intolerance of uncertainty. Neural Plast. 2020; 2020; 1–8. Hindawi Limited. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHartmann A: The role of organizational culture in motivating innovative behaviour in construction firms. Constr. Innov. 2006; 6(3): 159–172. Publisher Full Text\n\nHeimberg RG, Brozovich FA, Rapee RM: A Cognitive Behavioral Model of Social Anxiety Disorder: Update and Extension. Social Anxiety. Elsevier Inc.; 2010; pp. 395–422. Publisher Full Text\n\nHiggs M, Rowland D: Developing change leaders: Assessing the impact of a development programme. J. Chang. Manag. 2001; 2(1): 47–64. Publisher Full Text\n\nHiggs M, Rowland D: All changes great and small: Exploring approaches to change and its leadership. J. Chang. Manag. 2005; 5(2): 121–151. Publisher Full Text\n\nhofstede-insights.com: Country Comparison - Organisational Culture.2022. Reference Source\n\nHolt DT, Vardaman JM: Toward a Comprehensive Understanding of Readiness for Change: The Case for an Expanded Conceptualization. J. Chang. Manag. 2013; 13(1): 9–18. Publisher Full Text\n\nHughes M: Do 70 Per Cent of All Organizational Change Initiatives Really Fail? J. Chang. Manag. 2011; 11(4): 451–464. Publisher Full Text\n\nHuntington SP: The Clash of Civilizations? Foreign Aff. 1993; 72(3): 22–49. Publisher Full Text\n\nHussain ST, Lei S, Akram T, et al.: Kurt Lewin’s change model: A critical review of the role of leadership and employee involvement in organizational change. J. Innov. Knowl. 2018; 3(3): 123–127. Publisher Full Text\n\nHuston LA: Using total quality to put strategic intent into motion. Plan. Rev. 1992; 20(5): 21–23. Publisher Full Text\n\nHuther J, Shah A: Applying a Simple Measure of Good Governance to the Debate on Fiscal Decentralization.1998. Publisher Full Text\n\nIzard CE: Human Emotions. Izard CE, Singer JL, editors. Plenum Publishing Corporation; 1977. Publisher Full Text\n\nJafariani H, Mortazavi S, Nazemi S, et al.: Political behavior in organizational context: nature, research and paradigm. Manag. Sci. Lett. 2012; 2(8): 2987–3000. Publisher Full Text\n\nKantor JR: The Psychology of Feeling or Affective Reactions. Am. J. Psychol. 1923; 34(3): 433–463. Publisher Full Text Reference Source\n\nKeltner D, Gross JJ: Functional accounts of emotions. Cognit. Emot. 1999; 13(5): 467–480. Publisher Full Text\n\nKiefer T: Understanding the Emotional Experience of Organizational Change: Evidence from a Merger. Adv. Dev. Hum. Resour. 2002; 4(1): 39–61. Publisher Full Text\n\nKiefer T: Feeling bad: Antecedents and consequences of negative emotions in ongoing change. J. Organ. Behav. 2005; 26(8): 875–897. Publisher Full Text\n\nKotter JP, Cohen DS: The heart of change: real-life stories of how people change their organizations. Harvard Business School Press; 2002.\n\nLadd JM, Lenz GS: Reassessing the Role of Anxiety in Vote Choice. Polit. Psychol. 2008; 29(2): 275–296. Publisher Full Text Reference Source\n\nLang PJ, McTeague LM: The anxiety disorder spectrum: Fear imagery, physiological reactivity, and differential diagnosis. Anxiety Stress Coping. 2009; 22(1): 5–25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLerner JS, Keltner D: Beyond valence: Toward a model of emotion-specific influences on judgement and choice. Cognit. Emot. 2000; 14(4): 473–493. Publisher Full Text\n\nLewin K: Frontiers in Group Dynamics. Hum. Relat. 1947; 1(1): 1–5. Publisher Full Text\n\nLewin K: Group decision and social change.Macoby EE, Newcomb TM, Hartley EL, editors. Readings in Social Psychology. Winston: Holt, Rinehart; Third Edition1958; pp. 197–211.\n\nLewis LK, Seibold DR: Reconceptualizing Organizational Change Implementation as a Communication Problem: A Review of Literature and Research Agenda. Ann. Int. Commun. Assoc. 1998; 21(1):93–152. Publisher Full Text\n\nLuby JL, Essex MJ, Armstrong JM, et al.: Gender differences in emotional reactivity of depressed and at-risk preschoolers: Implications for gender specific manifestations of preschool depression. J. Clin. Child Adolesc. Psychol. 2009; 38(4): 525–537. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMacey WH, Schneider B: The Meaning of Employee Engagement. Ind. Organ. Psychol. 2008; 1(1): 3–30. Publisher Full Text\n\nMadsen SR, Miller D, John CR: Readiness for Organizational Change: Do Organizational Commitment and Social Relationships in the Workplace Make a Difference? Hum. Resour. Dev. Q. 2005; 16(2): 213–234. Publisher Full Text\n\nMalodia S, Dhir A, Mishra M, et al.: Future of e-Government: An integrated conceptual framework. Technol. Forecast. Soc. Chang. 2021; 173: 121102. Publisher Full Text\n\nManstead ASR, Semin GR: Social Transgressions, Social Perspectives, and Social Emotionality. Motiv. Emot. 1981; 5(3): 249–261. Publisher Full Text\n\nMartin AJ, Jones ES, Callan VJ: The role of psychological climate in facilitating employee adjustment during organizational change. Eur. J. Work Organ. Psy. 2005; 14(3): 263–289. Publisher Full Text\n\nMcFarlane DR: Statutory Coherence and Policy Implementation: The Case of Family Planning. J. Publ. Policy. 1995; 15(3): 281–298. PubMed Abstract \| Publisher Full Text\n\nMeyer AD, Goes J, Brooks GR: Organizations Reacting to Hyperturbulence. Huber G, Glick W, editors. Oxford University Press; 1993; pp. 66–111. Publisher Full Text\n\nMiles MB, Huberman AM: Qualitative data analysis: A sourcebook of new methods. Holland R, editor. 2nd ed.SAGE Publication Inc; 1994.\n\nMiles RH: Beyond the Age of Dilbert: Accelerating Corporate Transformations by Rapidly Engaging All Employees. Organ. Dyn. 2001; 29(4): 313–321. Publisher Full Text\n\nMilliken FJ: Three Types of Perceived Uncertainty About the Environment: State, Effect, and Response Uncertainty. Acad. Manag. Rev. 1987; 12(1): 133–143. Publisher Full Text\n\nMintzberg H: Patterns in Strategy Formation. Manag. Sci. 1978; 24(9): 934–948. Publisher Full Text\n\nMishra J, Attri V: Governance, Public Service Delivery and Trust in Government. Stud. Indian Politics. 2020; 8(2): 186–202. Publisher Full Text\n\nMsweli-Mbanga P, Potwana N: Modelling participation, resistance to change, and organisational citizenship behaviour: A South African case. S. Afr. J. Bus. Manag. 2006; 37(1): 21–29. Publisher Full Text\n\nNadia FND, Sukoco BM, Susanto E, et al.: Discomfort and organizational change as a part of becoming a world-class university. Int. J. Educ. Manag. 2020; 34(8): 1265–1287. Publisher Full Text\n\nNeubert MJ, Cady SH: Program Commitment: A Multi-Study Longitudinal Field Investigation Of Its Impact And Antecedents. Pers. Psychol. 2001; 54(2): 421–448. Publisher Full Text\n\nOreg S: Personality, context, and resistance to organizational change. Eur. J. Work Organ. Psy. 2006; 15(1): 73–101. Publisher Full Text\n\nOrosz JF: The Language of State Agency Executive Transitions. Am. Rev. Public Adm. 1994; 24(1): 43–66. Publisher Full Text\n\nPaterson JM, Cary J: Organizational Justice, Change Anxiety, and Acceptance of Downsizing: Preliminary Tests of an AET-Based Model. Motiv. Emot. 2002; 26(1). Publisher Full Text\n\nPatton MQ: Qualitative Research and Evaluation Methods. 3rd Edition.Laughton CD, Novak V, Axelsen DE, et al., editors. Sage Publications; 2002.\n\nPetracca MP: The Rational Choice Approach to Polities: A Challenge to Democratic Theory. Rev. Politics. 1991; 53(2): 289–319. Publisher Full Text Reference Source\n\nPettigrew A, Ferlie E, McKee L: Shaping strategic change-the case of the nhs in the 1980s. Public Money Manag. 1992; 12(3): 27–31. Publisher Full Text\n\nPiderit SK: Rethinking Resistance and Recognizing Ambivalence: A Multidimensional View of Attitudes Toward an Organizational Change. Acad. Manage. Rev. 2000; 25(4): 783–794. Publisher Full Text\n\nPierson P: Increasing Returns, Path Dependence, and the Study of Politics. Am. Polit. Sci. Rev. 2000; 94(2): 251–267. Publisher Full Text\n\nPieters RGM, Fred W, Raaij V: Functions and management of affect: Applications to economic behavior. J. Econ. Psychol. 1988; 9(2): 251–282. Publisher Full Text\n\nPihkala P: Toward a Taxonomy of Climate Emotions. Front. Clim. 2022; 3. Publisher Full Text\n\nProchaska JM, Prochaska JO, Levesque DA: A TRANSTHEORETICAL APPROACH TO CHANGING ORGANIZATIONS. Admin. Pol. Ment. Health. 2001; 28(4): 247–261. Publisher Full Text\n\nRafferty AE, Griffin MA: Perceptions of organizational change: A stress and coping perspective. J. Appl. Psychol. 2006; 91(5): 1154–1162. PubMed Abstract \| Publisher Full Text\n\nRafferty AE, Jimmieson NL, Armenakis AA: Change Readiness: A Multilevel Review. In. J. Manag. 2013; 39(1): 110–135. Publisher Full Text\n\nRafferty AE, Restubog SLD: The impact of change process and context on change reactions and turnover during a merger. J. Manag. 2010; 36(5): 1309–1338. Publisher Full Text\n\nReger RK, Mullane J v, Gustafson LT, et al.: Creating Earthquakes to Change Organizational Mindsets [and Executive Commentary]. Acad. Manage. Exec. (1993-2005). 1994; 8(4): 31–43. Publisher Full Text Reference SourceReference SourceReference Source\n\nReich MR: The politics of health sector reform in developing countries: three cases of pharmaceutical policy. Health Policy. 1995; 32(1): 47–77. PubMed Abstract \| Publisher Full Text\n\nRibeiro LCM, Munari DB, Souza ACSE, et al.: Planned organizational change to transform care to workers exposed to biological material. Rev. Bras. Enferm. 2020; 73(5): e20190314. PubMed Abstract \| Publisher Full Text\n\nRider CI, Negro G: Organizational failure and intraprofessional status loss. Organ. Sci. 2015; 26(3): 633–649. Publisher Full Text\n\nRobbins SP, Judge TA: Organizational Behavior Fifteenth Edition. 15th Edition.Yagan S, editor. Pearson Education, Inc; 2013.\n\nRobinson OJ, Vytal K, Cornwell BR, et al.: The impact of anxiety upon cognition: perspectives from human threat of shock studies. Front. Hum. Neurosci. 2013; 7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRodon T: The Spanish electoral cycle of 2019: a tale of two countries. West Eur. Polit. 2020; 43(7): 1490–1512. Publisher Full Text\n\nRomanelli E, Tushman ML: Organizational Transformation as Punctuated Equilibrium: An Empirical Test. Acad. Manag. J. 1994; 37(5): 1141–1166. Publisher Full Text\n\nRosenfeld LB, Richman JM, May SK: Information Adequacy, Job Satisfaction and Organizational Culture in a Dispersed-Network Organization. J. Appl. Commun. Res. 2004; 32(1): 28–54. Publisher Full Text\n\nSahay S: Communicative designs for input solicitation during organizational change.2017. Publisher Full Text\n\nSchaufeli WB, Bakker AB: Job demands, job resources, and their relationship with burnout and engagement: A multi-sample study. J. Organ. Behav. 2004; 25(3): 293–315. Publisher Full Text\n\nSchein EH: Organizational Culture and Leadership. 3rd ed.Jossey-Bass A Wiley Imprint; 2004.\n\nScherer KR: Appraisal Theory.Dalgleish T, Power MJ, editors. Handbook of Cognition and Emotion. John Wiley & Sons, Ltd.; 1999; pp. 637–663. Publisher Full Text\n\nSchneider IK, van Harreveld F , Rotteveel M, et al.: The path of ambivalence: tracing the pull of opposing evaluations using mouse trajectories. Front. Psychol. 2015; 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchumpeter JA: Capitalism, Socialism and Democracy. Routledge; 1976. Publisher Full Text\n\nSheffield J, Coleshill P: Developing best value in a Scottish local authority. Meas. Bus. Excell. 2001; 5(2): 31–38. Publisher Full Text\n\nShin J, Taylor MS, Seo MG: Resources for Change: The relationships of organizational inducements and psychological resilience to employees’ attitudes and behaviors toward organizational change. Acad. Manag. J. 2012; 55(3): 727–748. Publisher Full Text\n\nShvindina H: Leadership as a driver for organizational change. Business Ethics and Leadership. 2017; 1: 74–82. Publisher Full Text\n\nSmit CA, Lazarus RS: Emotion and Adaptation. Handbook of personality: Theory and research. Pervin LA, editor. The Guilford Press; 1990; Vol. 21(4): pp. 609–631. Publisher Full Text\n\nSmith BC: Decentralization: the Teritorial Dimension of the State. Nurdin N, Sartika I, editors. Masyarakat Ilmu Pemerintahan Indonesia; 2012.\n\nSmollan RK: Minds, hearts and deeds: Cognitive, affective and behavioural responses to change. J. Chang. Manag. 2006; 6(2): 143–158. Publisher Full Text\n\nSmollan RK, Sayers JG, Matheny JA: Emotional Responses to the Speed, Frequency and Timing of Organizational Change. Time Soc. 2010; 19(1): 28–53. Publisher Full Text\n\nSpector PE, Fox S: An emotion-centered model of voluntary work behavior Some parallels between counterproductive work behavior and organizational citizenship behavior. Hum. Resour. Manag. Rev. 2002; 12(2): 269–292. Publisher Full Text Reference Source\n\nStavros C, Westberg K: Using triangulation and multiple case studies to advance relationship marketing theory. Qualitative Market Research. 2009; 12(3): 307–320. Publisher Full Text\n\nSuhariadi F: Organizational Culture Change Effectiveness. Conference Paper. 2013. Reference Source\n\nSuwanda RP, Suhariadi F, Suyanto B, et al.: Underlying data for “Exploratory study of critical incidents within public organization leadership change”. [Dataset]. figshare. 2024. Publisher Full Text\n\nTiedens LZ, Linton S: Judgment under emotional certainty and uncertainty: The effects of specific emotions on information processing. J. Pers. Soc. Psychol. 2001; 81(6): 973–988. PubMed Abstract \| Publisher Full Text\n\nTodd AR, Forstmann M, Burgmer P, et al.: Supplemental Material for Anxious and Egocentric: How Specific Emotions Influence Perspective Taking. J. Exp. Psychol. Gen. 2015; 144(2): 374–391. Publisher Full Text\n\nTurnley WH, Feldman DC: The Impact of Psychological Contract Violations on Exit, Voice, Loyalty, and Neglect. Hum. Relat. 1999; 52(7): 895–922. Publisher Full Text\n\nTushman ML, Romanelli E: Organizational evolution: A metamorphosis model of convergence and reorientation. Res. Organ. Behav. 1985; 7: 171–222. Reference Source\n\nvan Dam K , Oreg S, Schyns B: Daily work contexts and resistance to organisational change: The role of leader-member exchange, development climate, and change process characteristics. Appl. Psychol. 2008; 57(2): 313–334. Publisher Full Text\n\nvan de Ven AH : Explaining Development and Change in Organizations. Acad. OI Manage. Rev. 1995; 20(3): 510–540. Publisher Full Text\n\nvan Harreveld F , Nohlen HU, Schneider IK: The ABC of Ambivalence: Affective, Behavioral, and Cognitive Consequences of Attitudinal Conflict. Adv. Exp. Soc. Psychol. 2015; 52: 285–324. Publisher Full Text\n\nVince R: Being Taken Over: Managers’ Emotions and Rationalizations During a Company Takeover. J. Manag. Stud. 2006; 43(2): 343–365. Publisher Full Text\n\nWagner M: Fear and Anger in Great Britain: Blame Assignment and Emotional Reactions to the Financial Crisis. Polit. Behav. 2014; 36(3): 683–703. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWeick KE, Quinn RE: Organizational Change and Development. Annu. Rev. Psychol. 1999; 50: 361–386. Publisher Full Text\n\nWeiss HM, Beal DJ: Reflections on Affective Events Theory.Ashkanasy NM, Zerbe WJ, Härtel CEJ, editors. The Effect of Affect in Organizational Settings (Research on Emotion in Organizations). Emerald Group Publishing Limited; 2005; Vol. 1. : pp. 1–21. Publisher Full Text\n\nWeiss HM, Cropanzano R: Affective Events Theory: A theoretical discussion of the structure, causes and consequences of affective experiences at work.Staw BM, Cummings LL, editors. Research in organizational behavior: An annual series of analytical essays and critical reviews. Elsevier Science/JAI Press; 1996; Vol. 18. : pp. 1–74.\n\nWeiss HM, Suckow K, Cropanzano R: Effects of justice conditions on discrete emotions. J. Appl. Psychol. 1999; 84(5): 786–794. Publisher Full Text\n\nWisse B, Sleebos E: When Change Causes Stress: Effects of Self-construal and Change Consequences. J. Bus. Psychol. 2016; 31(2): 249–264. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWoodman RW, Sawyer JE, Griffin RW: Toward a Theory of Organizational Creativity. Acad. Manag. Rev. 1993; 18(2): 293–321. Publisher Full Text\n\nWulandari RD, Supriyanto S, Qomaruddin MB, et al.: Role of leaders in building organizational readiness to change - Case study at public health centers in Indonesia. Probl. Perspect. Manag. 2020; 18(3): 1–10. Publisher Full Text" }	[ { "id": "282574", "date": "05 Sep 2024", "name": "Siti Kholifah", "expertise": [ "Reviewer Expertise My research areas in sociology of politic", "sociology of religion and gender studies" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI have some comments regarding this article: 1. The study uses some theories to frame the findings. However, the integration of these theories into the analysis could be more explicit. For instance, when discussing the cognitive and affective reactions, it would be helpful to directly tie these reactions back to specific theoretical concepts, illustrating how the data supports or challenges existing models. This is important to strengthen the theoretical contribution of the research. 2. This study provides a broad categorization of the causes, course and consequences of anxiety to the leadership change. The categorization is useful, but there is aneed for deeper analysis. For instance, the findings on political choices as a source of anxiety could benefit from further explanation of how different political alignments specifically influence anxiety levels and behaviour among department heads, also can provide an example. 3. The study explains valuable insights into the anxiety experienced by public organization leaders during leadership changes. However, the practical implication of these findings could be expanded. Consider providing more concrete recommendations for policymakers on how to address and manage the anxieties identified. This could include suggestions for leadership training, communication strategies, or organizational policies that could help mitigate the negative effect of anxiety and improve the overall success of leadership transitions in high-power distance cultures like Indonesia.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-357
https://f1000research.com/articles/13-354/v1	23 Apr 24	{ "type": "Study Protocol", "title": "A prospective randomized comparative study of effectiveness of simulation-based training in improving the performance of non-technical skill among postgraduate students during anaesthesia crisis resource management", "authors": [ "Karuna Taksande", "Dr. Amol Singam", "Varun Thawkar", "Dr. Amol Singam", "Varun Thawkar" ], "abstract": "Background Non-technical skills are pivotal in ensuring patient safety during anaesthesia crisis resource management. Simulation-based training has emerged as a promising educational approach for enhancing these skills. This study protocol outlines a prospective randomised comparative study aimed at assessing the impact of simulation-based training on the performance of anaesthesia residents during anaesthesia crisis resource management, with a focus on task management, teamwork, situational awareness, and decision-making skills, using the Assessment of Non-Technical Skills (ANTS) scoring system.\n\nMethods Anesthesia residents in postgraduate years 1 and 2 from the Department of Anesthesia at Acharya Vinoba Bhave Rural Hospital will be included as study participants. Informed consent will be obtained, and no exclusion criteria will be applied. Participants will undergo an orientation session covering essential crisis management and simulation knowledge. The study will employ advanced simulation equipment, including a Human Patient Simulator (HPS) mannequin, an anaesthesia machine, and a simulated operating room. Faculty members have selected six distinct perioperative emergency scenarios for simulation sessions. Participants will be grouped in pairs and exposed to three scenarios during each session. Debriefing and feedback will follow each scenario, reinforcing non-technical skills. Experienced staff anesthesiologists, trained in the Assessment of Non-Technical Skills (ANTS) scoring system, will serve as assessors to evaluate participant performance.\n\nExpected outcomes Data collected will include ANTS scores, debriefing feedback, and post-test results. Statistical analysis will be employed to assess the effectiveness of simulation-based training in enhancing non-technical skills among anaesthesia residents during anaesthesia crisis resource management.", "keywords": [ "Simulation-Based Training", "Anesthesia Crisis Resource Management", "Non-Technical Skills", "Assessment of Non-Technical Skills (ANTS)", "Postgraduate Anesthesia Residents", "Patient Safety." ], "content": "Introduction\n\nPatient safety and effective crisis management are paramount in anaesthesia, where even minor errors can have significant consequences. Anaesthesia providers, particularly residents in their early postgraduate years, face the demanding challenge of responding swiftly and adeptly to unexpected perioperative crises.1 The ability to navigate such crises hinges on clinical proficiency and non-technical skills, encompassing task management, teamwork, situational awareness, and decision-making. These non-technical skills are increasingly crucial to safe and high-quality healthcare delivery.2\n\nSimulation-based training has emerged as a transformative approach in healthcare education, offering a safe and immersive environment for learners to hone their clinical and non-technical skills. In recent years, simulation-based training has gained prominence in anaesthesia, providing a dynamic platform for anaesthesia residents to acquire and refine crisis resource management skills without exposing patients to unnecessary risk.3\n\nThis study protocol delineates a rigorous examination of the effectiveness of simulation-based training in enhancing the non-technical skills of postgraduate anaesthesia residents during anaesthesia crisis resource management. The Assessment of Non-Technical Skills (ANTS) scoring system will serve as the primary evaluative tool, allowing for the comprehensive assessment of task management, teamwork, situational awareness, and decision-making abilities in a controlled and standardized setting.4\n\nThe objective of this study is to bridge a critical knowledge gap by elucidating whether simulation-based training can significantly enhance anesthesia residents’ non-technical skills, ultimately contributing to improved patient safety during perioperative crises. As healthcare systems continually seek innovative approaches to optimize education and training, the findings of this research hold the potential to inform curricular advancements and healthcare practice standards.\n\nFurthermore, this study seeks to explore the relationship between participant characteristics, such as years of experience and prior training exposure, and the effectiveness of simulation-based training. Such insights may lead to tailored educational interventions that cater to the unique needs of anesthesia residents at various stages of their training.5\n\nThe study’s multifaceted approach, encompassing quantitative assessments, will provide a holistic understanding of the impact of simulation-based training on anesthesia residents’ non-technical skills. The ultimate aspiration is to empower anesthesia providers with the tools and knowledge to excel in crisis resource management, enhancing patient safety and the overall quality of anesthesia care.\n\n\nAim\n\nThe aim of this study is to assess the effectiveness of simulation-based training in improving the performance of anesthesia residents during anesthesia crisis resource management using the Assessment of Non-Technical Skills (ANTS) scoring system.\n\n\nObjectives\n\nTo evaluate and compare the performance of anesthesia residents in the following key non-technical skills domains during anesthesia crisis resource management:\n\n1. Task management: assess the ability to organize tasks efficiently during a crisis.\n\n2. Teamwork: evaluate teamwork skills, including communication, collaboration, and leadership within the anesthesia team.\n\n3. Situational awareness: measure the capacity to perceive and understand critical aspects of the situation, including early detection of potential issues.\n\n4. Decision-making: assess the quality and timeliness of decisions made by anesthesia residents in crisis scenarios.\n\n\n\n1. To enhance anesthesia residents’ cognitive abilities in recognizing complex and challenging clinical scenarios.\n\n2. To improve anesthesia residents’ social abilities in effective communication and interaction within the anesthesia team during crisis situations.\n\n3. To assess the retention of improved non-technical skills among anesthesia residents over a defined followup period.\n\n4. To gather participant feedback regarding their experiences with simulation-based training and its perceived impact on their clinical practice.\n\n5. To explore potential correlations between demographic factors (e.g., years of experience before training) and the effectiveness of simulation-based training in improving non-technical skills.\n\nThis will be a prospective, randomised comparative study.\n\nThe study will span a duration of three years.\n\nParticipants eligible for inclusion in this study will be anaesthesia residents in their first and second years of postgraduate study (PG).\n\nThe research will be carried out within the School of Virtual Learning premises at Acharya Vinoba Bhave Rural Hospital, Jawaharlal Nehru Medical College, Sawangi Meghe, Wardha.\n\nThe study will be conducted following the approval of the ethics and screening committee of Jawaharlal Nehru Medical College, DMIHER (DU), within the School of Virtual Learning at AVBRH, JNMC, Sawangi Meghe, Wardha.\n\n\n\n1. Improved non-technical skills: It is expected that participants who undergo simulation-based training will demonstrate a significant improvement in their non-technical skills, including task management, teamwork, situational awareness, and decision-making abilities. This improvement will likely be reflected in higher ANTS scores compared to baseline assessments.\n\n2. Enhanced crisis resource management: Simulation-based training is anticipated to enhance the ability of anaesthesia residents to manage crises effectively. This includes improved coordination within the anaesthesia team, quicker and more accurate decision-making, and a heightened awareness of critical situations.\n\n3. Positive participant feedback: Post-training feedback from participants is expected to reflect a positive experience and increased confidence in managing anaesthesia crisis scenarios. Participants are likely to find value in the hands-on, immersive nature of the training.\n\n4. Correlation with faculty interest: The study may reveal a correlation between faculty interest in teaching using Human Patient Simulator (HPS) mannequins and the selected perioperative emergency topics. This could influence the integration of simulation-based training into anaesthesia education curricula.\n\n5. Long-term retention of skills: The study may provide insights into the long-term retention of improved non-technical skills among anaesthesia residents. Follow-up assessments and feedback sessions after a month may indicate whether the skills acquired during training persist over time.\n\n6. Variability in performance: The study may identify variations in performance among anaesthesia residents, which could be influenced by factors such as years of experience and prior training. This information could inform tailored educational interventions.\n\n7. Validity of simulation-based training: The outcomes will contribute to the ongoing discussion on the validity and effectiveness of simulation-based training in healthcare education. Positive results would support the value of simulation in improving non-technical skills.\n\n8. Contribution to patient safety: Ultimately, the study’s outcomes have the potential to contribute to improved patient safety during anaesthesia procedures. Enhanced non-technical skills among anaesthesia residents may lead to better crisis management, reduced errors, and improved patient outcomes.\n\nAfter the approval from institutional ethics committee, the study will be conducted on 24 residents from department of anaesthesiology and will be randomly allocated into two groups: Group 1 (baseline session) n=12: performance of anaesthesia resident during first baseline session of simulation scenario; and Group 2 n=12: performance of anaesthesia resident during second session of simulation scenario.\n\nThe data collection process for the study involving anaesthesia residents in postgraduate years 1 and 2, focusing on simulation-based training for non-technical skills during anaesthesia crisis resource management, will be conducted with a high standard of American English. Below is a detailed description of the data collection process:\n\nSubject recruitment and informed consent: Anesthesia residents in postgraduate years 1 and 2 from the Department of Anesthesia will be included as study subjects following approval from the Institutional Research Board. There are no exclusion criteria, and residents can decline participation.\n\nOrientation session: Before the simulation sessions, all subjects will attend an orientation session. This session will cover the fundamentals of crisis evolution, patient simulation, and anaesthesia crisis resource management (ACRM). The initial hour of didactic instruction will include these key topics.\n\nSimulation setup and pretest: Subsequently, subjects will receive a hands-on introduction to the Human Patient Simulator (HPS) mannequin and monitors, the anaesthesia machine, and the simulated operating room setting. A pre-test will also be administered to assess the baseline knowledge and skills of the participants.\n\nAssessment for faculty: The study will assess faculty interest in teaching using HPS mannequins and select the topics of perioperative emergencies to be included in the simulation scenarios. A committee of faculty members will choose six specific perioperative emergencies:\n\n1. Laryngospasm during induction of general anaesthesia.\n\n2. Intraoperative ventricular tachycardia (VT).\n\n3. Anaphylaxis.\n\n4. Local anaesthetic toxicity (LA toxicity).\n\n5. Intraoperative myocardial infarction (MI).\n\n6. High spinal anesthesia.\n\nSimulation sessions: Participants will be divided into two groups for the simulator sessions. Each session will present three distinct scenarios. In each scenario, one participant will act as the primary anesthesiologist, while the other will assume the role of a secondary anesthesiologist, helping when requested.\n\nScenario execution: Each scenario will involve a verbal handoff from the chief investigator to the primary anesthesiologist, including crucial patient history, conducted studies, and the current state of anaesthesia and the surgical procedure. The entire simulation will be recorded, displaying the patient’s vital signs alongside the recorded procedure.\n\nSecondary anesthesiologist’s role: The secondary anesthesiologist will provide support as instructed but not offer crisis management advice or differential diagnoses during the scenarios.\n\nDebriefing and feedback: Following each scenario, all subjects will participate in a videotape-assisted debriefing session based on ACRM training principles. A post-test and feedback from participants will also be collected.\n\nRotational participation: Throughout the study, subjects will alternate between primary and secondary roles in the three scenarios. After the first three scenarios, a debriefing will occur. Subjects will remain in the same group for the study. They return to the simulation centre a month later for their second simulation session, including three new scenarios with debriefings.\n\nPerformance evaluation: Performance evaluation will primarily focus on non-technical skills and involve primary and secondary anesthesiologists. Subjects will participate in all six scenarios, with recurrent performance evaluations based on the initial three scenarios.\n\nAssessor training and ANTS scoring: Experienced staff anesthesiologists trained in simulation and ACRM concepts will serve as assessors, using the Assessment of Non-Technical Skills (ANTS) scoring system.4 Assessors will undergo training, which includes providing them with the user manual and background ANTS literature. After 4 hours of training, they can independently evaluate residents’ handling of simulated anaesthetic crises using videotapes. The ANTS scoring system will assess task management, teamwork, situational awareness, and decision-making skills.\n\nData comparison and analysis: Assessors will compare ANTS scores after evaluating videotapes of participants’ performance. ANTS uses a four-point scale to evaluate observable non-technical skills, with research videotapes sent to assessors after the study intervention phase is complete Table 1. This comprehensive data collection process will ensure a rigorous evaluation of the impact of simulation-based training on the non-technical skills of anaesthesia residents during anaesthesia crisis resource management.\n\n\nAllocation\n\nThe allocation of participants to the simulation-based training and control groups will be achieved through a randomisation process to ensure unbiased and equitable group assignment. Randomisation will be performed using a computer-generated randomisation sequence generated by an independent statistician or through a randomisation tool or software.\n\n1. Sequence generation: A randomisation sequence will be generated, assigning each participant a unique identification number. The sequence will be concealed from the study investigators until group assignment is required.\n\n2. Group assignment: Participants will be assigned to the simulation-based training or control group based on the generated sequence. Group assignments will be concealed until the time of allocation to minimise selection bias.\n\n3. Blinding: Due to the nature of the intervention (simulation-based training), it may not be feasible to blind participants or instructors. However, efforts will be made to ensure that the allocation sequence remains concealed from those involved in the allocation process.\n\nBaseline characteristics of participants, including demographic information, years of experience, and prior training exposure, will be collected to assess and report any potential group differences. Any significant differences in baseline characteristics between the groups will be considered during the data analysis phase.\n\nThe study will aim to allocate an equal number of participants to both the simulation-based training group and the control group to maintain balance. The allocation ratio will be 1:1. However, if there are practical constraints, such as an uneven number of participants, this ratio may be adjusted accordingly.\n\nThe allocation sequence and group assignments will be concealed from the study investigators and participants until the allocation point. This will be achieved using sealed envelopes or an independent party responsible for allocation. Allocation concealment is essential to prevent selection bias and maintain the integrity of the randomisation process.\n\nA designated study coordinator or research team member will ensure adherence to the randomisation process and proper group allocation. Monitoring will include periodic checks to confirm that the randomisation sequence is followed accurately.\n\nIn the event of protocol deviations or instances where participants cannot complete the assigned intervention (e.g., due to unforeseen circumstances), a protocol for addressing such deviations and maintaining data integrity will be established and documented.\n\nStatistical methods, including descriptive statistics, t-tests, and correlation analyses, will be employed to analyse the data using SPSS version 23. Data analysis in this study will be conducted meticulously to extract meaningful insights into the impact of simulation-based training on the non-technical skills of anaesthesia residents during anaesthesia crisis resource management. Our analytical approach encompasses several key facets:\n\nWe will perform a descriptive analysis to provide a comprehensive overview of the data collected. These entail calculating means and standard deviations for continuous variables, such as baseline participant characteristics, and computing frequencies for categorical variables. Descriptive statistics will help us understand the initial demographics and characteristics of the anaesthesia residents who participated in the study.\n\nTo assess the effectiveness of simulation-based training, we will employ comparative analysis. Specifically, we will conduct paired t-tests or Wilcoxon signed-rank tests to compare pre-training and post-training Assessment of Non-Technical Skills (ANTS) scores within groups. These tests will reveal whether the simulation-trained group exhibited statistically significant improvements in non-technical skills following the training sessions. Additionally, independent t-tests or Mann-Whitney U tests will be utilised to compare ANTS scores between the simulation-trained group and the control group, shedding light on the differential impact of the training program.\n\nCorrelation analyses will explore potential relationships between participant characteristics and training outcomes. For instance, we will investigate whether years of experience or prior training significantly affect the extent of skill improvement achieved through simulation-based training. These correlation analyses will enable us to identify any factors that may influence the effectiveness of the training program.\n\nThe findings of this study will be reported in a comprehensive research report, which may also be submitted for publication in peer-reviewed scientific journals. Our aim in data reporting is to present the results in a clear, organised, and transparent manner to facilitate understanding and interpretation by both the scientific community and stakeholders in healthcare education.\n\nEnsuring secure, organised, and ethical data management is paramount to this study’s integrity and success. The following procedures will be implemented to safeguard data at every stage of the research process:\n\n\n\n1. Secure data collection: All data collected during the study, including Assessment of Non-Technical Skills (ANTS) scores, participant feedback, demographic information, and video recordings, will be collected using secure electronic or paper forms.\n\n2. Anonymization: Participants’ identifiers will be replaced with unique identification codes to ensure confidentiality and privacy. Any paper documents with personal information will be securely stored in locked cabinets.\n\n\n\n3. Electronic storage: Electronic data will be stored on secure, password-protected servers accessible only to authorised personnel. Access controls will be implemented to limit data access to study investigators and authorised assessors\n\n\nBias\n\nBias: Participants in the study may not represent the entire anaesthesia resident population, potentially leading to skewed results.\n\nOvercome: Implement a randomisation process to allocate participants to the simulation-based training group and the control group. Randomisation helps ensure that each participant has an equal chance of being assigned to either group, reducing the risk of selection bias.\n\nBias: The assessors evaluating participants’ performance during simulation sessions may be aware of group assignments, which could lead to biased scoring.\n\nOvercome: Implement blinding or masking of assessors to group assignments. Ensure that assessors know whether a participant belongs to the simulation-based training or control group to minimise observer bias.\n\nBias: Researchers or assessors may unintentionally interpret data in a way that confirms their expectations or hypotheses.\n\nOvercome: Maintain objectivity throughout the study. Use validated assessment tools like the Assessment of Non-Technical Skills (ANTS) scoring system to minimise subjective judgment. Pre-specify analysis plans to reduce the likelihood of post-hoc data interpretation that aligns with preconceived notions.\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol (Reference number: DMIHER (DU)/IEC/2023/977) Date: 10/05/2023. Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has yet to start. After the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nThe field of anaesthesia is marked by a critical need for anaesthesia providers, particularly residents, to possess clinical proficiency and robust non-technical skills, encompassing task management, teamwork, situational awareness, and decision-making.6 These non-technical skills are pivotal in ensuring patient safety during perioperative crises. Simulation-based training has emerged as a promising educational approach, offering a controlled environment for learners to develop clinical and non-technical competencies.7\n\nOur study protocol outlines a rigorous examination of the potential benefits of simulation-based training for anaesthesia residents. The primary aim of this study is to evaluate whether such training significantly enhances non-technical skills, as assessed by the Assessment of Non-Technical Skills (ANTS) scoring system. The ANTS scoring system is a validated tool that comprehensively evaluates anaesthesia providers’ performance in high-stress scenarios.8 Through this study, we aim to contribute to the growing body of evidence supporting the integrating of simulation-based training into anaesthesia education curricula.\n\nThe anticipated outcomes of this study align with prior research that has demonstrated the efficacy of simulation-based training in improving non-technical skills among healthcare providers. For example, studies in surgical and medical specialities have shown that simulation-based training can significantly improve teamwork and communication skills, situational awareness, and decision-making.9,10 Given the parallels between the demands of perioperative care and other healthcare settings, we anticipate that anaesthesia residents will likewise benefit from simulation-based training.\n\nOur study also seeks to explore potential correlations between participant characteristics, such as years of experience and prior training exposure, and the effectiveness of simulation-based training. Previous research has suggested that learners at different stages of their education and training may respond differently to simulation interventions.11 By considering these factors, we may gain insights into how to tailor educational interventions to the unique needs of anaesthesia residents at different points in their training journey.\n\nThis study’s findings can inform educational strategies and best practices in anaesthesia crisis resource management. Improved non-technical skills among anaesthesia residents can lead to more effective crisis management, reduced errors, and enhanced patient safety.4 As the healthcare landscape continues to evolve, optimising the education and training of anaesthesia providers is essential to meet the demands of complex and rapidly changing clinical environments.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nGaba DM: Anaesthesiology as a model for patient safety in health care. BMJ. 2000; 320: 785–788. Publisher Full Text\n\nBijok B, Jaulin F, Picard J, et al.: Guidelines on human factors in critical situations 2023. Anaesth. Crit. Care Pain Med. 2023; 42: 101262. PubMed Abstract \| Publisher Full Text\n\nLateef F: Simulation-based learning: Just like the real thing. J. Emerg. Trauma Shock. 2010; 3: 348. Publisher Full Text\n\nFletcher G, Flin R, McGeorge P, et al.: Anaesthetists’ Non-Technical Skills (ANTS): evaluation of a behavioural marker system† †Declaration of interest: The ANTS system was developed under research funding from the Scottish Council for Postgraduate Medical and Dental Education, now part of NHS Education for Scotland, through grants to the University of Aberdeen from September 1999 to August 2003. The views presented in this paper are those of the authors and should not be taken to represent the position or policy of the funding body. Br. J. Anaesth. 2003; 90: 580–588. Publisher Full Text\n\nTorrano V, Zadek F, Bugada D, et al.: Simulation-Based Medical Education and Training Enhance Anesthesia Residents’ Proficiency in Erector Spinae Plane Block. Front. Med. 2022; 9: 870372. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRadhakrishnan B, Katikar MD, Myatra SN, et al.: Importance of non-technical skills in anaesthesia education. Indian J. Anaesth. 2022; 66: 64–69. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGordon M, Darbyshire D, Baker P: Non-technical skills training to enhance patient safety: a systematic review. Med. Educ. 2012; 46: 1042–1054. Publisher Full Text\n\nFlin R, O’Connor P, Crichton M: Safety at the Sharp End: A Guide to Non-Technical Skills. 1st ed.CRC Press; 2017. Publisher Full Text\n\nZiv A, Ben-David S, Ziv M: Simulation based medical education: an opportunity to learn from errors. Med. Teach. 2005; 27: 193–199. Publisher Full Text\n\nArora S, Aggarwal R, Sirimanna P, et al.: Mental practice enhances surgical technical skills: a randomized controlled study. Ann. Surg. 2011; 253: 265–270. Publisher Full Text\n\nCheng A, Grant V, Dieckmann P, et al.: Faculty Development for Simulation Programs: Five Issues for the Future of Debriefing Training. Simul. Healthc J. Soc. Simul. Healthc. 2015; 10: 217–222. Publisher Full Text" }	[ { "id": "301986", "date": "22 Aug 2024", "name": "Lisa Osborne Smith", "expertise": [], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study design is described as a randomized comparative study, but the description of the control group is not adequate, and it also doesn’t appear to be a control group per se. A pre-post-test design is a reasonable option for this type of study. A pre-test post-test design would allow an evaluation of the within-subject impact of the intervention, and it would also provide between-subject assessment to evaluate the secondary objectives such as the years of training. The addition of a study flowchart would assist the reader to quickly understand the methods. It’s also not clear why 3 scenarios were chosen for testing if the subjects are to work in pairs (taking turns being the primary and secondary anesthesiologist which results in an uneven distribution of being in the primary role– this is problematic). The ANTS scoring system has been widely used to assess non-technical skills and it is likely a good choice for this study. It would help to know more about the decision to have a follow-up at 1 month. The justification for this short timeframe has not been provided. The scenarios chosen for six simulation sessions represent a range of adverse events are appropriate for evaluation.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "297393", "date": "28 Oct 2024", "name": "Wenlong Yao", "expertise": [ "Reviewer Expertise anesthesia and pain medicine" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a study protocol to investigate the role of simulated-based training in improving non-technical skills. Overall, the purpose is very clear.\n\nI have several detailed questions about design.\n1. The two groups were not clearly defined. As far as I am concerned, one group: receiving simulated-based training, the other one: not receiving training. But the authors defined group 1 and group 2. It could be pre-training and post-training sessions. I am not sure whether the participants in two groups received the same courses.\n\n2. There are 6 cases for simulation. Does each participant take part in all of 6 cases by two sessions?\n3.I suggest use a Figure to show the flow chart, including grouping, training, data collection and analysis.\n\n4. How was the sample size calculated ?\n5. How many assessors were involved in the study ？and How were they blinded to groups ?\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "335695", "date": "22 Nov 2024", "name": "Aliya Ahmed", "expertise": [ "Reviewer Expertise Medical Education", "Acute Pain Management", "Anaesthesiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the request to review this protocol. We have reviewed it closely and our comments are as follows:\nObjectives:\nHow will it be assessed that secondary objectives number 1 and 2 have been achieved?\nMethodology:\nThere are many points in Methodology that need clarification. The details provided are not sufficient for the study to be replicated by other researchers.\nSample size: How was the total number of participants decided? Are there only 12 trainees each in year 1 and year 2 of training? If so, what would be the strategy if some of the trainees decline to participate? It might lead to the sample size being too small, or there being unequal numbers of Year-1 and Year-2 trainees.\nThe group assignments also need clarification: Please clarify the statement: “Group 1 (baseline session) n=12: performance of anaesthesia resident during first baseline session of simulation scenario; and Group 2 n=12: performance of anaesthesia resident during second session of simulation scenario”.\nThere is mention of a ‘control group’ much further down in the protocol, but the description of the control group is not adequately provided.\nWe recommend that a flow chart be provided. It would help in understanding the methodology. Moreover, it seems to us that this type of study would be better conducted with a pre-post test method rather than comparison between two groups.\nThe scenarios selected are pertinent to assessment of ANTS. However, more details are required in Methodology. It is mentioned that 3 scenarios will be selected for the first session. How many simulation sessions will be conducted to enable every participant a chance to become the primary anesthesiologist? Elaboration is required about the number of sessions to be conducted to give every participant an equal chance to play the role of primary anesthesiologist.\n“Rotational participation”: Please clarify.\nRetention of skills: Please provide the reason for choosing a gap of one month for assessing retention of skills?\nAssessors: Please mention how many assessors will be involved in the study? Will the assesors be the same for the two sessions?\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-354
https://f1000research.com/articles/13-352/v1	23 Apr 24	{ "type": "Opinion Article", "title": "Immigrants are crucial to U.S. Health System Resilience", "authors": [ "Maria Duque", "Aaron Clark-Ginsberg", "Seth J. Schwartz", "Aaron Clark-Ginsberg", "Seth J. Schwartz" ], "abstract": "A polycrisis of climate and non-climate related shocks and stresses are straining U.S. health systems and affecting mental health. In contrast to negative rhetoric surrounding immigrants and immigration, immigrants make contributions that are fundamental to ensuring health system resilience. As in many other countries, in the United States foreign born compensate for health care worker shortages; help subsidize health programs with their labor; and support response, recovery, and rebuilding following disaster. However, immigrants are often trapped in political inflammatory narratives and public’s clashing sentiments. To harness the power of immigrants’ contributions in facilitating health system resilience, policies that help pair the pool of global talent with the needs of America’s public health systems are needed. This may require redressing harmful policies that reduce participation on the labor pool and crafting more humane policies that encourage migration. Doing so may result in a stronger health system better able to weather converging crises.", "keywords": [ "health system resilience", "health system workforce", "polycrisis", "immigration" ], "content": "Introduction\n\nHealth systems in the United States and across the world are increasingly challenged by a polycrisis of converging shocks and stresses, both climate- and non-climate related.1 These shocks and stresses include (a) the COVID-19 pandemic, which continues to burden health agencies; (b) an uptick in disasters induced by a changing climate, adding to health needs and compromising health infrastructure; and (c) demographic shifts characterized by an aging population coupled with a steady decline in fertility that shape expenditures and labor availability.2–5 It is difficult and relatively unproductive to attempt to disentangle the effects of climate change on these crises.6 Instead, these and other crises should be examined together; understood as placing incredible stress on an already stressed health system. In this context, as a recognized mechanism for managing health system risk, health system resilience, or the capacity of health systems to prepare for, respond to, recover from and transform in response to shocks and stresses,7 is critical for maintaining mental health and more general well-being.\n\nWe argue that, in contrast to the often-negative rhetoric surrounding immigrants and immigration,8 in the United States immigrants’ contributions are crucial to ensuring a resilient health system that is responsive to mental health needs amidst polycrisis. Far from being a drain on health systems and resources, immigrants are an asset: they contribute to the economy, to the labor force pool, and to responses to acute and chronic disasters. Yet, immigrants’ contributions have been traditionally overlooked as a health system strength.\n\nTo substantiate this argument, we illustrate how immigrants play a fundamental role in addressing three shocks and stresses impacting the US health systems: economic volatility, a changing workforce, and accelerating disaster threats. We conclude with a discussion of how, despite their contributions to American society, immigrants face challenges related to invisibility, stigma, and multiple obstacles workforce entry, which exacerbates challenges to U.S. public health preparedness.\n\n\nImmigrants Contribute to the Economy in Ways that Alleviate Health System Fiscal Shocks\n\nTwo fiscal shocks are impacting US health systems: growing healthcare expenditures and large-scale reductions in the tax base attributable to population shifts. Baby Boomers are exiting the workforce, representing a significant decline in payroll taxes and an increase in health care expenditures. Americans are living longer than ever, and as a result, they spend greater amounts of time drawing Medicare health benefits, including more expensive benefits typically used at older ages. Given expenses associated with Medicare, this reduction in the workforce and increase in the retired population could translate to about a 30% increase in the health care costs for older adults.9\n\nThe US fertility rate has reached a record low, mirroring long-term reductions in the workforce and consequent declines in revenue collection required to subsidize health programs.10 In turn, the doubly-amplified demographic shift of an aging population coupled with decreasing fertility is likely to affect several major revenue streams (e.g., tax revenues) in the coming decades.11 Simultaneously, unemployment spikes associated with the COVID-19 pandemic and associated mitigation strategies created additional short-term fiscal stress as job losses led to an additional drop in payroll taxes.\n\nImmigrants impact the economy in ways that help alleviate public health fiscal shocks and stresses. In contrast to people born in the United States, who, between 2006 and 2018, consumed $98 billion more in Medicare than they contributed through taxes (making them net consumers of Medicare services), immigrants are net contributors to Medicare, contributing nearly $75 billion more in taxes than they spent in that same period.12 This is partly due to the demographic profile of immigrants, who, compared to people born in the United States, are more likely to be working-age taxpayers, thus contributing taxes and using fewer health system resources.13\n\n\nImmigrants Contribute to the Health Labor Pool to Reduce Labor Stresses\n\nProviding health services is labor intensive, to the extent that the health care industry constitutes the largest source of employment in the United States.14 This industry is also projected to grow rapidly over the coming decades, with demands outstripping supply, partly due to increases in health needs as Americans age out of the workforce and into retirement at rates that outpace new workers coming into the labor pool,15 but also partly due to factors such as staff burnout and turnover associated with the COVID-19 pandemic.16 Together, the changing ratio of workers to retirees, the shrinking labor force pool, and labor shortages in health care associated with public health emergencies could represent a potentially significant strain affecting the tax base available to maintain health systems.\n\nBefore the COVID-19 pandemic, predictions forecast a US shortfall of up to 139,160 physicians by 2030.17 Shortfalls may be particularly acute in rural America, where nearly one-third of practicing doctors are over 60 and nearing retirement age.18 When the pandemic hit, shortfalls increased further as healthcare workers resigned due to safety and burnout while needs expanded.19\n\nImmigration can help counteract some of these demographic shifts. Almost 30% of America’s physicians are foreign-born,20 and compared to their US-born counterparts, immigrants are twice as likely to be physicians, and more frequently fill positions in medically underserved areas. For instance, immigrants are twice as likely to work as home health aides, clinical technicians, and other front-line occupations critical to a functional health system.21\n\n\nImmigrants Support Health System Disaster Preparedness, Response, and Recovery\n\nAccelerating disaster threats, including climate- and non-climate related natural hazards as well as public health crises, require large amounts of resources and effectively take these resources away from other priorities. These disaster threats therefore pose a challenge to the health system by constraining the provision of health services and reducing the pool of available essential workers.\n\nImmigrants are instrumental to public health readiness and play a crucial role in delivering essential health services during public health emergencies. During the COVID-19 pandemic, for instance, 74% of undocumented immigrants were employed as essential workers.22 Response and recovery to natural hazards is similar. A sizeable workforce is needed to rebuild and recover following many disasters. For example, prompt rebuilding and repair of critical infrastructure impacted by hurricanes and wildfires, including hospitals, roads, and energy and water supply plants, are critical for providing continuity in care provision to prevent further loss of health and lives. Furthermore, 25% of immigrants work in construction,23 where they play a valuable role in rebuilding infrastructure post-disaster.\n\nExposure to disasters is also associated with increases in mental and behavioral health challenges, where again immigrants provide valuable mental health services. For instance, there is a critical shortage of psychiatrists in the United States – a deficit of 3400 as of 2016 – and this shortage is expected only to grow given the age of the current workforce (60% of psychiatrists are 55 or older).24 Foreign-licensed physicians constitute almost a third of practicing psychiatrists,25 and outside of psychiatry, immigrants working as clinical psychologists, therapists, counselors, and psychiatric aides are also participating in the US mental health workforce in growing numbers.\n\n\nConclusions\n\nA polycrisis of converging shocks and stresses have underscored the challenges facing health systems in the United States, including those related to providing essential mental health services. Immigrants can enhance health system resilience by leveraging the availability of global talent to support health systems before, during, and after crises. Nonetheless, the invisibility of immigrants’ crucial role in health system resilience is three-fold, including for immigrants who are skilled and highly trained in medical professions critical to US health systems. First, immigrants’ contributions have been traditionally overlooked as an asset to health systems. Second, immigrants often face deeply entrenched social prejudice that frames them as fiscal burdens and social threats.26 Third, working in the United States as a foreigner requires navigating an ever-changing series of legal restrictions and policies. Navigating these laws and policies can be time consuming and costly, and successfully securing a pathway to permanently and legally work in the country is by no means guaranteed.\n\nAs a result, a first step towards leveraging immigrants for a resilient health system involves making the relative invisibility of immigrants’ contributions to American society – including in the area of health – visible. Immigrants’ contributions represent a critical component for a functioning health system in general and a health system resilient to crisis. For the United States to capture and value the resources that immigrants provide and bolster public health system resilience, the country needs to shift from old paradigms that portray immigrants as a burden to society to a new approach that focuses on immigrants’ contributions as an asset to health systems and to broader societal well-being.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nFootnotes\n\n1 Homer-Dixon, T., Renn, O., Rockstrom, J., Donges, JF. Janzwood, S. A call for an international research program on the risk of a global polycrisis. SSRN 2. 2021; 405859.\n\n2 Jeff Chapman. The Long-Term Decline in Fertility—and What It Means for State Budgets; 2022. https://www.pewtrusts.org/en/research-and-analysis/issue-briefs/2022/12/the-long-term-decline-in-fertility-and-what-it-means-for-state-budgets Accessed April 3, 2023.\n\n3 Federal Hospital Insurance and Federal Supplementary Medical Insurance Trust Funds. Board of Trustees. The 2021 Annual Report of the Boards of Trustees of the Federal Hospital Insurance and Federal Supplementary Medical Insurance Trust Funds; 2021. https://www.cms.gov/files/document/2021-medicare-trustees-report.pdf. Accessed April 3, 2023.\n\n4 Ayanian JZ. Saving Medicare for Baby Boomers and Beyond-A Looming Fiscal Crisis. JAMA Health Forum. 2020;1(11):e201387. Published 2020 Nov 2. doi:10.1001/jamahealthforum.2020.1387\n\n5 Skinner L, Staiger DO, Auerbach DI, Buerhaus PI. Implications of an Aging Rural Physician Workforce. N Engl J Med. 2019;381(4):299-301. doi:10.1056/NEJMp1900808\n\n6 Kelman, Ilan, Jean-Christophe Gaillard, and Jessica Mercer. “Climate change’s role in disaster risk reduction’s future: Beyond vulnerability and resilience.” International Journal of Disaster Risk Science 6 (2015): 21-27.\n\nKelman, Ilan. “Linking disaster risk reduction, climate change, and the sustainable development goals.” Disaster Prevention and Management: An International Journal 26, no. 3 (2017): 254-258.\n\n7 Clark-Ginsberg, Aaron, and Anita Chandra. “Climate change-related mass migration requires health system resilience.” Environmental Research: Health 1, no. 4 (2023): 045004.\n\n8 Banulescu-Bogdan N, Malka H, Culbertson S. The Migration Policy Institute. How We Talk about Migration: The Link between Migration Narratives, Policy, and Power; 2021. https://www.migrationpolicy.org/sites/default/files/publications/narratives-about-migration-2021_final.pdf. Accessed April 3, 2023.\n\n9 Federal Hospital Insurance and Federal Supplementary Medical Insurance Trust Funds 2021.\n\n10 Ibid.\n\n11 Ibid.\n\n12 Moore S, Mawji A, Shiell A, Noseworthy T. Public health preparedness: a systems-level approach. J Epidemiol Community Health. 2007;61(4):282-286. doi:10.1136/jech.2004.030783\n\n13 Ward N and Batalova J. Frequently Requested Statistics on Immigrants and Immigration in the United States. Migration Policy Institute; 2023. https://www.migrationpolicy.org/article/frequently-requested-statistics-immigrants-and-immigration-united-states . Accessed October 10, 2023.\n\n14 Ibid.\n\n15 Ayanian et al 2020.\n\n16 Garrett AL, Park YS, Redlener I. Mitigating absenteeism in hospital workers during a pandemic. Disaster Med Public Health Prep. 2009;3 Suppl 2:S141-S147. doi:10.1097/DMP.0b013e3181c12959\n\n17 Zhang X, Lin D, Pforsich H, Lin VW. Physician workforce in the United States of America: forecasting nationwide shortages. Hum Resour Health. 2020;18(1):8. Published 2020 Feb 6. doi:10.1186/s12960-020-0448-3\n\n18 Skinner et al 2019.\n\n19 Garrett et al 2009.\n\n20 Gelatt J. The Migration Policy Institute. Immigrant Workers: Vital to the US COVID-19 Response, Disproportionately Vulnerable; 2020. https://www.migrationpolicy.org/sites/default/files/publications/COVID-19-EssentialWorkers-FS_Final.pdf. Accessed April 3, 2023.\n\n21 Aho, K. The American Immigration Council. Amid a Severe Shortage of Home Health Aides, Immigrants Help Care for Our Seniors; 2023. https://www.newamericaneconomy.org/issues/healthcare/. Accessed April 3, 2023.\n\n22 Kerwin D, Warren R. US foreign-born workers in the global pandemic: essential and marginalized. J Migration Hum Sec. 2020;8(3):282-300.\n\n23 Porter E. Short of Workers, U.S. Builders and Farmers Crave More Immigrants. New York Times. April, 2019. Accessed April 3, 2023. https://www.nytimes.com/2019/04/03/business/economy/immigration-labor-economy.html\n\n24 Mangurian C, Lee CM, Rodriguez C. Contributions of immigrants to the field of US psychiatry. Lancet Psychiatry. 2017;4(8):584-585. doi:10.1016/S2215-0366(17)30292-4\n\n25 Ibid.\n\n26 Commodore-Mensah Y, DePriest K, Samuel LJ, Hanson G, D’Aoust R, Slade EP. Prevalence and Characteristics of Non-US-Born and US-Born Health Care Professionals, 2010-2018. JAMA Netw Open. 2021;4(4):e218396. Published 2021 Apr 1. doi:10.1001/jamanetworkopen.2021.8396" }	[ { "id": "297672", "date": "15 Jul 2024", "name": "Kanchan Marcus", "expertise": [ "Reviewer Expertise health workforce", "migrants", "healthcare access", "heath systems" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study highlights a pressing need to emphasise a strengths-based approach to underline the significant impact that immigrants have upon the US healthcare system, which is important. Further contextual information, reorganising some of the arguments and structure of the paper will improve this study.\n\nRephrase text for ease of understanding: “In this context, as a recognized mechanism for managing health system risk, health system resilience, or the capacity of health systems to prepare for, respond to, recover from and transform in response to shocks and stresses, is critical for maintaining mental health and more general well-being.” Consider adding contextual information here: “…and to responses to acute and chronic disaster” to something like “and responding to acute and chronic distasters through…? community care? Low-paid care work?...” Add ‘to’ here: “immigrants face challenges related to invisibility, stigma, and multiple obstacles to workforce entry, which exacerbates challenges to U.S. public health preparedness“ Please add some information about the Medicare system in the US/Medicaid or Obamacare and whether immigrants have access to these. Would be useful to add context regarding the numbers of immigrants in the US; key source countries; overseas born professionals on visas etc.\n\nIt might be useful to add fiscal aspects related to increasing health expenditures (maybe describe an example of bundled payment models) because there are multiple reasons presented in the evidence base for increasing health costs. Is it possible that immigrants consumed less Medicare services due to costs associated with services or temporary visa status or fear of being reported? Include references if there’s evidence that there is “accelerating disaster threats to climate…” or rephrase Please include a sample size for this or rephrase: “For instance, 74% of undocumented immigrants were employed as essential workers”. What about statistics of immigrants in the care sector or rural areas? Do internationally qualified nurses support mental health for populations in the US?\n\nMental health argument here could be strengthened or expanded upon Given that the authors argue that it is difficult to disentangle the three crises, I offer a suggestion to amending the three headings (which are all interlinked with the health system). Possibly 1) “Background to the US health system and immigrants” (provide contextual information about the country as suggested above – Medicaid/numbers of immigrants etc) 2) “Immigrants support health systems through labor workforce, reducing fiscal shocks and disaster recovery” (which is the body of the interlinked arguments presented) and 3) Recommendations or how to move forward Conclusion – invisibility argument should move up into the body of the text. The same goes for legal policies as these should be described above. The conclusion should present a summary of the information and argument without introducing new information.\n\nPlease choose one consistent way of describing the US. There is U.S or US or United States throughout the paper\nThis paper is an important study, and a good effort has been made in triangulating the three interlinked crises. Editing the paper will help clarify these links and solidify the paper.\n\nAll the best with your paper.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-352
https://f1000research.com/articles/13-350/v1	23 Apr 24	{ "type": "Review", "title": "Benzydamine hydrochloride: an overview on a well-established drug with news in mechanisms of action", "authors": [ "Antonio Ferrer-Montiel" ], "abstract": "Pain and inflammation are the consequences of sore throat, dental and oral procedures, infections, ulcers and head and neck chemotherapy/radiotherapy, and their management is of fundamental importance to avoid distress in patients. Benzydamine hydrochloride (HCl) is a topical indolic nonsteroidal anti-inflammatory drug, endowed with analgesic and anesthetic activity, and with antimicrobial (including both gram-positive and gram-negative bacteria) and antifungal properties (targeting Candida albicans and non-albicans strains), used in odontostomatology, otorhinolaryngology, and gynecology for its properties. This molecule has a lipophilic nature, showing high affinity with cell membranes and exhibiting membrane stabilization properties, resulting in local anesthesia, an effect related also to the interaction of the drug with cationic channels. In addition, benzydamine HCl is able to inhibit the production of pro-inflammatory cytokines, with consequent analgesia. Moreover, benzydamine HCl is able to inhibit leukocyte-endothelial interactions and platelet aggregation. Unlike other non-steroidal anti-inflammatory drugs, benzydamine HCl does not inhibit cyclooxygenase or lipoxygenase. Here we review the most updated clinical data available on benzydamine HCl local application as spray, mouthwash or gargling and evidence of its effectiveness in inflammatory and/or septic conditions in the otorhinolaryngology and odontostomatology settings, with particular reference to sore throat, oral inflammation, dental plaque, tonsillitis/tonsillectomy and chemo- or radiotherapy-induced oral mucositis. Novel formulations for oral administration of benzydamine HCl are also reviewed, including in situ gelling formulations to be sprayed onto the damaged oral mucosa. Finally, novel data on the potential role of benzydamine HCl in nociceptor excitability are introduced.", "keywords": [ "Benzydamine hydrochloride", "sore throat", "oropharyngeal disorders", "inflammation", "pain relief", "nociceptor excitability" ], "content": "Introduction\n\nBenzydamine, available as hydrochloride (HCl) salt, is an indolic nonsteroidal anti-inflammatory drug (NSAID) that shares properties with other NSAIDs, but displays also some peculiar characteristics, including local anaesthetic and analgesic activities, as well as antimicrobial and antifungal properties (Figure 1).1 Benzydamine HCl is currently formulated as topical preparations for the treatment of oropharyngeal and gynaecological conditions.2 It has been approved also for pediatric use in oropharyngeal conditions. The main characteristics of this molecule, as well as the main available clinical data and perspectives in its use and effectiveness are summarized in this narrative review.\n\nBenzydamine HCl shares some properties with other nonsteroidal antiinflammatory drugs, but also displays some unique characteristics.\n\n(↓) indicates downregulation; (↑) indicates upregulation.\n\nA comprehensive search and critical review have been conducted in PubMed database using the keywords benzydamine hydrochloride, sore throat, oropharyngeal disorders, inflammation, oral mucositis, pain relief through the use of the Boolean operators AND, OR, and identifying the articles relevant to this review. The literature search has been limited to English language articles. Manual search for related articles has been performed as well.\n\n\nPharmacology of benzydamine hydrochloride\n\nBenzydamine HCl has high lipid solubility in the unionized form, but low protein-binding capacity, and is consequently taken up by cells with high efficiency.1 Benzydamine HCl is metabolized mainly by conjugation, dealkylation and oxidation, with benzydamine N-oxide as the major metabolite.2\n\nBenzydamine HCl is characterized by a high volume of distribution and a relatively low systemic clearance.2 Plasma drug concentrations of oral benzydamine HCl reach a peak rapidly and decline with a half-life of about 13 h. Less than 20% of the drug results to be bound to plasma proteins.3 The systemic absorption of benzydamine HCl through the skin and non-specialized mucosae is relatively low compared to oral administration,2 thereby limiting unrequired systemic exposure to this drug and the potential for any systemic side-effect.\n\nBenzydamine HCl shares some properties with other NSAIDs, but exhibits also some distinctive characteristics. Benzydamine HCl has several properties that may contribute to its anti-inflammatory activity, as summarized in Figure 1. Among others, it may exert an anti-inflammatory activity by decreasing the release of pro-inflammatory cytokines, such as tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), but not IL-6 and IL-8, without affecting the production of anti-inflammatory molecules, such as IL-10 and IL-1 receptor antagonist (IL-1ra).4 At lower concentrations (3–30 μmol/L), this drug is also able to inhibit leukocyte-endothelial interactions, while at concentration of 10–100 μmol/L, benzydamine HCl may stabilize the mucosal membrane by virtue of its general high affinity for membranes, and may inhibit the release of azurophilic granules from neutrophils, rich in serine proteases, further contributing to its anti-inflammatory effects.1,5 Benzydamine HCl also reduces the histamine-induced vasodilation and vascular permeability.6 Benzydamine HCl shows antithrombotic activity7 and the inhibition of the collagen-induced aggregation appears to be rather selective vs. other NSAIDs.4 Finally, benzydamine HCl is a weak inhibitor of cyclooxygenase and lipoxygenase, and needs high concentrations to inhibit effectively prostaglandin and thromboxane biosynthesis.4\n\nBenzydamine HCl has also anti-microbial properties, supporting its anti-inflammatory activity when applied to the mouth. It proved to be effective in growth inhibition of Candida albicans and non-albicans strains, with minimal inhibitory concentrations ranging from 12.5 to 50.0 μg/mL, and with cytotoxic activity at higher concentration, through a membrane-damaging action, consistently with the lipophilic properties of this drug.8 A very recent study confirmed the effectiveness of benzydamine HCl on Candida albicans inhibition through the impairment of its adhesion, biofilm formation, regrowth and persistence in vitro.9 Benzydamine HCl proved to be effective also against gram-negative and gram-positive bacteria in vitro within a few minutes from exposure, at concentrations equal to or lower than those generally used to exert an anti-inflammatory action.10\n\n\nThe role of benzydamine hydrochloride in prevention and treatment of sore throat: insights from the clinical data\n\nAcute sore throat is a symptom often caused by an inflammation of pharynx, tonsils or nasopharynx and can occur as a part of a common cold of viral origin or can be due to pharyngeal bacterial infections.11 The effectiveness of benzydamine HCl oral rinse for pain relief in acute sore throat has been initially supported by a double-blind study involving 44 patients, where it showed a greater effect on hyperemia and edema at 24 hours vs. the placebo solution.12 More recently, a study revealed that chlorhexidine gluconate and benzydamine HCl mouth spray, added to standard antibiotic treatment with penicillin, significantly alleviated the intensity of clinical signs in patients with streptococcal tonsillopharyngitis.13 Of major interest, a novel multicenter, phase IV randomized study proved that both benzydamine HCl 0.3% oromucosal spray and benzydamine HCl 3 mg lozenges were effective in providing a sore throat relief in patients with at least one symptom of upper respiratory tract infection already 2 minutes after a single drug administration, thus addressing the patients’ priority of rapid symptoms’ relief in the setting of upper respiratory tract infections. Clinical efficacy after 7 days of treatment and a good safety profile were also demonstrated.14\n\nSore throat following tonsillectomy both in adults and children can cause discomfort in the immediate post-operative period. Moreover, since the nerve supplying the tonsil has a branch in the ear, otalgia, i.e. pain along the glossopharyngeal nerve, is commonly referred by patients submitted to tonsillectomy. Benzydamine HCl spray was more effective than placebo in the control of post-operative pain in patients submitted to tonsillectomy in a double-blind trial.15 Another double-blind study confirmed the effectiveness of benzydamine HCl as a local agent in alleviating symptoms of dysphagia and sore throat, but not the earache, thus reducing the requirement of analgesic medication in adult post-tonsillectomy patients.16 However, a prospective, double-blind randomized clinical trial (RCT) did not reveal any difference between mouthwash benzydamine HCl and placebo in intensity and duration of post operative pain,17 suggesting the need for further research studies.\n\nPost-operative sore throat (POST) is an adverse outcome of intubation for general anesthesia that can affect patient’s condition and the care quality, with multifactorial etiology and an incidence ranging from 21% to 66%, in function of the different surgical and anesthetic procedures.18 Different methods have been applied to alleviate POST. Among them, different studies tested the effectiveness of benzydamine HCl by virtue of its analgesic, anesthetic and anti-inflammatory properties. A prospective, double-blind study verified the effectiveness of an approach based on spraying the endotracheal tube cuff and/or the oropharyngeal cavity with benzydamine HCl. The results clearly indicated that spraying benzydamine HCl on the endotracheal tube lowers the incidence and severity of POST without increased benzydamine-related adverse effects.18 These data are consistent with the results of a subsequent meta-analysis of five trials that included 824 patients, showing that the incidence of POST was significantly reduced in the group treated with benzydamine HCl, without major benzydamine-related complications.19 A prospective randomized double-blind comparative study also confirmed the effectiveness of a gargle with benzydamine HCl for 30 seconds before undergoing surgery under general anaesthesia in alleviating the POST, the severity of cough and the voice hoarseness vs. a control group treated with placebo.20 Of note, benzydamine HCl gargle proved to be effective in reducing the consumption of propofol, an agent of choice used for sedation during endoscopic retrograde cholangiopancreatography. The combination of propofol and benzydamine HCl mouthwash reduced POST, cumulative propofol consumption/min/kg body weight and desaturation vs. the control group that received propofol and water mouthwash.21 These results are of particular interest, as they support the use of a combination of propofol and benzydamine HCl as topical analgesic to reduce propofol consumption and to provide adequate sedation while avoiding propofol side effects, including hypotension and respiratory depression, with a relevant advantage for patients. The combination of sedation with topical anaesthetics in endoscopic procedures is not new and has been tested also in previous studies, where lidocaine in the form of spray or gel was locally applied.22 However, benzydamine HCl mouthwash is becoming an alternative for this approach in the clinical practice as it can induce lower side effects than lidocaine.\n\nOnly a few studies did not confirm the effectiveness of prophylactic benzydamine HCl spray on POST following endotracheal intubation.23\n\n\nThe role of benzydamine hydrochloride in prevention and treatment of chemoradiotherapy-induced oral mucositis: insights from the clinical data\n\nOropharyngeal mucositis is one of the main adverse events of cancer treatment with chemotherapy or radiation therapy, and is characterized by generalized inflammation, erythema, atrophy and ulceration of oral mucosa.24,25 Oral mucositis can also follow hematopoietic stem cell transplantation, and can be caused by infections, diabetes and smoking as well. Oropharyngeal mucositis can induce several debilitating symptoms and functional impairment, with consequences on body weight and nutritional status. Moreover, cancer patients could need an unscheduled temporary stop of treatments due to severe oral mucositis, with the risk of a negative impact both on treatment outcome and on survival rates. Oral care is of great importance for prevention or limitation of oropharyngeal mucositis, as it can have an interplay with microbiota and oral infections, including candidiasis and herpes simplex virus-1 infections.25 Benzydamine HCl is widely used in the control of oral mucositis, thanks to its capacity to interact with different inflammation pathways and at the same time to act on pain. The Clinical Practice Guidelines for mucositis issued by the Multinational Association of Supportive Care in Cancer and by the International Society of Oral Oncology recommend the use of benzydamine HCl mouthwash for the prevention of oral mucositis in head and neck cancer (HNC) patients receiving radiotherapy, without concomitant chemotherapy. A recent systematic review of 11 papers further supported the use of benzydamine HCl mouthwash in the prevention and/or treatment of oral mucositis in patients submitted to radiotherapy while also adding chemotherapy.26,27 However, another systematic review of interventions used to mitigate the radiotherapy-induced oral mucositis in HNC patients did not support the use of benzydamine HCl or other interventions, such as honey and oral glutamine, in radiation-induced oral mucositis. This discrepancy highlights the need for additional high-quality studies with a consensus on the methodology to reduce heterogeneity, and an examination of the cost effectiveness of the interventions.28 Indeed, the discrepancies among study results may be due to dosing and timing of product administration, type of cancer and of patients characteristics, as well as to heterogeneity in anticancer treatments. Several other clinical studies supported the positive effects of benzydamine HCl in preventing and/or reducing the severity of oral mucositis in cancer submitted to radiotherapy. Among others, Chitapanarux et al. demonstrated the superiority of benzydamine HCl vs. sodium bicarbonate in reducing the severity of oral mucositis in locally advanced HNC patients treated with high-dose radiotherapy concurrently with platinum-based chemotherapy.29 Similar positive results have been obtained by Rastogi et al. in the prevention of oral mucositis in HNC patients treated with radiotherapy (>50 Gy) without chemotherapy, while the efficacy of benzydamine HCl in patients receiving concurrent chemotherapy was not confirmed.30 Positive results have been obtained also in pediatric patients affected by chemotherapy-induced oropharyngeal mucositis.31\n\nThis overview mostly supports the beneficial effect of benzydamine HCl in oral mucositis following anticancer treatments. Importantly, to the best of our knowledge, there is no evidence of any interference of benzydamine HCl with the activity of anticancer treatments. Moreover, the treatment with benzydamine HCl has been proved not only effective, but also safe and well tolerated in the setting of radiation-induced oral mucositis.32\n\n\nThe role of benzydamine hydrochloride in prevention and treatment of oral disorders: insights from the clinical data\n\nRecurrent aphthous stomatitis (RAS) is a common and painful disease of oral mucosa of unknown etiology and pathogenesis, not associated with systemic diseases and characterized by the formation of round or oval mouth ulcers.\n\nSince the underlying cause triggering RAS remains to be elucidated, at present the emergence of new lesions cannot be prevented, and therapy focuses mainly on pain reduction, through corticosteroids and topical analgesics plus antiseptics.33 A trial involving patients with minor RAS and comparing the effectiveness of 0.15% benzydamine HCl, 0.2% aqueous chlorhexidine and placebo mouthwashes administered consecutively for 3 months/each, for a total of 9 months, did not reveal any difference between the treatments tested. However, a subgroup of patients preferred the benzydamine HCl preparation because of the temporary topical anesthetic effect, which gave some pain relief.34 A greater control of pain by benzydamine HCl vs. other proprietary agents was also highlighted in a study involving hospital out-patients with aphthae in the UK.35 More recently, a prospective, parallel, double-blind, active control, preliminary study compared the flavonoid quercetin with 0.15% benzydamine HCl (Tantum oral rinse) in patients with RAS. The study revealed that both the drugs led to a similar reduction in pain scores from baseline up to day 7 during the treatment period, despite quercetin was able to significantly accelerate ulcer healing vs. benzydamine HCl.36\n\nDental plaque is a microbial biofilm adhering to the tooth surfaces and composed by microorganisms and by an extracellular matrix, i.e. a mix of molecules derived from both the biofilm microorganisms and from the host.37 Dental plaque is the most important etiological factor for oral diseases and is known to have also systemic effects on health. Oral antiseptics in mouth-rinse formulations are often used to reduce the microbial load in the oral cavity and can play an important role in preservation of oral health, together with mechanical oral hygiene procedures.38 Benzydamine HCl 0.15% as a mouthwash was well tolerated with no reported side effects in a double-blind RCT, and was as effective as chlorhexidine digluconate 0.2% in reducing gingival inflammation due to plaque accumulation, thus controlling further disease progression.39 However, these data were not confirmed by another study comparing chlorhexidine and benzydamine HCl administered as oral sprays to patients affected by gingival inflammation.40\n\nOral antiseptics can potentially cause irritation and have cytotoxic effects on cells of oral mucosa. The cytotoxic effect of benzydamine HCl has been recently assessed on primary human gingival fibroblasts in parallel with other oral antiseptics. The 2,3-bis (2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino) carbonyl]-2H-tetrazo-lium hydroxide (XTT) cytotoxicity test revealed low cytotoxic effects of benzydamine HCl on fibroblasts, suggesting that it can be used safely to achieve faster wound healing for conditions such as post-operative period.41\n\nPeriodontal surgery aims to prevent or improve different types of defects in the bone, gingiva or alveolar mucosa. Acute pain is one of the most frequent postoperative complications after periodontal surgery, and several analgesics have been tested so far. In this setting, a recent RCT compared the efficacy of 0.15% benzydamine HCl mouthwash vs. 400 mg ibruprofen tablets in the reduction of postoperative pain in a period of 24 hours following the crown lengthening, a surgical procedure that addresses excessive gingival display. The trial revealed comparable results for the level of pain in the two groups of patients treated with either benzydamine HCl or ibruprofen; however the investigators supported the use of benzydamine HCl mouthwash to decrease pain after periodontal surgery, because of its fewer side effects and lower price vs. ibuprofen.42 Another double-blind RCT involving patients affected by periodontitis demonstrated the superiority of 0.15% benzydamine HCl vs. 50 mg diclofenac sodium tablets in reduction of pain perceived by patients submitted to periodontal surgery.43\n\n\nThe potential role of benzydamine hydrochloride in nociceptor excitability: insights from novel preclinical data\n\nIn addition to the anti-inflammatory, analgesic and antimicrobial effects described above (Figure 1), some studies are revealing the ability of benzydamine HCl to block the neuronal excitability as well. A first indication came from a study investigating the effect of four different NSAIDs, including benzydamine HCl, on neuronally evoked contractile responses to a submaximal dose of prostaglandin E1 (PGE1) or cholecystokinin-octapeptide (CCK-8) in isolated guinea-pig ileum. All the four NSAIDs tested in the study were able to inhibit the CCK-8- or PGE1-induced contractile response in the isolated guinea-pig ileum at very low concentration, thus indicating their ability to interfere with a neuronally-evoked response. Moreover, all the NSAIDs tested were able to depress the opioid system activated by PGE1 or CCK-8.44 A more recent study verified the effect of benzydamine HCl on nociceptor excitability in primary cultures of sensitized rat nociceptors treated with the anti-mycotic compound econazole. This drug, belonging to the imidazole class, is able, at a clinically relevant concentration, to modulate directly the cytosolic Ca2+ homeostasis. Overall, the consequence of econazole action on sensory neurons is an increase in their excitability, augmenting the triggering of action potentials in silent nociceptors and, more evidently, in ATP-sensitized nociceptors, consistently with the higher Ca2+ fluxes. Of interest, a treatment with benzydamine HCl in vitro was able to inhibit the econazole-induced nociceptor excitability through the blockade of voltage-gated Na+ (Nav) channels.45 These data suggest an alternative pathway to inflammatory cytokine inhibition for the analgesic activity of benzydamine HCl.\n\nAdditional studies tested the capacity of benzydamine HCl to decrease the neuronal activity in an inflammatory sensitized neuronal model through electrophysiological recordings. Nociceptors were sensitized through a 24-hours incubation with an inflammatory soup containing histamine, serotonin, ATP and Prostaglandin E2. Action potential firing was induced by acute exposure to an identical inflammatory soup and acid pH, in order to mimic a local inflammatory process. Benzydamine HCl showed a dose-related inhibition of neuronal excitability mediated by either the inflammatory cocktail or the acidic pH in sensitized nociceptors and in basal conditions. Of note, higher potency was shown under inflammatory sensitized conditions compared to basal conditions.46 These novel results support the idea of complementary and synergistic effects of benzydamine HCl in the treatment of local inflammatory symptoms as well as in the painful processes, not only by reducing the inflammation cascade but also by reducing the inflammatory-mediated neuronal signaling.\n\n\nThe safety of benzydamine HCl administration as spray, mouthwash or gargling: insights from the clinical studies\n\nThe safety of benzydamine HCl when administered as spray, mouthwash or gargling in the setting of otorhinolaryngology and odontostomatology, has been verified by several studies. Among them, a multicenter phase IV study showed that both benzydamine HCl 0.3% spray and benzydamine HCl 3 mg lozenges formulations were well tolerated and showed a good safety profile, without any clinically significant abnormality when administered to patients with acute sore throat.14 The absence of significant adverse events related to benzydamine HCl has been showed also by a systematic review and meta-analysis of 13 RCT assessing the efficacy and safety of topical application of benzydamine HCl to prevent POST.47 The safety of benzydamine HCl oral spray administered as adjuvant therapy was further confirmed in a study including 210 children and adults submitted to tonsillectomy, adenoidectomy, or both, when compared to a similar group receiving a Salvia officinalis preparation.48 Finally, benzydamine HCl oral spray showed proper safety and was well tolerated, with no serious adverse events reported, when administered to patients with an acute tonsillopharyngitis associated with a common cold.49 Generally, the most commonly reported adverse effects after a topical administration of benzydamine HCl were mild numbness in tissues and tingling sensation in oral cavity after the rinse. These effects are presumably related to the mechanism of action of benzydamine HCl, characterized by a marked, local anesthetic activity, with a rapid onset and transience.50,51\n\n\nResearch insights for novel benzydamine HCl formulations\n\nSome studies are testing novel formulations for the administration of benzydamine HCl. An in-situ gelling formulation of benzydamine HCl, whose composition includes a thermosensitive polymer to be sprayed onto the damaged oral mucosa by self-administration, showed a sustained drug release and reduced the number of daily administrations of benzydamine HCl, while protecting the damaged mucosa from mechanical and chemical solicitations.52 The chemical and physical characteristics of benzydamine HCl also make this drug ideal for nanosponge complexes, i.e. stable nanostructures able to cross multiple barriers, as the pore size of the oral cavity is 2 μm, and particles that are less than this pore size can cross the mucus membrane.53 A recent study tested in the oral mucosa of murine models the local administration of benzydamine HCl in nanosponge-loaded hydrogels, able to increase the drug stability and to make its release more target-specific, for a potential application to mouth ulcers.54 A mucoadhesive buccal film for the mucosal delivery of benzydamine HCl has been recently developed for the treatment of aphthous stomatitis. The film showed adequate physicochemical properties and was able to provide prolonged residence time and sustained delivery vs. conventional therapies.40 Finally, nanoparticles composed by chitosan, a linear polysaccharide, have been recently developed and tested in vitro for benzydamine HCl delivery.55\n\nAn easier application and a higher contact time of benzydamine HCl with the oral mucosa thanks to the novel formulations described above could lead to a greater local bioavailability of the drug with a consequent grater control of pain and inflammation and/or infection, greater management of drug administration and a decrease of potential side effects.\n\n\nConclusions\n\nPain and inflammation are the consequences of sore throat, dental and oral procedures, infections, ulcers and HNC chemotherapy/radiotherapy, and their management is of fundamental importance to avoid distress in patients. The pharmacokinetics and clinical data summarized in this review revealed that the topical application of benzydamine HCl has several advantages, as the drug is well tolerated and effective, with a marked reduction of the side effects and complications potentially occurring during the systemic administration of other NSAIDs. Benzydamine HCl proved to be safe and efficient in pain relief, and novel properties and formulations are currently under investigation with promising results and new interesting perspectives for this well-established drug.\n\n\nEthics and consent\n\nEthical approval and written consent were not required.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nAmalia Forte, Ph.D., provided the medical writing support on behalf of Menthalia S.r.l., Naples, Italy.\n\n\nReferences\n\nQuane PA, Graham GG, Ziegler JB: Pharmacology of benzydamine. Inflammopharmacology. 1998; 6(2): 95–107. Publisher Full Text\n\nBaldock GA, Brodie RR, Chasseaud LF, et al.: Pharmacokinetics of benzydamine after intravenous, oral, and topical doses to human subjects. Biopharm. Drug Dispos. 1991; 12(7): 481–492. PubMed Abstract \| Publisher Full Text\n\nChasseaud LF, Catanese B: Pharmacokinetics of benzydamine. Int. J. Tissue React. 1985; 7(3): 195–204. PubMed Abstract\n\nSironi M, Massimiliano L, Transidico P, et al.: Differential effect of benzydamine on pro- versus anti-inflammatory cytokine production: lack of inhibition of interleukin-10 and interleukin-1 receptor antagonist. Int. J. Clin. Lab. Res. 2000; 30(1): 17–19. PubMed Abstract \| Publisher Full Text\n\nBaggiolini M, Mauderli P, Näf U, et al.: Effect of benzydamine on exocytosis and respiratory burst in human neutrophils and mononuclear phagocytes. Agents Actions. 1985; 16(5): 346–352. PubMed Abstract \| Publisher Full Text\n\nSironi M, Pozzi P, Polentarutti N, et al.: Inhibition of inflammatory cytokine production and protection against endotoxin toxicity by benzydamine. Cytokine. 1996; 8(9): 710–716. PubMed Abstract \| Publisher Full Text\n\nMüller-Peddinghaus R: New pharmacologic and biochemical findings on the mechanism of action of the non-steroidal antiphlogistic, benzydamine. A synopsis. Arzneimittelforschung. 1987; 37(5A): 635–645. PubMed Abstract\n\nPina-Vaz C, Rodrigues AG, Sansonetty F, et al.: Antifungal activity of local anesthetics against Candida species. Infect. Dis. Obstet. Gynecol. 2000; 8(3-4): 124–137. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArdizzoni A, Boaretto G, Pericolini E, et al.: Effects of benzydamine and mouthwashes containing benzydamine on Candida albicans adhesion, biofilm formation, regrowth, and persistence. Clin. Oral Investig. 2022; 26(4): 3613–3625. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFanaki NH, el-Nakeeb MA: Antimicrobial activity of benzydamine, a non-steroid anti-inflammatory agent. J. Chemother. 1992; 4(6): 347–352. PubMed Abstract \| Publisher Full Text\n\nFarah B, Visintini S: Benzydamine for Acute Sore Throat: A Review of Clinical Effectiveness and Guidelines. Ottawa (ON): Canadian Agency for Drugs and Technologies in Health; PubMed Abstract 2018.\n\nWethington JF: Double-blind study of benzydamine hydrochloride, a new treatment for sore throat. Clin. Ther. 1985; 7(5): 641–646. PubMed Abstract\n\nCingi C, Songu M, Ural A, et al.: Effect of chlorhexidine gluconate and benzydamine hydrochloride mouth spray on clinical signs and quality of life of patients with streptococcal tonsillopharyngitis: multicentre, prospective, randomised, double-blinded, placebo-controlled study. J. Laryngol. Otol. 2011; 125(6): 620–625. PubMed Abstract \| Publisher Full Text\n\nValerio C, Di Loreto G, Salvatori E, et al.: Comparative evaluation of rapidity of action of benzydamine hydrochloride 0.3% oromucosal spray and benzydamine hydrochloride 3 mg lozenges in patients with acute sore throat: A phase IV randomized trial. Medicine (Baltimore). 2023; 102(13): e33367. Publisher Full Text\n\nYoung JR: A comparative study of benzydamine hydrochloride 0.15% w.v. (‘Difflam’ pump spray) and placebo as analgesics following tonsillectomy. J. Int. Med. Res. 1985; 13(4): 245–247. PubMed Abstract \| Publisher Full Text\n\nRaj TB, Wickham MH: The effect of benzydamine hydrochloride (difflam) spray on post-tonsillectomy symptoms: a double-blind study. J. Laryngol. Otol. 1986; 100(3): 303–306. PubMed Abstract \| Publisher Full Text\n\nHanani T, Gadban H, Jahshan F, et al.: Tantum verde mouthwash for tonsillectomy: A prospective, double-blind, randomized control trial. Int. J. Pediatr. Otorhinolaryngol. 2019; 121: 173–178. PubMed Abstract \| Publisher Full Text\n\nHuang YS, Hung NK, Lee MS, et al.: The effectiveness of benzydamine hydrochloride spraying on the endotracheal tube cuff or oral mucosa for postoperative sore throat. Anesth. Analg. 2010; 111(4): 887–891. PubMed Abstract \| Publisher Full Text\n\nChen CY, Kuo CJ, Lee YW, et al.: Benzydamine hydrochloride on postoperative sore throat: a meta-analysis of randomized controlled trials. Can. J. Anaesth. 2014; 61(3): 220–228. PubMed Abstract \| Publisher Full Text\n\nGaikwad S, Rupwate K, Tendolkar B: A prospective, randomized, double blind, placebo controlled clinical trial to study efficacy and safety of benzydamine 0.15% gargles in prevention of postoperative sore throat. J. Res. Med. Sci. 2016; 4(6): 2420–2427. Publisher Full Text\n\nSugiarto A, Kapuangan C, Tantri AR, et al.: Effectivity of benzydamine hydrochloride gargle to reduce propofol consumption in endoscopic retrograde cholangiopancreatography procedure: a randomized controlled trial. BMC Anesthesiol. 2020; 20(1): 123. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBasturk A, Artan R, Yılmaz A: Investigation of Efficacy of Lidocaine Spray for Sedated Esophagogastroduodenoscopy in Children. Pediatr. Gastroenterol. Hepatol. Nutr. 2017; 20(2): 87–93. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYhim HB, Yoon SH, Jang YE, et al.: Effects of benzydamine hydrochloride on postoperative sore throat after extubation in children: a randomized controlled trial. BMC Anesthesiol. 2020; 20(1): 77. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTrotti A, Bellm LA, Epstein JB, et al.: Mucositis incidence, severity and associated outcomes in patients with head and neck cancer receiving radiotherapy with or without chemotherapy: a systematic literature review. Radiother. Oncol. 2003; 66(3): 253–262. Publisher Full Text\n\nNicolatou-Galitis O, Bossi P, Orlandi E, et al.: The role of benzydamine in prevention and treatment of chemoradiotherapy-induced mucositis. Support Care Cancer. 2021; 29: 5701–5709. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLalla RV, Bowen J, Barasch A, et al.: Mucositis Guidelines Leadership Group of the Multinational Association of Supportive Care in Cancer and International Society of Oral Oncology (MASCC/ISOO). MASCC/ISOO clinical practice guidelines for the management of mucositis secondary to cancer therapy. Cancer. 2014; 120(10): 1453–1461. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAriyawardana A, Cheng KKF, Kandwal A, et al.: Mucositis Study Group of the Multinational Association of Supportive Care in Cancer/International Society for Oral Oncology (MASCC/ISOO). Systematic review of anti-inflammatory agents for the management of oral mucositis in cancer patients and clinical practice guidelines. Support. Care Cancer. 2019; 27(10): 3985–3995. PubMed Abstract \| Publisher Full Text\n\nDavy C, Heathcote S: A systematic review of interventions to mitigate radiotherapy-induced oral mucositis in head and neck cancer patients. Support. Care Cancer. 2021; 29(4): 2187–2202. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChitapanarux I, Tungkasamit T, Petsuksiri J, et al.: Randomized control trial of benzydamine HCl versus sodium bicarbonate for prophylaxis of concurrent chemoradiation-induced oral mucositis. Support. Care Cancer. 2018; 26(3): 879–886. PubMed Abstract \| Publisher Full Text\n\nRastogi M, Khurana R, Revannasiddaiah S, et al.: Role of benzydamine hydrochloride in the prevention of oral mucositis in head and neck cancer patients treated with radiotherapy (>50 Gy) with or without chemotherapy. Support. Care Cancer. 2017; 25(5): 1439–1443. Publisher Full Text\n\nCheng KK: Children’s acceptance and tolerance of chlorhexidine and benzydamine oral rinses in the treatment of chemotherapy-induced oropharyngeal mucositis. Eur. J. Oncol. Nurs. 2004; 8(4): 341–349. PubMed Abstract \| Publisher Full Text\n\nEpstein JB, Silverman S Jr, Paggiarino DA, et al.: Benzydamine HCl for prophylaxis of radiation-induced oral mucositis: results from a multicenter, randomized, double-blind, placebo-controlled clinical trial. Cancer. 2001; 92(4): 875–885. PubMed Abstract \| Publisher Full Text\n\nRivera C: Essentials of recurrent aphthous stomatitis. Biomed. Rep. 2019; 11(2): 47–50. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMatthews RW, Scully CM, Levers BG, et al.: Clinical evaluation of benzydamine, chlorhexidine, and placebo mouthwashes in the management of recurrent aphthous stomatitis. Oral Surg. Oral Med. Oral Pathol. 1987; 63(2): 189–191. PubMed Abstract \| Publisher Full Text\n\nEdres MA, Scully C, Gelbier M: Use of proprietary agents to relieve recurrent aphthous stomatitis. Br. Dent. J. 1997; 182(4): 144–146. PubMed Abstract \| Publisher Full Text\n\nPandya M, Kalappanavar AN, Annigeri RG, et al.: Relative Efficacy of Quercetin Compared with Benzydamine Hydrochloride in Minor Aphthae: A Prospective, Parallel, Double Blind, Active Control, Preliminary Study. Int. J. Dent. 2017; 2017: 7034390–7034396. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJakubovics NS, Goodman SD, Mashburn-Warren L, et al.: The dental plaque biofilm matrix. Periodontology. 2021; 86(1): 32–56. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHerrera D, Santos S, Ferrús J, et al.: Efficacy of a 0.15% benzydamine hydrochloride and 0.05% cetylpyridinium chloride mouth rinse on 4-day de novo plaque formation. J. Clin. Periodontol. 2005; 32(6): 595–603. PubMed Abstract \| Publisher Full Text\n\nSeshan H, Shanavas S, Ashwini S: Effective evaluation of benzydamine hydrochloride as a mouth wash in subjects with plaque induced gingival inflammation. Int. J. Oral Health Dent. 2016; 2(3): 161–170. Publisher Full Text\n\nBozkurt FY, Oztürk M, Yetkin Z: The effects of three oral sprays on plaque and gingival inflammation. J. Periodontol. 2005; 76(10): 1654–1660. PubMed Abstract \| Publisher Full Text\n\nAlpaslan Yayli NZ, Tunc SK, Degirmenci BU, et al.: Comparative evaluation of the cytotoxic effects of different oral antiseptics: A primary culture study. Niger. J. Clin. Pract. 2021; 24(3): 313–320. PubMed Abstract \| Publisher Full Text\n\nKhabazian A, Tavakoli A, Soltani S, et al.: Comparison of Benzydamine Hydrochloride Mouthwash 0.15% and Ibuprofen in Reducing Postoperative Pain during 24 hours after Crown Lengthening: a Randomized Clinical Trial. Open Dent. J. 2021; 14: 66–70. Publisher Full Text\n\nPeddengatagari S, Mutyala SG: Efficacy of benzydamine hydrochloride mouthwash versus diclofenac tablet in postoperative pain after periodontal surgery: a comparative study. Int. J. Med. Biomed. Studies. 2020; 4(6): 47–51. Publisher Full Text\n\nValeri P, Morrone LA, Romanelli L, et al.: Aspirin-like drugs inhibit neuronally evoked responses in isolated guinea-pig ileum. Ann. Ist. Super. Sanita. 1993; 29(3): 379–385. PubMed Abstract\n\nMathivanan S, de la Torre-Martinez R , Wolf C, et al.: Effect of econazole and benzydamine on sensory neurons in culture. J. Physiol. Pharmacol. 2016; 67(6): 851–858. PubMed Abstract\n\nNikolaeva-Koleva M, Espinosa A, Vergassola M, et al.: Benzydamine plays a role in limiting inflammatory pain induced by neuronal sensitization. Mol. Pain. 2023; 19: 17448069231204191. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKuriyama A, Aga M, Maeda H: Topical benzydamine hydrochloride for prevention of postoperative sore throat in adults undergoing tracheal intubation for elective surgery: a systematic review and meta-analysis. Anaesthesia. 2018; 73(7): 889–900. PubMed Abstract \| Publisher Full Text\n\nLalićević S, Djordjević I: Comparison of benzydamine hydrochloride and Salvia officinalis as an adjuvant local treatment to systemic nonsteroidal anti-inflammatory drug in controlling pain after tonsillectomy, adenoidectomy, or both: an open-label, single-blind, randomized clinical trial. Curr. Ther. Res. Clin. Exp. 2004 Jul; 65(4): 360–372. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGolac-Guzina N, Novaković Z, Sarajlić Z, et al.: Comparative Study of the Efficacy of the Lysozyme, Benzydamine and Chlorhexidine Oral Spray in the Treatment of Acute Tonsillopharyngitis - Results of a Pilot Study. Acta Med. Acad. 2019 Aug; 48(2): 140–146. PubMed Abstract \| Publisher Full Text\n\nPassàli D, Volonté M, Passàli GC, et al.: Efficacy and safety of ketoprofen lysine salt mouthwash versus benzydamine hydrochloride mouthwash in acute pharyngeal inflammation: a randomized, single-blind study. Clin. Ther. 2001 Sep; 23(9): 1508–1518. PubMed Abstract \| Publisher Full Text\n\nBlanchard A, Yarom N, Levi L, et al.: Atask force of the Mucositis Study Group of the Multinational Association of Supportive Care in Cancer/International Society of Oral Oncology (MASCC/ISOO). Clinicians’ experience with topical benzydamine and morphine for the management of oral mucositis: adverse effects and barriers. Support. Care Cancer. 2022 Dec; 30(12): 10255–10262. PubMed Abstract \| Publisher Full Text\n\nPagano C, Giovagnoli S, Perioli L, et al.: Development and characterization of mucoadhesive-thermoresponsive gels for the treatment of oral mucosa diseases. Eur. J. Pharm. Sci. 2020 Jan 15; 142: 105125. PubMed Abstract \| Publisher Full Text\n\nShaji J, Vaswani T: Formulation optimization of benzydamine hydrochloride nanosponges loaded hydrogel for treatment against mouth ulcers. Int. J. Pharm. Sci. Res. 2020; 11(10): 4945–4956. Publisher Full Text\n\nSharma D, Sharma A, Garg R: Design, Development and In vitro/Ex vivo Evaluation of Mucoadhesive Buccal Film of Benzydamine Hydrochloride for the Effective Treatment of Aphthous Stomatitis. Recent Pat. Drug Deliv. Formul. 2018; 12(4): 277–294. PubMed Abstract \| Publisher Full Text\n\nMarudova M, Zahariev N, Milenkova S, et al.: Development and In-Vitro Characterization of Benzydamine-Loaded Chitosan Nanoparticles. Macromol. Symp. 2021; 395(1): 2000279. Publisher Full Text" }	[ { "id": "279009", "date": "05 Jun 2024", "name": "Jian-Xin Liu", "expertise": [ "Reviewer Expertise Kidney disease and inflammation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article provides an overview of benzydamine hydrochloride and a detailed analysis of its mechanism of action. Benzamine hydrochloride has been proven to be safe and effective in anti-inflammatory, antibacterial, and pain relief, and its research is an interesting topic. However, the article still has the following issues to consider. Comment 1 “Unlike other non-steroidal anti inflammatory drugs, benzydamine HCl does not inhibit cyclooxygenase or lipoxygenase.” The ending with \" Unlike other non-steroidal antiinflammatory drugs, benzydamine HCl does not inhibit cyclooxygenase or lipoxygenase.\" in the abstract is too abrupt, and a sentence can be added at the end. Unlike other nonsteroidal anti-inflammatory drugs, what happens if cyclooxygenase is not inhibited, and whether it improves or deteriorates. Comment 2 “The mechanisms of action of benzydamine HCl” The description of the mechanism of action of benzydamine HCl in \"The mechanisms of action of benzydamine HCl\" is too simplistic. Comment 3 “The role of benzydamine hydrochloride in prevention and treatment of sore throat: insights from the clinical data” It is best to add a table to make it clearer and more clear. How does benzidine hydrochloride affect these diseases of throat pain, and what data supports this viewpoint, presented in a table format for a more intuitive understanding. Comment 4 As a review paper, the literature cited in this paper is too outdated to reflect the latest research progress. Is there any literature support from the past three years. Comment 5 “Only a few studies did not confirm the effectiveness of prophylactic benzydamine HCl spray on POST following endotracheal intubation.”\nIs there any other literature here that proves this drug is ineffective? Comment 6 \"The role of benzydamine hydrochloride in prevention and treatment of sore throat” There is a lack of more in-depth insights into the clinical data here, and it is recommended to delete 1~2 articles inserted into the literature. Comment 7 “Research insights for novel benzydamine HCl formulations” There is little description of the new dosage form here, and there is a lack of recent advances.\nAbstract\nPain and inflammation are the consequences of sore throat, dental and oral procedures, infections, ulcers and head and neck chemotherapy/radiotherapy, and their management is of fundamental importance to avoid distress in patients. Benzydamine hydrochloride (HCl) is a topical indolic nonsteroidal anti-inflammatory drug, endowed with analgesic and anesthetic activity, and with antimicrobial (including both gram-positive and gram-negative bacteria) and antifungal properties (targeting Candida albicans and non-albicans strains), used in odontostomatology, otorhinolaryngology, and gynecology for its properties. This molecule has a lipophilic nature, showing high affinity with cell membranes and exhibiting membrane stabilization properties, resulting in local anesthesia, an effect related also to the interaction of the drug with cationic channels. In addition, benzydamine HCl is able to inhibit the production of pro-inflammatory cytokines, with consequent analgesia. Moreover, benzydamine HCl is able to inhibit leukocyte-endothelial interactions and platelet aggregation. Unlike other non-steroidal anti-inflammatory drugs, benzydamine HCl does not inhibit cyclooxygenase or lipoxygenase.\nHere we review the most updated clinical data available on benzydamine HCl local application as spray, mouthwash or gargling and evidence of its effectiveness in inflammatory and/or septic conditions in the otorhinolaryngology and odontostomatology settings, with particular reference to sore throat, oral inflammation, dental plaque, tonsillitis/tonsillectomy and chemo- or radiotherapy-induced oral mucositis. Novel formulations for oral administration of benzydamine HCl are also reviewed, including in situ gelling formulations to be sprayed onto the damaged oral mucosa. Finally, novel data on the potential role of benzydamine HCl in nociceptor excitability are introduced.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-350
https://f1000research.com/articles/13-349/v1	23 Apr 24	{ "type": "Study Protocol", "title": "VDR mRNA Expression And Serum Vitamin D Levels in Post-Covid Vaccinated Patients", "authors": [ "Sandesh Shende", "Jaishriram Rathored", "Sandesh Shende" ], "abstract": "The emergence of COVID-19 vaccines has reshaped the trajectory of the ongoing pandemic, offering hope for widespread immunity. Beyond conferring protection against SARS-CoV-2, these vaccines have exhibited intriguing immunomodulatory effects. This research explores the dynamic interplay among VDR mRNA expression levels, calcium (ionized and total), and intact parathyroid hormone (iPTH) concentrations in individuals post-COVID-19 vaccination. The Vitamin D Receptor (VDR) plays a pivotal role in immune regulation and is closely intertwined with calcium homeostasis. This study investigates the hypothesis that COVID-19 vaccination may induce alterations in VDR mRNA expression, subsequently influencing calcium metabolism and iPTH secretion. Our findings reveal dynamic shifts in VDR mRNA expression following COVID-19 vaccination, with distinct patterns observed across individuals. Concurrently, we observe ionized and total calcium levels alterations, hinting at potential links between VDR activity and calcium metabolism post-vaccination. Furthermore, iPTH levels exhibit intriguing fluctuations, suggesting a regulatory role of VDR in parathyroid hormone secretion. The integration of clinical outcomes and vaccine response data sheds light on the significance of these molecular and biochemical alterations. This research underscores the multifaceted impact of COVID-19 vaccination on VDR mRNA expression, calcium homeostasis, and iPTH regulation. Beyond the scope of vaccination, our findings may bear implications for immunomodulation in various disease contexts, particularly in individuals with pre-existing calcium-related disorders. In conclusion, our study unveils the intricate relationships among VDR mRNA expression, calcium levels, and iPTH concentrations in the context of post-COVID-19 vaccination. These discoveries extend our understanding of vaccine-induced immunomodulation and may pave the way for personalized vaccination strategies, while also opening new avenues for investigating the role of VDR in immune responses and calcium regulation beyond the pandemic.", "keywords": [ "Vitamin D Receptor", "mRNA expression", "COVID-19", "intact Parathyroid Hormone", "Calcium level", "Serum vitamin D" ], "content": "Introduction\n\nIn the global pursuit of ending the COVID-19 pandemic, vaccination campaigns have emerged as a beacon of hope, ushering in a new era of resilience and recovery. While vaccines have played a main role in mitigating the devastating impact of virus,1 they have also prompted numerous questions about their effects on the human body, especially in molecular biology.2 Among the myriad questions that have arisen, one has particularly intrigued scientists and clinicians alike: How do COVID-19 vaccines impact the expression of the Vitamin D Receptor (VDR) mRNA in the human body, and what could this mean for our understanding of immune responses and overall health?\n\nThe COVID-19 outbreak has challenged healthcare professionals throughout the world with challenges that have never been encountered before.3 Numerous lives have been saved as a result of the vital role that quick vaccine development and distribution have played in controlling the virus’s spread.4 But there is still much to learn about the complex interactions between vaccinations, the immune system’s function, and other biological functions.5\n\nThe VDR, a vital part of the immune system in humans, is well-known for its crucial function in controlling immunological responses, regulating pathways of inflammation, and maintaining general health.6 Vitamin D, also known as “sunshine vitamin,” plays a crucial part in regulating VDR expression.7–9 Variations in VDR mRNA levels of expression may affect how each person reacts to vaccines and viral illnesses, according to recent research.10\n\nGaining a thorough grasp of how COVID-19 immunization affects VDR mRNA expression is crucial as the globe struggles with COVID-19 and its continuous mutations.11 This information could provide insight into the long-term implications of side effects as well as the processes underlying them. Additionally, it can provide insightful information on individualized vaccination plans and the creation of innovative treatments to improve vaccine responses.\n\nIn this investigation, we set out to understand the complex molecular dynamics of VDR mRNA expression in post-COVID-vaccinated patients. I hope to give a comprehensive view of how COVID-19 vaccinations affect the expression of this important receptor by diving into the worlds of molecular biology, and immunology. In order to understand the molecular symphony that directs our immune response to COVID-19 immunization, our work makes use of cutting-edge methodologies, extensive data analysis, and multidisciplinary collaboration.\n\nI want to further my knowledge of the intricate relationships among vaccines, the immune system, and human genetics through this endeavour, bridging the gap between scientific curiosity and useful healthcare applications. As we journey through the labyrinthine pathways of VDR mRNA expression, my goal is not only to shed light on its modulation but also to illuminate new avenues for harnessing this knowledge to strengthen our defences against current and future pandemics.\n\n\nReview of literature\n\nUnderstanding the interplay between Vitamin D and the VDR is crucial in deciphering the complexities of post-vaccination immune responses.12 Vitamin D is known for its pleiotropic effects on the immune system, and the VDR serves as the key mediator in this process.13 The modulation of innate and adaptive immunological responses, cytokine synthesis, and T-cell activity have all been connected to vitamin D.6 Therefore, any changes in VDR expression may have profound effects on immunological homeostasis.6 The synthesis of calcitriol in monocytes and macrophages is likely necessary for vitamin D to exert immunomodulatory effects.14 To completely comprehend the overall impact of vitamin D on the human immune system, further questions need to be addressed.6\n\nSeveral studies have demonstrated the variable expression of VDR mRNA in different tissues and among individuals. Environmental factors, such as polymorphisms in VDR gene and exposure to sunlight, contribute to this variability.15 However, the specific impact of COVID-19 vaccination on VDR mRNA expression patterns remains a relatively unexplored territory.16 Investigating how vaccination influences these expression patterns is essential for understanding vaccine responsiveness and potential long-term effects.17\n\nAltered VDR mRNA expression may affect immune responses in multiple ways.18 It may influence the production of antimicrobial peptides, cytokines, and chemokines.19,20 Understanding these consequences could provide insights into vaccine efficacy and the risk of immune-related adverse events, offering guidance for tailored vaccination strategies.21\n\nExploring the modulation of VDR mRNA expression could open new avenues for therapeutic interventions.22 Fine-tuning VDR expression may offer ways to enhance vaccine responses in specific populations or mitigate adverse effects.23 Moreover, VDR agonists have been investigated for their potential in managing inflammatory and autoimmune conditions, making this receptor an intriguing target for future research.24\n\n\nResearch gap analysis\n\nOne of the primary research gaps in the field is the paucity of comprehensive studies examining VDR mRNA expression following COVID-19 vaccination.25 There is a pressing need for large-scale, multi-center studies encompassing diverse populations to capture the full spectrum of VDR expression changes post-vaccination.26\n\nWhile some studies have provided insights into VDR expression shortly after vaccination, there is a notable lack of research investigating the temporal dynamics of VDR mRNA expression.27 Understanding how VDR expression evolves over time, especially in the context of booster shots and potential long-term effects, is crucial for informed vaccination strategies.28\n\nThe VDR is expressed in a tissue-specific manner, with varying levels in different organs and cell types.29 Yet, research often overlooks the importance of tissue-specific analysis. A comprehensive examination of VDR mRNA expression across relevant tissues, such as immune cells, respiratory epithelium, and lymphoid organs, is essential to grasp the full immunological implications of vaccination.30\n\nWhile changes in VDR mRNA expression are intriguing, their functional consequences remain underexplored.31 Investigating the downstream effects of altered VDR expression on immune responses, and cytokine profiles is paramount to connect molecular changes with clinical outcomes.32\n\nEnvironmental factors like sunlight exposure are known to influence VDR expression.33 However, research often neglects these variables. Examining how these factors interact with vaccination-induced changes in VDR mRNA expression could provide insights into personalized vaccine responses.\n\nComparative studies between different COVID-19 vaccines and vaccine platforms are scarce.34 Investigating whether different vaccines induce distinct patterns of VDR mRNA expression could inform vaccine selection and development strategies.35\n\nWhile some studies hint at the therapeutic potential of modulating VDR expression,36 there is a dearth of research specifically designed to harness this knowledge for clinical applications.37 Developing targeted interventions based on VDR expression changes could revolutionize vaccine strategies and benefit populations with suboptimal responses.23\n\nResearch question: Is VDR mRNA expression and serum Vit D deficiency lead to susceptibility to various infections in post-COVID vaccinated patients?\n\n\nHypothesis\n\nTo study the VDR mRNA expression in post covid vaccinated patient and correlate with different biochemical parameters like Vit D level, Intact Parathyroid Hormone (iPTH) and calcium level (ionized and total) and try to rule out whether this mRNA expression is responsible for deficiency of Vit D and susceptible for covid infection.\n\nVDR mRNA Expression and serum Vit. D levels in Post COVID-Vaccinated Patients\n\n\n\n1. To study the mRNA expression levels of the VDR genes in PBMCs of post COVID-vaccinated patients.\n\n2. To identify the potential associations between VDR mRNA expression levels and other biochemical parameters in post-vaccinated patients.\n\n3. To study the Correlation of VDR mRNA expression with vit D, calcium (ionized & total) and iPTH levels\n\n4. To study the possible correlation of vitamin D deficiency in post covid infection and normal controls (Normal control is defined as “healthy Subjects without Covid infection”)\n\n\nMethods\n\nStudy design: Cross-sectional study\n\nPlace of study: Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi (Meghe), Wardha\n\nInformed consent form (ICF): All participants will be enrolled after obtaining ICF.\n\nParticipant recruitment: Participants will be recruited based on strict exclusion and inclusion criteria mentioned below\n\n\n\n1. Participants of either gender aged between 18-65 years\n\n2. Covid-19 Vaccination done (Covishield, Covaxin, Sputnik-V and other related brands)\n\n3. Free from Co-morbid diseases (TB, HIV, Diabetes, Hypertension, etc)\n\n4. Participants ready to provide written, informed consent.\n\n\n\n1. Pregnant and lactating Mother\n\n2. Comorbid conditions (TB, HIV, Diabetes, Hypertension)\n\n3. Those who have not received any vaccination for COVID-19\n\n4. Those who have received any vaccination other than COVID-19 in the last 5 years at the time of recruitment.\n\nHealthy subjects will be recruited from the general population with the same socioeconomic status and those who are free from any diseases and comorbidities.\n\nDemographic and clinical data: Structured questionaries will be used to collect demographic information, vaccination history, and relevant medical history from each participant.\n\nBlood sampling: Peripheral blood samples (5-10 ml) will be obtained from participants by a trained phlebotomist.\n\nIsolation of peripheral blood mononuclear cells (PBMCs): PBMCs will be collected from whole blood with the help of density gradient centrifugation protocol as per manufacturer instructions.\n\nRNA isolation: It will be done by Insta NX Mag16 automated Nucleic acid extractor machine and RNA Extraction kits, HiMedia Lab, India, followed by manufacturer’s instructions.\n\ncDNA synthesis and Real-time PCR: cDNA synthesis will be done in RT-PCR machine (QuantStudioTM 5 Real-Time PCR System, Thermo Fisher Scientific, Waltham, Massachusetts, USA) followed by reverse transcriptase PCR. After cDNA synthesis real-time PCR will be done as per manufacturer instructions followed by RTPCR kits.\n\nSunlight exposure assessment: Sunlight exposure history was assessed through participant questionnaires, including information on average daily sun exposure, and sunscreen use.\n\nData storage: All data, including demographic, clinical, and molecular data, were securely stored in Excel to ensure data integrity and participant confidentiality. Double data entry will be done to maintain the quality and integrity.\n\nStatistical analysis: For Statistical analysis, all data will be presented as mean standard deviation (SD) CV % and P-values for statistical significance. Comparison between Post Vaccinated COVID-19 patients with Healthy subjects will be done using unpaired T-test. All analyses will be performed using statistical SPSS software.\n\nParticipant confidentiality: All participants’ personal information and data will be kept confidential.\n\nInformed consent: Informed consent procedures will be followed, and participants will be informed about the study’s purpose, risks, and benefits.\n\nEthics approval: Applied and will be obtained before the study starts.\n\nThe study will be completed in 3 years, including participant recruitment, data collection, laboratory analyses, and data analysis.\n\nThe findings will be presented in the form of tables, graphs, and figures related to VDR mRNA expression and different biochemical other potential parameters used in the present study.\n\nThe findings will be discussed in the context of existing literature, and implications and will be able to draw the relevant conclusion.\n\nFormula:\n\nWhere: Z = 1.96 for a confidence level (α) of 95%,\n\np = Prevalence of Covid 19 vaccination in India 95%\n\ne = margin of error.\n\nn = 203\n\nThe sample size is 203 total subjects\n\n(for equal distribution of cases and control we will take 204 sample size)38\n\nIEC Approval: Got the approval of my Synopsis from Datta Meghe Institute of Higher Education and Research. IEC Approval Letter No. is DMIHER (DU)/IEC/2023/56.\n\nTrial Registration: Applied for Registration on CTRI website and Reference No. is. REF/2024/01/077535 AU.\n\nPrimary outcome\n\nTo identify the possible mechanism of VDR signalling molecules through mRNA expression leads to Vitamin D deficiency in post vaccinated covid patients.\n\nSecondary outcome\n\nTo address the factors responsible for defective VDR signalling of post vaccinated covid patients through different biochemical parameters (Vitamin D, Total Calcium, Ionized calcium, iPTH hormone).", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nMoghadas SM, Vilches TN, Zhang K, et al.: The impact of vaccination on COVID-19 outbreaks in the United States. medRxiv. 2021 Jan 2. 2020.11.27.20240051.\n\nRodrigues CMC, Plotkin SA: Impact of Vaccines; Health, Economic and Social Perspectives. Front. Microbiol. 2020 Jul 14; 11: 1526. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRazu SR, Yasmin T, Arif TB, et al.: Challenges Faced by Healthcare Professionals During the COVID-19 Pandemic: A Qualitative Inquiry From Bangladesh. Front. Public Health. 2021 Aug 10; 9: 647315. Publisher Full Text\n\nFang E, Liu X, Li M, et al.: Advances in COVID-19 mRNA vaccine development. Signal Transduct. Target. Ther. 2022 Mar 23; 7: 94.\n\nPulendran B, Ahmed R: Immunological mechanisms of vaccination. Nat. Immunol. 2011 Jun; 12(6): 509–517. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAranow C: Vitamin D and the Immune System. J Investig Med Off Publ Am Fed Clin Res. 2011 Aug; 59(6): 881–886. Publisher Full Text\n\nNair R, Maseeh A: Vitamin D: The “sunshine” vitamin. J. Pharmacol. Pharmacother. 2012 Jun; 3(2): 118–126. PubMed Abstract \| Publisher Full Text\n\nRathored J, Sharma SK, Singh B, et al.: Risk and outcome of multidrug-resistant tuberculosis: vitamin D receptor polymorphisms and serum 25(OH)D. Int. J. Tuberc. Lung Dis. 2012 Nov 1; 16(11): 1522–1528. PubMed Abstract \| Publisher Full Text\n\nRathored J, Sharma SK, Chauhan A, et al.: Low serum vitamin D in North Indian multi-drug resistant pulmonary tuberculosis patients: the role of diet and sunlight. Ann. Med. 2023 Dec 12; 55(2): 2291554. PubMed Abstract \| Publisher Full Text\n\nGhelani D, Alesi S, Mousa A: Vitamin D and COVID-19: An Overview of Recent Evidence. Int. J. Mol. Sci. 2021 Sep 29; 22(19): 10559. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYap C, Ali A, Prabhakar A, et al.: Comprehensive literature review on COVID-19 vaccines and role of SARS-CoV-2 variants in the pandemic. Ther. Adv. Vaccines Immunother. 2021 Nov 24; 9: 251513552110597. Publisher Full Text\n\nChillon TS, Demircan K, Heller RA, et al.: Relationship between Vitamin D Status and Antibody Response to COVID-19 mRNA Vaccination in Healthy Adults. Biomedicines. 2021 Nov 18; 9(11): 1714. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKamen DL, Tangpricha V: Vitamin D and molecular actions on the immune system: modulation of innate and autoimmunity. J. Mol. Med. Berl. Ger. 2010 May; 88(5): 441–450. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRosa MD, Malaguarnera M, Nicoletti F, et al.: Vitamin D3: a helpful immuno-modulator. Immunology. 2011 Oct; 134(2): 123–139. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUsategui-Martín R, De Luis-Román DA, Fernández-Gómez JM, et al.: Vitamin D Receptor (VDR) Gene Polymorphisms Modify the Response to Vitamin D Supplementation: A Systematic Review and Meta-Analysis. Nutrients. 2022 Jan 15; 14(2): 360. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHatmal MM, Al-Hatamleh MAI, Olaimat AN, et al.: Side Effects and Perceptions Following COVID-19 Vaccination in Jordan: A Randomized, Cross-Sectional Study Implementing Machine Learning for Predicting Severity of Side Effects. Vaccines. 2021 Jun; 9(6): 556. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZimmermann P, Curtis N: Factors That Influence the Immune Response to Vaccination. Clin. Microbiol. Rev. 2019 Mar 13; 32(2): e00084–e00018. Publisher Full Text\n\nKongsbak M, Levring TB, Geisler C, et al.: The Vitamin D Receptor and T Cell Function. Front. Immunol. 2013 Jun 18; 4: 148. Publisher Full Text\n\nGombart AF: The vitamin D–antimicrobial peptide pathway and its role in protection against infection. Future Microbiol. 2009 Nov; 4: 1151–1165. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYoussef DA, Miller CW, El-Abbassi AM, et al.: Antimicrobial implications of vitamin D. Dermatoendocrinology. 2011 Oct; 3(4): 220–229. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFalahi S, Kenarkoohi A: Host factors and vaccine efficacy: Implications for COVID-19 vaccines. J. Med. Virol. 2022 Apr; 94(4): 1330–1335. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nApprato G, Fiz C, Fusano I, et al.: Natural Epigenetic Modulators of Vitamin D Receptor. Appl. Sci. 2020 Jan; 10(12): 4096. Publisher Full Text\n\nSadarangani S, Whitaker JA, Poland GA: “Let There Be Light”: The Role of Vitamin D in the Immune Response to Vaccines. Expert Rev. Vaccines. 2015; 14(11): 1427–1440. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang S, Li A, Wang J, et al.: Vitamin D Receptor: A Novel Therapeutic Target for Kidney Diseases. Curr. Med. Chem. 2018 Aug; 25(27): 3256–3271. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYap C, Ali A, Prabhakar A, et al.: Comprehensive literature review on COVID-19 vaccines and role of SARS-CoV-2 variants in the pandemic. Ther. Adv. Vaccines Immunother. 2021 Nov 24; 9: 251513552110597. Publisher Full Text\n\nBrisse M, Vrba SM, Kirk N, et al.: Emerging Concepts and Technologies in Vaccine Development. Front. Immunol. 2020 Sep 30; 11: 583077. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBass JJ, Nakhuda A, Deane CS, et al.: Overexpression of the vitamin D receptor (VDR) induces skeletal muscle hypertrophy. Mol. Metab. 2020 Aug 7; 42: 101059. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu N, Joyal-Desmarais K, Ribeiro PAB, et al.: Long-term effectiveness of COVID-19 vaccines against infections, hospitalisations, and mortality in adults: findings from a rapid living systematic evidence synthesis and meta-analysis up to December, 2022. Lancet Respir. Med. 2023 May; 11(5): 439–452. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPike JW, Meyer MB, Lee SM, et al.: The vitamin D receptor: contemporary genomic approaches reveal new basic and translational insights. J. Clin. Invest. 127(4): 1146–1154. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGreiller CL, Martineau AR: Modulation of the Immune Response to Respiratory Viruses by Vitamin D. Nutrients. 2015 May 29; 7(6): 4240–4270. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZenata O, Vrzal R: Fine tuning of vitamin D receptor (VDR) activity by post-transcriptional and post-translational modifications. Oncotarget. 2017 Feb 25; 8(21): 35390–35402. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAggeletopoulou I, Thomopoulos K, Mouzaki A, et al.: Vitamin D–VDR Novel Anti-Inflammatory Molecules—New Insights into Their Effects on Liver Diseases. Int. J. Mol. Sci. 2022 Jul 30; 23(15): 8465. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShraim R, MacDonnchadha C, Vrbanic L, et al.: Gene-Environment Interactions in Vitamin D Status and Sun Exposure: A Systematic Review with Recommendations for Future Research. Nutrients. 2022 Jun 30; 14(13): 2735. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMorales-Núñez JJ, Muñoz-Valle JF, Machado-Sulbarán AC, et al.: Comparison of three different COVID-19 vaccine platforms (CoronaVac, BTN162b2, and Ad5-nCoV) in individuals with and without prior COVID-19: Reactogenicity and neutralizing antibodies. Immunol. Lett. 2022 Dec; 251-252: 20–28. Publisher Full Text\n\nAl Fayez N, Nassar MS, Alshehri AA, et al.: Recent Advancement in mRNA Vaccine Development and Applications. Pharmaceutics. 2023 Jul; 15(7): 1972. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDankers W, Colin EM, van Hamburg JP , et al.: Vitamin D in Autoimmunity: Molecular Mechanisms and Therapeutic Potential. Front. Immunol. 2017 Jan 20; 7: 697. Publisher Full Text\n\nGlowka E, Stasiak J, Lulek J: Drug Delivery Systems for Vitamin D Supplementation and Therapy. Pharmaceutics. 2019 Jul 18; 11(7): 347. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChoudhary R, Choudhary RR, Pervez A: COVID-19 Vaccination and Gaps in India. Cureus. 2023 Apr; 15(4): e37490. PubMed Abstract \| Publisher Full Text" }	[ { "id": "285926", "date": "14 Jun 2024", "name": "Gaurav Kaushik", "expertise": [ "Reviewer Expertise Molecular Biology", "Molecular Diagnostics", "Clinical Research", "Molecular Genetics", "Infectious Diseases." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper proposes an investigation into the effects of COVID-19 vaccination on Vitamin D Receptor (VDR) mRNA expression and its relationship with calcium metabolism and intact parathyroid hormone (iPTH) levels. The study aims to explore the immunomodulatory effects of COVID-19 vaccines beyond their primary role in providing immunity against SARS-CoV-2. By examining the interplay among VDR mRNA expression, calcium levels, and iPTH concentrations, the research seeks to uncover potential mechanisms underlying vaccine-induced changes in immune and calcium homeostasis. This study is particularly relevant as it addresses an underexplored aspect of COVID-19 vaccination and can have significant implications for personalized vaccination strategies and the management of individuals with pre-existing calcium-related disorders.\nMajor Points: 1. The study addresses a novel aspect of COVID-19 vaccination by focusing on VDR mRNA expression and its downstream effects on calcium metabolism and iPTH levels.\n2. The hypothesis is well-defined, aiming to explore the relationship between VDR mRNA expression and various biochemical parameters post-vaccination.\n3. The objectives are clear and align well with the overall aim of the study, providing a structured approach to investigating the proposed research questions.\nConstructive Feedback: Overall, the proposed study is well-conceived and addresses a pertinent and novel question in the context of COVID-19 vaccination.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-349
https://f1000research.com/articles/13-347/v1	23 Apr 24	{ "type": "Study Protocol", "title": "Randomised control trial comparing postoperative analgesia between nalbuphine and fentanyl as an adjuvant with intrathecal levobupivacaine for lower abdominal gynaecological surgeries", "authors": [ "SAELY PAUNIKAR", "Dr. Sanjot Ninave", "Dr. Sanjot Ninave" ], "abstract": "Background Effective post-operative pain management is crucial for patient comfort and recovery following lower abdominal gynaecological surgeries. This study protocol outlines a randomised control trial designed to compare the efficacy and safety of two intrathecal adjuvants, nalbuphine and fentanyl, in conjunction with hyperbaric levobupivacaine for postoperative analgesia.\n\nMethods The study will be conducted at the Department of Anaesthesiology, Jawaharlal Nehru Medical College, DMIMS (DU), and affiliated institutions. Sixty eligible patients aged 35-75 years undergoing lower abdominal gynaecological surgeries under subarachnoid block will be randomly assigned to one of two groups. Group A will receive nalbuphine with levobupivacaine, while Group B will receive fentanyl with levobupivacaine. Patients will be monitored for the duration of post-operative analgesia, onset of sensory and motor block, hemodynamic effects, and side effects.\n\nOutcomes The primary outcome is the comparison of post-operative analgesia duration between nalbuphine and fentanyl. Secondary outcomes include assessing sensory and motor block onset, hemodynamic changes, ephedrine usage, and side effects.\n\nAim To evaluate the efficacy and safety of intrathecal nalbuphine and fentanyl as adjuvants with hyperbaric levobupivacaine for postoperative analgesia in lower abdominal gynaecological surgeries.", "keywords": [ "Intrathecal", "Nalbuphine", "Fentanyl", "Levobupivacaine", "Gynecological surgeries", "postoperative analgesia" ], "content": "Introduction\n\nEffective post-operative pain management is a cornerstone of modern healthcare, as it directly influences patient comfort, recovery, and overall satisfaction with medical interventions. Lower abdominal gynaecological surgeries, including procedures such as hysterectomies and ovarian surgeries, often present unique challenges in the context of pain management. Patients undergoing these surgeries require a balance between adequate postoperative analgesia and minimising adverse effects to facilitate a smooth recovery process.1\n\nIntrathecal anaesthesia, particularly when combined with adjuvants, is a well-established method for managing perioperative pain in lower abdominal surgeries.2 The choice of adjuvant, however, can significantly impact the quality and duration of post-operative pain relief. Nalbuphine and fentanyl are two commonly employed adjuvants, each with distinct pharmacological properties and potential advantages in this context.3\n\nNalbuphine, a synthetic opioid, exhibits mixed agonist-antagonist properties at opioid receptors, which may provide potent analgesia while minimising the risk of respiratory depression and other opioid-related side effects.4 Fentanyl, a highly potent opioid, offers rapid onset and profound analgesic effects but may be associated with a higher risk of certain adverse events. Therefore, selecting the optimal intrathecal adjuvant is a critical consideration for healthcare providers.5\n\nThis study protocol outlines a randomised control trial designed to compare the efficacy and safety of intrathecal nalbuphine and fentanyl when used as adjuvants with hyperbaric levobupivacaine for postoperative analgesia in lower abdominal gynaecological surgeries. The primary objective is to assess the duration of post-operative analgesia. At the same time, secondary outcomes include the onset of sensory and motor block, hemodynamic effects, ephedrine usage, and the incidence of side effects. The results of this study are anticipated to provide valuable insights into the optimal choice of intrathecal adjuvants for pain management in lower abdominal gynaecological surgeries. By enhancing our understanding of the benefits and potential risks associated with nalbuphine and fentanyl, this research may improve clinical practice and patient outcomes in this specific surgical population.\n\n\n\n1. To compare the duration of postoperative analgesia between intrathecal nalbuphine and intrathecal fentanyl when administered as adjuvants with hyperbaric levobupivacaine in lower abdominal gynaecological surgeries.\n\n\n\n1. To compare the onset of the sensory and motor block between intrathecal nalbuphine and intrathecal fentanyl in conjunction with hyperbaric levobupivacaine.\n\n2. To assess the impact of intrathecal nalbuphine and intrathecal fentanyl on hemodynamic parameters during lower abdominal gynaecological surgeries and the requirement for ephedrine to manage hypotension.\n\n3. To evaluate and compare any potential side effects associated with the use of intrathecal nalbuphine and intrathecal fentanyl in combination with hyperbaric levobupivacaine for postoperative analgesia.\n\n\nMethods\n\nStudy setting: The study will be conducted at the Department of Anaesthesiology at Jawaharlal Nehru Medical College, DMIMS (DU), Acharya Vinoba Bhave Rural Hospital (AVBRH), and Datta Meghe Institute of Medical Sciences, Sawangi (M), Wardha.\n\n\n\n1. Patients aged between 35-75 years old.\n\n2. Patients scheduled for lower abdominal gynaecological surgeries under subarachnoid block.\n\n3. The duration of surgery is expected to be at most 120 minutes.\n\n4. Patients classified under the American Society of Anesthesiologists (ASA) as class I or II.\n\n5. Patients with Mallampati classification I or II.\n\n6. Patients who willingly provide informed written consent to participate in the study.\n\n\n\n1. Patients who do not provide valid informed written consent.\n\n2. Patients with ASA grades III and IV.\n\n3. Patients with active infection at the injection site for subarachnoid block.\n\n4. Patients diagnosed with significant neurological and musculoskeletal diseases.\n\n5. Patients with known bleeding disorders.\n\n6. Patients who are taking anticoagulants.\n\n7. Patients with a documented history of allergy to local anaesthetics, fentanyl, and nalbuphine.\n\nThis study will include two groups:\n\nGroup A: Participants in this group will receive the following intrathecal medication:\n\n• Inj. Levobupivacaine 3 ml (15 mg) of 0.5%.\n\n• Nalbuphine 0.1 ml (1 mg).\n\n• 0.4 ml of normal saline.\n\nGroup B: Participants in this group will receive the following intrathecal medication:\n\n• Inj. Levobupivacaine 3 ml (15 mg) of 0.5%.\n\n• Fentanyl 0.5 ml (25 mcg).\n\nPatients in both groups will undergo spinal anaesthesia after a thorough pre-anaesthetic checkup and confirmation of their vital parameters before the start of surgery Table 1. Patients who experience failed spinal anaesthesia or require additional interventions will be excluded from the study.\n\nThe primary difference between the two groups lies in the adjuvants administered intrathecally - Group A receiving nalbuphine and Group B receiving fentanyl in conjunction with levobupivacaine. The study will assess the impact of these different adjuvants on postoperative analgesia and related parameters.\n\nPrimary outcome:\n\n1. The primary objective of this study is to compare the duration of postoperative analgesia between intrathecal nalbuphine and intrathecal fentanyl when administered as adjuvants with hyperbaric levobupivacaine for lower abdominal gynaecological surgeries. The primary outcome will be assessed by measuring the time from the end of surgery to the first request for analgesia by the patient.\n\nSecondary outcomes:\n\n1. Onset of sensory and motor block: The time to onset of sensory and motor block will be compared between the nalbuphine and fentanyl groups. Sensory block onset will be determined by assessing the interval between the injection of the local anaesthetic drug and the loss of sensation to a pinprick at a predetermined dermatomal level. Motor block onset will be assessed using a modified Bromage scale.\n\n2. Hemodynamic effects and ephedrine usage: The study will evaluate the impact of intrathecal nalbuphine and intrathecal fentanyl on hemodynamic parameters during lower abdominal gynaecological surgeries. The requirement for intravenous ephedrine to manage hypotension, defined as a systolic blood pressure less than 90 mm Hg or a drop of more than 20% from baseline, will be recorded.\n\n3. Side-effects: Any potential side effects associated with the use of intrathecal nalbuphine and intrathecal fentanyl in combination with hyperbaric levobupivacaine will be documented and compared. This includes adverse events such as nausea, vomiting, pruritus, and respiratory depression.\n\nTo achieve the target sample size of 60 patients who meet the inclusion criteria, the following recruitment process will be followed:\n\n1. Patient counseling and explanation: Potential study participants will be identified during the pre-anesthetic check-up. Patients will be thoroughly counselled and explained the study’s purpose, procedures, and potential benefits. They will be informed about the need for the study and the expected outcomes, particularly the potential for enhanced intraoperative and postoperative pain relief with either nalbuphine or fentanyl as adjuvants in their spinal anaesthesia.\n\n2. Informed consent: Patients who express their willingness to participate in the study will receive a detailed informed consent form. The form will outline the study’s objectives, procedures, potential risks, and benefits. Patients can ask questions and clarify any concerns they may have. Those who provide valid informed written consent will be enrolled in the study.\n\n3. Patient selection: Patients recruited for the study will meet all the inclusion criteria, ensuring they fall within the specified age range, require lower abdominal gynaecological surgeries under the subarachnoid block, and meet the specified ASA and Mallampati classifications.\n\n4. Preoperative evaluation: Each recruited patient will undergo a thorough preoperative evaluation the day before surgery to assess their overall fitness. This evaluation will include various measurements and tests, as outlined in the protocol.\n\n5. Randomization: Patients will be randomly assigned to one of the two study groups, Group A (nalbuphine) or Group B (fentanyl), using a predetermined randomisation method, such as computer-generated random numbers. Randomisation will be conducted by personnel not directly involved in the study to ensure unbiased allocation.\n\n6. Blinding: Patients and the anesthesiologist responsible for recording perioperative data will be blinded to the study drug assignment. This double-masked approach will ensure that the patients and the medical personnel know the administered drug at the end of the study.\n\nThe research will be conducted on 60 patients who meet all the inclusion criteria and provide informed written consent to participate. These patients will be divided into two study groups: Group A (n=30), which will receive nalbuphine with levobupivacaine, and Group B (n=30), which will receive fentanyl with levobupivacaine.\n\nThe sample size calculation is based on the formula for the difference between two means:\n\nWhere:\n\n• Zα is the level of significance at 5% (95% confidence interval) = 1.96.\n\n• Zβ is the power of the test = 80% = 0.84.\n\n• σ1 is the standard deviation of the onset of sensory block in Group C = 1.05.\n\n• σ2 is the standard deviation of the onset of sensory block in Group M = 0.44.\n\n• Δ is the difference in the means of the two groups (3.04-1.95 = 0.61), and k is set to 1.\n\nPlugging these values into the formula:\n\nn ≈ 30 patients needed in each group (Reference study6)\n\n\n\n1. The allocation of patients into the two study groups, Group A and Group B, will be done using a randomisation process. A predetermined randomisation method, such as computer-generated random numbers or randomisation software R studio Version 4.3.1, will ensure that the allocation is unbiased and not influenced by the researchers or healthcare providers.\n\n\n\n1. This study will be conducted as a double-blind trial. Double blinding means that the patients and the medical personnel involved in the study will be blinded to the drugs administered. The blinding ensures that neither the patients nor the healthcare providers are aware of whether the patient is receiving nalbuphine or fentanyl with levobupivacaine.\n\n2. To maintain blinding, the study conductors and anesthesiologists responsible for patient care will only know about the study drug administered at the end of the study. The actual drugs (nalbuphine or fentanyl) will be concealed, and the patients will not be informed about which drug they are receiving.\n\n3. Blinding is essential to eliminate potential biases and ensure that the patients’ or healthcare providers’ expectations or beliefs do not influence the study results. Blinding is a crucial method to maintain the integrity of the research and reduce the risk of bias in the study’s outcomes.\n\n\n\n1. Preoperative data collection: Before surgery, preoperative data will be collected, including demographic information, patient history, and clinical assessments. This may include age, sex, medical history, ASA classification, and Mallampati classification.\n\n2. Randomization and blinding: Patients will be randomly assigned to either Group A (nalbuphine with levobupivacaine) or Group B (fentanyl with levobupivacaine) using a predetermined randomisation method. The allocation will be concealed to maintain double-blinding.\n\n3. Intraoperative monitoring: Patients will be continuously monitored for hemodynamic parameters during the surgery, including peripheral oxygen saturation, non-invasive blood pressure, and pulse rate. Data will be recorded at regular intervals throughout the procedure.\n\n4. Onset of sensory and motor block: The time to onset of sensory and motor blocks will be recorded. Sensory block onset will be determined by assessing the interval between the injection of the local anaesthetic drug and the loss of sensation to a pinprick at a predetermined dermatomal level. Motor block onset will be assessed using a modified Bromage scale.\n\n5. Hemodynamic changes and medication use: Any hemodynamic changes, such as hypotension (systolic blood pressure < 90 mm Hg) or bradycardia (heart rate < 50 beats/min), will be documented. In cases of hypotension, intravenous ephedrine (5-10 mg) will be recorded. For bradycardia, the administration of intravenous atropine (0.6 mg) will be documented.\n\n6. Sedation assessment: Intraoperative sedation levels will be assessed using the Ramsey Sedation Score at baseline (before the subarachnoid block), post-op before shifting to the Post Anesthesia Care Unit, and at the time of the first complaint of pain.\n\n7. Postoperative data collection: In the recovery and postoperative ward, patients will be routinely followed up for pain assessment using the Visual Analogue Scale (VAS). Patients will be educated about the VAS scale, and their pain scores will be assessed regularly.\n\n8. Assessment of primary and secondary outcomes: The primary outcome, the duration of postoperative analgesia, will be assessed by measuring the time from the end of surgery to the first request for analgesia by the patient. The secondary outcomes will also be assessed and recorded, including sensory and motor block characteristics, hemodynamic changes, ephedrine usage, and side effects.\n\n9. Data monitoring: Data will be monitored by a resident doctor not involved in the study. They will ensure the accurate collection and recording of data as per the study protocol.\n\n10. Data management: Collected data will be stored and managed according to standard research and data management practices, ensuring data integrity and confidentiality.\n\nThis study has been approved by the Datta Meghe Institute of Higher Education and Research (approval number: DMIMS (DU)/IEC/2022/94; approval date: 20/07/2022). CTRI (REF/2023/06/06827; 13/06/2023).\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has yet to start. After the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nIntrathecal anaesthesia has become an indispensable tool in the armamentarium of anesthesiologists, offering precise and efficient pain management for various surgical procedures, including lower abdominal gynaecological surgeries. The choice of intrathecal adjuvants plays a pivotal role in determining the quality and duration of postoperative analgesia while managing the risks associated with opioid use. The present study is designed to investigate the comparative efficacy of two intrathecal adjuvants, nalbuphine and fentanyl, in combination with hyperbaric levobupivacaine for postoperative pain control.\n\nOne of the primary objectives of this study is to assess the duration of postoperative analgesia achieved with intrathecal nalbuphine and fentanyl. Extending the duration of effective pain relief is crucial for patient comfort and recovery. In a study by Arghya Mukherjee et al., intrathecal nalbuphine demonstrated a significantly longer duration of postoperative analgesia compared to intrathecal fentanyl in orthopaedic surgery patients.7 Our study aims to evaluate whether similar results can be observed in the context of lower abdominal gynaecological surgeries.\n\nAnother critical aspect of intrathecal anaesthesia is sensory and motor block onset. The rapidity with which the block is achieved impacts the overall quality of the anaesthetic technique. In a study by Biswas et al., nalbuphine was shown to produce a faster onset of sensory block compared to fentanyl when used as an adjuvant to intrathecal hyperbaric bupivacaine in urological surgeries.8 Our study will investigate whether the same trend is observed in the context of gynaecological surgeries.\n\nHemodynamic stability during surgery is of paramount importance. The choice of intrathecal adjuvant can influence the incidence of hypotension and bradycardia. A study by Mahnaz S Shah et al. found that nalbuphine, when used as an adjuvant to intrathecal bupivacaine, resulted in significantly less hypotension compared to fentanyl in patients undergoing cesarean sections.9 We will closely monitor our study’s hemodynamic parameters and ephedrine use to evaluate any differences.\n\nThe incidence of side effects, such as nausea, vomiting, pruritus, and respiratory depression, is a critical consideration when selecting intrathecal adjuvants. With its unique receptor binding profile, Nalbuphine may offer advantages in terms of a lower risk of respiratory depression. However, fentanyl’s rapid onset of action and potent analgesic effects may necessitate a balanced assessment. A comprehensive understanding of the side-effect profiles of these adjuvants is essential to ensure patient safety and satisfaction.10 This study protocol offers a robust framework for systematically comparing nalbuphine and fentanyl as intrathecal adjuvants in the specific context of lower abdominal gynaecological surgeries. The results of this study are expected to provide valuable insights for clinicians in selecting the most appropriate adjuvant to optimise post-operative pain control while minimising adverse effects.", "appendix": "References\n\nOhnesorge H, Günther V, Grünewald M, et al.: Postoperative pain management in obstetrics and gynecology. J. Turk. Ger. Gynecol Assoc. 2020; 21: 287–297. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan AL, Singh RB, Tripathi RK, et al.: A comparative study between intrathecal dexmedetomidine and fentanyl as adjuvant to intrathecal bupivacaine in lower abdominal surgeries: A randomized trial. Anesth. Essays Res. 2015; 9: 139–148. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrabhakaraiah UN, Narayanappa AB, Gurulingaswamy S, et al.: “Comparison of Nalbuphine Hydrochloride and Fentanyl as an Adjuvant to Bupivacaine for Spinal Anesthesia in Lower Abdominal Surgeries:” A Randomized, Double-blind Study. Anesth. Essays Res. 2017; 11: 859–863. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEdinoff AN, Kaplan LA, Khan S, et al.: Full Opioid Agonists and Tramadol: Pharmacological and Clinical Considerations. Anesthesiol. Pain Med. 2021; 11: e119156. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGupta R, Verma R, Bogra J, et al.: A Comparative study of intrathecal dexmedetomidine and fentanyl as adjuvants to Bupivacaine. J. Anaesthesiol. Clin. Pharmacol. 2011; 27: 339–343. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNazli B, Oguzalp H, Horasanli E, et al.: The Effects on Sensorial Block, Motor Block, and Haemodynamics of Levobupivacaine at Different Temperatures Applied in the Subarachnoid Space. Biomed. Res. Int. 2014; 2014: 132687–132687. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMukherjee A, Pal A, Agrawal J, et al.: Intrathecal nalbuphine as an adjuvant to subarachnoid block: What is the most effective dose? Anesth. Essays Res. 2011; 5: 171–175. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBajwa BS, Singh AP, Rekhi AK: Comparison of intrathecal clonidine and fentanyl in hyperbaric bupivacaine for spinal anesthesia and postoperative analgesia in patients undergoing lower abdominal surgeries. Saudi J. Anaesth. 2017; 11: 37–40. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShah MS, Masoodi T, Hussain SY, et al.: Nalbuphine as an Intrathecal Adjuvant to 0.5% Hyperbaric Bupivacaine in Two Different Doses for Postoperative Analgesia After Abdominal Hysterectomy: A Prospective, Randomized, Double-Blind Control Study. Cureus. 14: e25044. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharma A, Chaudhary S, Kumar M, et al.: Comparison of nalbuphine versus fentanyl as intrathecal adjuvant to bupivacaine for orthopedic surgeries: A randomized controlled double-blind trial. J. Anaesthesiol. Clin. Pharmacol. 2021; 37: 529–536. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "288368", "date": "24 Jun 2024", "name": "Philippe Richebe", "expertise": [ "Reviewer Expertise Acute pain management", "Transition from acute to chronic pain", "Regional anesthesia", "Adjuvants for pain managements", "Nociception and EEG monitoring" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a study protocol proposed here. Lower abdominal gynaecological surgeries could be more precise and better describe to avoid biases due to too many different types of approach which lead to different type and level of postoperative pain. Please avoid too much heterogeneity. Nalbuphine and fentanyl will be added to the intrathecal injection of hyperbaric levobupivacaine. Intraoperative pain assessments and patients’ satisfaction could also be reported, not only intraoperative side effects or postoperative outcomes. Primary outcome is duration of postoperative analgesia. This could be more precisely described. A better definition is warranted: time for 1st need or requirement of analgesics? Time for the pain level to reach a certain threshold? … Please provide a clear and precise definition, also in the abstract. Impact on hemodynamic parameters: the same protocol for blood pressure management as well as fluid loading must be respected and described precisely, so there is no bias due to heterogeneity in hypovolemia prior or during the anesthesia. The procedure of blinding for the anesthesiologist and the research team who will follow-up on the patients must be clearly stated. Power calculation: it seems that the power calculation was made using “onset of the sensory block”, but the primary objective of the study is not this outcome. The primary outcome is Time for requirement of analgesia. Power calculation must be done on the primary objective.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] }, { "id": "314397", "date": "29 Aug 2024", "name": "Samar Rafik Amin", "expertise": [ "Reviewer Expertise Anaesthesia", "pain therapy", "perioperative medicine", "and intensive care" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis protocol was proposed for conducting a comparative study between fentanyl and nalbuphine as adjuvant to local anesthetics during the subarachnoid block for lower abdominal gynecological surgeries based on randomized study design. the protocol is well written, however i have the following concerns:\n1- Title includes the description as randomized controlled trial, but no control group in the methods. two active comparators will be compared without control group! It is better to identify the type of operation as open not laparoscopic.\n2- In the abstract : Move the aim paragraph at the end of the background and the no need for outcomes paragraph separated from the methods. also, write the study design and duration in the methods\n3- The introduction is where you build your hypothesis based on the previous literature. the study point of search has been utilized in many researches before ( fentanyl versus nalbuphine as local anesthetic adjuvants so, what are the conflicts or issues regarding previous reports , your study will try to resolve? clear this point in your hypothesis in the introduction. Also, avoid repetition of your objectives many times .. enumerate them briefly in your study objectives then mention their details in the methods\n4- Methods: Add the anticipated study duration time. Clarify the procedure as open not laparoscopic in the inclusion criteria Mention the dermatomal level that will be established as onset level, and the bromage score that will be considered as onset of motor block. Define the type of hemodynamic parameters (MAP -SBP- DBP- HR- CVP ... etc) that will be measured and the time points of measurements define the duration time for Side effects follow up.\n5- In sample size calculation: what is group C and group M .. Please add the reference from which you obtained the mean and SD of the onset of sensory block. Additionally, sample size should be calculated based on the study 1ry outcome (duration of analgesia) not the 2ry outcome\nAlso, add a section to define the statistical analysis method.\n6- Allocation concealment is a process of concealing the allocation sequence from the investigator responsible for recruiting patients, it is different from randomization. Some standard methods of ensuring allocation concealment include sequentially numbered, opaque, sealed envelopes (SNOSE); sequentially numbered containers; pharmacy controlled randomization; and central randomization.\n7- Define who will perform the block and the operation .. the same team or different ones ?\n8- There is a discrepancy between the parameters that were mentioned in the measured outcomes and the collected data as you add the sedation score and the VAS score .. please unify your intended outcomes.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-347
https://f1000research.com/articles/13-346/v1	23 Apr 24	{ "type": "Study Protocol", "title": "A study to assess the effectiveness of planned teaching regarding the harmful effect of oil application on anterior fontanels of newborn among post-natal mothers", "authors": [ "Kajal Raut", "MS. Manjusha mahakarkar", "Kajal Raut" ], "abstract": "The anterior fontanelle, sometimes known as the “soft spot,” is an important anatomical component in neonates that allows brain growth and development. Possible harm is caused by such practices, as they may result in unfavorable outcomes, such as skin irritation and a delay in fontanelle closure. The goal of this study was to see how effective pre-planned education was at informing postpartum women about the dangers of applying oil to newborns’ anterior fontanelles. The study was conducted with the goal of increasing the understanding of the adverse effects of oil application on the anterior fontanels of newborns among postnatal mothers, The study will be thoroughly described to the participants, and their written Consent will be taken for the participate in the study and publishing the information. Sampling technique will be convenient. Population and sampling techniques will be examined. Mothers will be the target group with a sample size of 60 postnatal mothers. The sample will be drawn using The Purposive sampling approach. Prior authorization will be acquired from the designated hospitals’ higher authority. The inclusion criteria will be used to select samples. Information will be gathered from the hospital’s obstetric ward. First, pretest knowledge of the adverse effects of applying oil to newborns’ anterior fontanels among postnatal mothers was assessed. Postnatal mothers will be taught about the detrimental effects of placing oil on the anterior fontanels of their newborns. The post-test assessment of knowledge regarding the adverse effects of applying oil to anterior fontanels was performed after 7 days. If the hypothesis of our study is helpful in improving mothers’ knowledge in the post-test rather than pre-test following the intended training.", "keywords": [ "Newborn", "Anterior", "Fontanelles", "Application", "Harmful." ], "content": "Introduction\n\nThe fragile, delicate bodies of babies necessitate extra care and attention throughout their first few days of life. The infant’s anterior fontanelle, a soft part of the skull where the cranial bones have not yet fused, must be maintained.1 Despite the fact that this area is already delicate and sensitive, some cultural norms or well-meaning but wrong views have encouraged the use of oils in the anterior fontanelle.2\n\nThe purpose of this introduction is to highlight the need for adequate infant care practices and shed light on the detrimental consequences of oil application on babies’ anterior fontanelles. The anterior fontanelle, also known as the “soft spot,” is a membrane-covered space in the baby’s skull that allows it to grow and bend throughout the early stages of development.3 Oils or other substances applied to the anterior fontanelle in many cultures can improve brain development, increase brain growth, or even fend off evil spirits.4\n\nFirst, certain oils may include allergens or irritants that might result in skin reactions or infections when in contact with a baby’s sensitive skin. Second, oils can hinder sweat from normal evaporation, increase body heat retention, and increase the newborn’s vulnerability to heat-related disorders. In addition, improper soft spot handling during oil delivery may result in mechanical injuries such as pressure on the fontanelle or an inadvertent puncture, which can lead to serious problems such as infections or brain damage.5 Promoting evidence-based practices and educating parents and communities about the dangers of applying oils to the anterior fontanelle are crucial tasks for healthcare providers and caregivers.\n\nEncouragement of suitable infant care practices, such as routine washing, keeping the environment clean, and avoiding superfluous practices, can significantly lower the risk of neonatal injuries. Finally, the anterior fontanelle of a newborn is a delicate and vulnerable structure that requires special care and preservation.6 Applying oils to this sensitive part of the baby’s head may have negative consequences, including skin difficulties, heat-related disorders, and the possibility of mechanical harm. By raising awareness of the negative consequences of oil application on the anterior fontanelle, we may work to protect newborn’s health and safety and develop evidence-based practices for baby care.7\n\nThe purpose of this study was to assess how well postpartum mothers understood the harmful effects of oil application on their newborn’s anterior fontanelles through a structured education session.\n\n\n\n1. To improve knowledge regarding the harmful effects of oil application on the anterior fontanels of newborns among postnatal mothers.\n\n2. To Evaluate the effectiveness of planned teaching regarding the harmful effects of oil on anterior fontanels of newborn postnatal mothers.\n\nThe participants’ written agreement will be sought from their mothers at Sawangi Meghe Hospital in Wardha, Maharashtra, as this study is cantered on postnatal mothers. Pre- and post-test knowledge will be collected after obtaining ethical approval with the inclusion and exclusion criteria based on creating planned instructions for mothers to impart knowledge. Mothers were the study’s target demographic for the interventional approach research design, which consisted of a single group pre- and post-test. The target population of this study will be mothers. participants In the study will be new mothers. A non-probability sampling technique will employed in this investigation. 60 mothers will make up a convenient sample size for this investigation. The study tools consisted of structured lectures and questionnaires. The variable consists of two variables: independent and dependent. The awareness of mothers regarding the detrimental impact of oil application on a newborn’s anterior fontanelles will the dependent variable, while the planned education of postnatal mothers on this knowledge will the independent variable. We plan to gather this information using questionnaires. Descriptive and inferential statistics will used for interpretation, followed by report-writing.\n\n\n\n• Postnatal mothers admitted and presenting in ward.\n\n• Postnatal mothers who can read and write English and Marathi.\n\n• Mother available during data collection.\n\n\n\n• Postnatal mothers who are known cases of psychiatric illness.\n\n• Postnatal mothers who had already been a part of a similar study from 6 months to 1 year.\n\n• Mother who is not willing to participate in the study.\n\nIn this study, an interventional method will be used in conjunction with a pretest and post-test design. We recruited 60 postpartum mothers. The total knowledge of postnatal mothers will be measured using a structured knowledge questionnaire. Sections A and B constitute the two sections that constitute the tool. The demographic information in Section A includes age, education level, type of home, monthly income, and prior awareness of the harmful effects of oil application on a newborn’s anterior fontanel. Ten items comprise Section B’s structured knowledge questionnaire on negative impacts. Experts received the instrument to guarantee content authenticity. Following consultation with the guide and expert guidance, the instrument underwent necessary modifications. The details will be gathered between October 5, 2023, and November 5, 2023.\n\nA standardized questionnaire will be used to assess the participants’ current knowledge of the detrimental effects of oil application on the anterior fontanels of newborns among postnatal mothers.\n\nWe will create a 30-minute teaching plan on the adverse effects of oil application on newborn anterior fontanels.\n\nA post-test questionnaire will be administered after seven days to assess the success of the intended education on the adverse effects of oil application on the anterior fontanels of newborns.\n\nThe primary goal of this study was to improve postnatal mothers’ understanding of the adverse effects of oil application on the anterior fontanels of newborns. This was determined by comparing postnatal pre- and post-test results.\n\nA feedback survey and questionnaires used to assess participant satisfaction with the planned educational program and their assessment of its worth in terms of knowledge improvement were used to assess participant satisfaction. Planned instruction had little effect on postnatal moms’ practice of administering oil to their newborns’ anterior fontanels. It monitors whether there is a decrease in the amount or frequency of oil applied to this sensitive spot, indicating an improvement in the procedures.\n\n“Eligibility criteria are the postnatal mothers who are interested in participating in the study.”\n\nThe sample size calculation is based on a similar study.\n\nIn the present study, the sample is postnatal mothers selected hospitals.\n\nSample size – 60\n\nI took this sample size from this reference to obtain the sample size.\n\nCochran’s formula for sample size (this formula is referred as per Cochran W.G. et al)8\n\nZ = 1.96\n\nP = Subjects received jaundice education\n\n= 11% = 0.11\n\nd = Desired error of margin = 8% = 0.08\n\nT-tests and other analytical tests will be also performed. All statistical analyses will be performed using SPSS version 27.09 p0.05 as the significance threshold. This research will be conducted at the A.V.B.R.H. hospital Sawangi Meghe Wardha.\n\nThe pre-test and post-test will be used to assess knowledge levels; knowledge will change as a result of the intended training, and knowledge will improve.\n\nBias is conceivable at the statistical analysis level and can be mitigated by utilizing appropriate analytical software and double checking of the outputs.\n\nWhen the study is completed, it will be published in Scopus, Web of Science, PubMed, and other nursing-related indexed journals.\n\nCurrently, the study is yet to be started.\n\n\nDiscussion\n\nIn this study, a descriptive research design was adopted. Purposive sampling was used to obtain 157 samples from a single institution. A structured dichotomous questionnaire and demographic data were used to gather the subjects’ data. Results: The information acquired from 157 samples was analyzed using descriptive statistics. (149) Of the mothers, 95% massaged their infants with oil before bathing. (83) 53% of mothers have given their infants over-the-counter medications. When their babies’ skin turned yellow, (87) 55% of the mothers gave their children ash, soot, powder, or dried cow dung; (115) 73% of the mothers exposed their children to sunshine. (129) To avoid bad eyesight, 82% of mothers apply “Kajal” to their infant’s face. (92%). 59% of mothers follow the adage “An empty cradle should not be moved.” In summary, the study’s conclusions showed a significant correlation between parents’ cultural practices and beliefs about baby care and demographic traits, including family structure and religion. The postnatal ward should offer regular health education on the dos and don’ts of newborn care. This will help curtail the detrimental customs.10 To determine the customary remedies Turkish mothers utilized to treat their newborns’ jaundice, a cross-sectional descriptive study was conducted. In one university hospital and one public children’s hospital in Sanliurfa, 229 mothers of newborns aged 0-28 days were assessed using knowledge questionnaires on the customs and beliefs of mothers regarding jaundice. Data were analyzed using descriptive and inferential methods. According to this study, mothers apply traditional practices when dealing with health issues such as jaundice, and these methods are important to them. In addition, mothers mentioned employing dangerous traditional therapies for neonatal jaundice, such as severing the space between the infant’s brows with a knife, which is not customary in other societies. The study’s conclusions were used to support the recommendation that families should receive education regarding the consequences of conventional techniques and that future research examining the effects of this type of education should be guided by these findings.3 All babies admitted to the paediatrics department at SVP PGIP & SCBMCH, CUTTACK, or those who presented to the outpatient department at SVPPGIP, CTC, were eligible for this descriptive study a two-year span beginning on August 1, 2014, and ending on July 31, 2016. Critically ill neonates were excluded from the study. A structured dichotomous questionnaire was developed, verified, and used to gather, examine, and aggregate the data. Of the 170 mothers, 64.1% were under 25 years of age, and 61.8% were part of a combined or extended family. Over 40% (40.6%) of mothers had a family income of less than Rs. 9794, the majority (>80%) were in Matric, and 91.2% of mothers were identified as Hindu. Eleven infants were wrapped in old fabric within 30 min of delivery, making up the bulk of newborns (69.4%). A total of 95.9% of mothers massaged their infants with oil prior to bathing, and 92.4% massaged their infants with oil. week on earth. Of the mothers who began breastfeeding, 54% did so within one hour, 24.7% did so between one and four hours, and 15.9% did so more than that. Ethic-related issues.11\n\nThe institutional ethics committee approved the title of the Study with reference number DMIHER (DU)/IEC/2023/1133 ON DATE 01/07/2023 this approval has been granted on the assumption that the proposed research work will be carried out in accordance with the ethical guideline prescribed by central ethics committee on human research (C.E.C.H.R.).", "appendix": "Data availability\n\nNo dada associated with this article.\n\n\nAcknowledgements\n\nI would like to thanks Ms. Manjusha Mahakarkar for her invaluable advice, Mr. Vijay Babar for his assistance with the sample size calculation and analytic design, and Mr. Laximakant Umate for his assistance in developing the study Protocol.\n\n\nReferences\n\nNethra N, Udgiri R: A study on traditional beliefs and practices in newborn care among mothers in a tertiary health care centre in Vijayapura, North Karnataka. Int. J. Commun. Med. Public Health. 2018 Feb 24; 5: 1035. Publisher Full Text\n\nOumer M, Tazebew A, Alemayehu M: Anterior Fontanel Size Among Term Newborns: A Systematic Review and Meta-Analysis. Public Health Rev. 2021; 42: 1604044. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReshma, Sujatha R: Cultural practices and beliefs on newborn care among mothers in a selected hospital of mangalore taluk. J. Health Allied Sci. Nu. 2014 jun 1; 04: 021–026. Publisher Full Text\n\nFurtado LMF, Filho JA d CV, Freitas LS, et al.: Anterior fontanelle closure and diagnosis of non-syndromic craniosynostosis: a comparative study using computed tomography. J. Pediatr. 2021 Nov 30; 98(4): 413–418. Publisher Full Text\n\nBangari A, Thapliyal S, Ruchi R, et al.: Traditional beliefs and practices in newborn care among mothers in a tertiary care centre in Dehradun, Uttarakhand, India. Int. J. Commun. Med. Public Health. 2019 May 27; 6: 2600. Publisher Full Text\n\nArumugam L, Kamala S, Ganapathy K, et al.: Traditional Newborn Care Practices in a Tribal Community of Tamilnadu, South India: A Mixed Methods Study. Indian J. Community Med. Off. Publ. Indian Assoc. Prev. Soc. Med. 2023 Feb; 48(1): 131. Publisher Full Text\n\nAnsong J, Asampong E, Adongo PB: Socio-cultural beliefs and practices during pregnancy, child birth, and postnatal period: A qualitative study in Southern Ghana. Cogent Public Health. 2022 Dec 31; 9(1): 2046908. Publisher Full Text\n\nYılmaz A: Cochran 1977 Sampling Techniques Third Edition.[cited 2024 Feb 18]. Reference Source\n\nStamm A: FileCR. IBM SPSS Statistics 27.0.1 IF026; 2022 [cited 2024 Feb 18]. Reference Source\n\nSharma A, Pandya A: Traditional Beliefs and Practices in New Born Care at Different Communities-Literature Review. Int. J. Nurs. Care. 2017 Jan 1; 5: 80. Publisher Full Text\n\nNethra N, Udgiri R: A study on traditional beliefs and practices in newborn care among mothers in a tertiary health care centre in Vijayapura, North Karnataka. Int. J. Commun. Med. Public Health. 2018 Feb 24; 5: 1035. Publisher Full Text" }	[ { "id": "285281", "date": "01 Jul 2024", "name": "Mary Ani-Amponsah", "expertise": [ "Reviewer Expertise Newborn health", "child migration." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe protocol has relevance for practice and potential to improve newborn health but it has several gaps.Â Harmful practices are best addressed before they happen; hence will the researchers sample mothers with newborns who have applied the oil to the fontanel or any mother seeking postnatal service?Â Â\n\nThe protocol does not specify why postnatal mothers alone are the population of interest. Antenatal mothersÂ and newborn gatekeepers could be included as the population of interest if the aim is to generate the evidence needed to change this cultural practice or generate evidence needed to address this issue.Â Postnatal mothers often are not the ones implementing the practice of oil application to fontanels due to cultural norms.Â Besides, conducting training and assessing maternal knowledge and the practice of oil application during the postnatal period leaves room for non compliance to best newborn practices.\nThere is heavy confusion in the language text presentation between the proposal language and the study conduct; it appears the study has already been conducted; language editing needed.Â The discussion section needs to be improved; the content is linked to a different study not linked so well to the study topic.Â\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-346
https://f1000research.com/articles/13-345/v1	23 Apr 24	{ "type": "Study Protocol", "title": "Interventional cross-sectional study of extra-cardiac anomalies in children with congenital heart diseases in tertiary care hospital in central India", "authors": [ "Rahul Y Khandelwal", "Jayant Vagha", "Jayant Vagha" ], "abstract": "Background Congenital heart diseases (CHDs) in neonates often present complex clinical scenarios, and the association with extra-cardiac anomalies adds a layer of intricacy to their management. This study protocol outlines a comprehensive investigation into the prevalence and clinical outcomes of extra-cardiac anomalies in neonates diagnosed with CHDs. The study addresses gaps in current knowledge regarding this specific patient population, situated in the Neonatology unit of Jawaharlal Nehru Medical College and AVBR Hospital, Sawangi, Wardha, Central India.\n\nMethods Utilizing a descriptive, interventional cross-sectional design, the study will enrol neonates meeting inclusion criteria—diagnosis of CHDs with concurrent extra-cardiac anomalies. Rigorous data collection will involve detailed clinical histories, thorough physical examinations, and the compilation of relevant investigations, including diagnostic imaging and laboratory results. The study’s temporal scope spans three years, ensuring a robust representation of the neonatal population. Statistical analysis, employing chi-square tests, Fischer’s tests, and independent t-tests, will explore relationships between demographic and clinical characteristics, contributing to a nuanced understanding of this complex interplay.\n\nExpected Results Anticipated outcomes of this study include a precise estimation of the prevalence of extra-cardiac anomalies in neonates with CHDs. Furthermore, insights into this specific patient cohort’s clinical outcomes and management will be gained. The study aims to unravel the intricate relationship between demographic factors, clinical characteristics, and extra-cardiac anomalies in CHD patients through meticulous data analysis. These findings are poised to inform clinical practice, enhance patient care strategies, and set the stage for further research in this critical area of neonatal medicine.", "keywords": [ "Congenital Heart Diseases", "Neonates", "Extra-cardiac Anomalies", "Tertiary Care Hospital", "Cross-sectional Study", "Clinical Outcomes" ], "content": "Introduction\n\nCongenital heart diseases (CHDs) constitute a significant burden of morbidity and mortality among neonates globally, posing multifaceted challenges to healthcare systems.1 While advancements in medical science have improved diagnostics and interventions, the coexistence of extra-cardiac anomalies in neonates with CHDs introduces additional layers of complexity to their clinical management.2 This study protocol outlines a comprehensive investigation into the prevalence and clinical outcomes of extra-cardiac anomalies in neonates diagnosed with CHDs within a tertiary care hospital in Central India.\n\nGlobally, CHDs are recognised as the most prevalent group of congenital anomalies, affecting approximately 8 in 1,000 live births.3 These anomalies often necessitate intricate medical interventions, making CHDs a leading cause of neonatal morbidity and mortality.4 The simultaneous presence of extra-cardiac anomalies further compounds the challenges faced by clinicians in providing effective and tailored care.\n\nThe prevalence of CHDs varies across populations, and recent evidence suggests that the presence of extra-cardiac anomalies might influence both the clinical course and outcomes of neonates with CHDs.5 Despite advancements in medical research, there is a paucity of population-specific data on the association between CHDs and extra-cardiac anomalies in the Central Indian context. Understanding the nuanced relationship between these anomalies is crucial for optimising diagnostic strategies, clinical management, and resource allocation.\n\nThe primary aim of this interventional cross-sectional study is to investigate the association between extra-cardiac anomalies and congenital heart diseases (CHDs) in neonates within a tertiary care hospital in Central India.\n\n\n\n1. To estimate the prevalence of extra-cardiac anomalies in neonates diagnosed with congenital heart diseases.\n\n2. To evaluate and compare the clinical outcomes of neonates with CHDs who have additional extra-cardiac anomalies against those without such anomalies.\n\n3. To explore the relationship between demographic factors (e.g., gestational age, birth weight) and clinical characteristics (e.g., serum electrolyte levels) with extra-cardiac anomalies in CHD patients.\n\n4. To identify and analyse potential etiological factors contributing to the co-occurrence of extra-cardiac anomalies in neonates with CHDs.\n\n5. To document the clinical course, interventions, and management strategies employed in neonates with CHDs and extra-cardiac anomalies, providing insights into the challenges and opportunities for improving patient care.\n\n\nMethod\n\nThis study will adopt a descriptive, interventional cross-sectional design.\n\nThe study population comprises neonates diagnosed with congenital heart diseases (CHDs) admitted to the Neonatology unit at the Department of Pediatrics, Jawaharlal Nehru Medical College & AVBR Hospital, Sawangi, Wardha, Central India.\n\nThe study will be conducted at the Neonatology unit within the hospital. This unit encompasses the Outpatient Department (OPD), Pediatrics Ward, Pediatric Intensive Care Unit (PICU), and Neonatal Intensive Care Unit (NICU).\n\nNeonates meeting the following criteria will be included in the study:\n\n• Diagnosis of congenital heart diseases (CHDs).\n\n• Presence of extra-cardiac anomalies.\n\nNeonates meeting any of the following criteria will be excluded from the study:\n\n• Refusal of consent from parents or guardians.\n\nDuring this study, several potential biases may influence the interpretation of results. Selection bias is a concern, given that the study population is drawn from a tertiary care hospital, possibly skewing the representation towards individuals seeking specialised care. Efforts will be made to diversify the study population by including patients from various socioeconomic backgrounds, and findings will be interpreted with the acknowledgement of potential selection biases.\n\nInformation bias is another consideration, particularly in the retrospective components relying on medical records. To minimise this bias, the study team will adhere to standardised protocols for data collection, and regular training sessions will be conducted. Cross-referencing with multiple sources will be employed to validate the accuracy of the collected data.\n\nRecall bias may affect the quality of information parents or guardians provide regarding the neonate’s medical history. To address this, the research team will use detailed and structured questionnaires, and interviews will be conducted as promptly as possible after relevant events to ensure accurate recollection.\n\nChallenges related to inclusion criteria may arise, particularly when the diagnosis of congenital heart diseases (CHDs) or extra-cardiac anomalies is not straightforward. To navigate this, the study will establish clear and standardised diagnostic criteria, with consultations sought from specialists to ensure accurate inclusion. Diagnostic confirmation will be based on comprehensive reviews of medical records and expert consultations.\n\nRefusal of consent poses a potential challenge, as excluding cases based on consent refusal may introduce bias. Those who decline participation may differ systematically from those who provide consent. Mitigation strategies include effective communication with parents or guardians, providing clear and understandable information about the study, and emphasising sensitivity to concerns and questions to encourage informed consent.\n\nAddressing these potential biases and enrollment challenges is essential to bolster the study’s internal validity, ensuring that the findings accurately reflect the relationship between extra-cardiac anomalies and congenital heart diseases in the population under investigation.\n\nBefore embarking on the data collection process, the study will begin with a crucial step: obtaining informed consent from the parents or legal guardians of neonates participating. Clear explanations about the study’s purpose, procedures, potential risks, and benefits will be provided, and participants will be assured of the voluntary nature of their involvement, along with the commitment to maintaining confidentiality. The study will unfold within the Neonatology unit at the Department of Pediatrics in Jawaharlal Nehru Medical College and AVBR Hospital, Sawangi, Wardha, Central India. This unit encompasses the Outpatient Department (OPD), Pediatrics Ward, Pediatric Intensive Care Unit (PICU), and Neonatal Intensive Care Unit (NICU).\n\nIdentifying eligible participants is the next step, with neonates meeting the inclusion criteria—diagnosis of congenital heart diseases (CHDs) with accompanying extra-cardiac anomalies—being selected during their visits to the various units mentioned earlier. To ensure a systematic approach to data collection, a pre-designed and pre-validated proforma will serve as the primary tool. This comprehensive document covers demographic details, medical history, clinical examination findings, diagnostic results, and specifics about interventions and management.\n\nCollecting pertinent information begins with a detailed clinical history, drawing on perinatal, family, and prenatal aspects. This data will be sourced from medical records and interviews with parents or guardians. Trained healthcare professionals will conduct a meticulous physical examination focusing on cardiac and extra-cardiac anomalies. In addition to clinical history and examination, relevant investigations such as diagnostic imaging, echocardiograms, and laboratory results (including serum electrolytes) will be meticulously recorded from the patient’s medical records.\n\nThroughout their stay in the Neonatology unit, the clinical course of each neonate will be closely documented. This includes any complications encountered, treatments administered, and interventions employed. Once the necessary information has been gathered, a crucial step involves entering the data into a Microsoft Excel spreadsheet. This task will be performed by trained research personnel, ensuring accuracy and consistency in the recorded data.\n\nTo maintain the quality and integrity of the data, regular checks for accuracy and completeness will be implemented as part of a robust quality control process. Any discrepancies or missing information will be promptly addressed by verifying the source documents. The study will progress to the statistical analysis stage after the data collection phase. This analysis, guided by the study protocol, will explore relationships between demographic and clinical characteristics, shedding light on the nuanced association between extra-cardiac anomalies and congenital heart diseases in neonates within the hospital setting.\n\n\n\n1. Prevalence estimation: The investigation seeks to provide a precise estimate of the prevalence of extra-cardiac anomalies among neonates diagnosed with CHDs in the specified population. This information is crucial for healthcare planning and resource allocation.\n\n2. Clinical outcomes: By evaluating the clinical course, morbidity, and mortality of neonates with both CHDs and extra-cardiac anomalies, the study aims to uncover patterns and associations that may influence patient outcomes. This knowledge can guide clinicians in tailoring interventions for this specific patient population.\n\n3. Demographic and etiological factors: The study will explore the influence of demographic factors such as gestational age and birth weight on the occurrence of extra-cardiac anomalies in CHD patients. Additionally, it will investigate potential etiological factors contributing to the coexistence of these conditions, providing valuable insights into risk factors and possible preventive measures.\n\n4. Clinical management challenges: Documenting the clinical course and management strategies employed for neonates with CHDs and extra-cardiac anomalies will shed light on the challenges faced by healthcare providers. This information can inform the development of targeted interventions and improve the overall quality of care for these complex cases.\n\n5. Contribution to existing knowledge: The study aims to contribute to the existing body of knowledge regarding the association between CHDs and extra-cardiac anomalies, particularly in Central India. The findings may enhance existing clinical guidelines and pave the way for further research in neonatal cardiology.\n\nThe calculation of the sample size for this study involves several vital parameters. With a defined population size (N) of 1000, a hypothesised percentage frequency of the outcome factor (p) set at 8% with a margin of error of ±5%, and confidence limits (d) set at 5% of 100, the sample size is determined to be 114. The design effect (DEFF), used for cluster surveys and, in this case, is considered 1, is factored into the calculation. Additionally, a confidence level of 95% is applied to ensure the reliability and statistical significance of the study findings. Consequently, the calculated sample size of 114 is expected to provide a representative and robust dataset for investigating the association between extra-cardiac anomalies and congenital heart diseases in neonates within the specified tertiary care hospital setting.\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol (Reference number: DMIHER (DU)/IEC/2023/900. Date:31-03-2023). Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study is yet to be started. After the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nUnderstanding the prevalence of extra-cardiac anomalies in neonates with CHDs is essential for informing clinical decision-making and resource allocation. Previous studies have demonstrated varying prevalence rates globally, emphasising the need for population-specific investigations.5 By focusing on a Central Indian population, this study seeks to contribute data that can enhance the accuracy of prevalence estimates and provide insights into the disease burden in this region.\n\nExploring the clinical outcomes of neonates with CHDs and additional extra-cardiac anomalies is paramount for optimizing patient care. The literature indicates that the presence of extra-cardiac anomalies can significantly impact prognosis and management strategies.6 This study aims to provide a comprehensive understanding of the challenges encountered in the management of these complex cases, potentially guiding the development of tailored intervention strategies.\n\nThe examination of demographic factors such as gestational age and birth weight, alongside an exploration of potential etiological factors, adds depth to our understanding of the complex interplay between genetic and environmental influences in the development of CHDs and extra-cardiac anomalies.3 The proposed study aligns with current research trends that emphasize the importance of elucidating these factors to inform preventive measures and genetic counseling.\n\nThe adoption of a descriptive, interventional cross-sectional study design provides a snapshot of the prevalence and clinical outcomes in a specific timeframe, allowing for efficient data collection and analysis. While the study is conducted within a tertiary care hospital, the findings can contribute valuable insights that may be applicable to similar settings in Central India.\n\nThe proposed statistical analysis, including chi-square tests, Fischer’s tests, and independent t-tests, reflects a robust approach to exploring relationships between demographic and clinical characteristics. This aligns with best practices in quantitative research, enhancing the rigor and validity of the study’s conclusions.7\n\nAnticipated results from this study will likely contribute to the existing body of knowledge by shedding light on the prevalence and clinical implications of extra-cardiac anomalies in neonates with CHDs in Central India. The findings can inform evidence-based clinical guidelines and may serve as a foundation for future longitudinal studies and interventions aimed at improving outcomes in this vulnerable population.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nRepository: Proforma for the data collections ‘Interventional Cross-sectional study of extra-cardiac anomalies in children with congenital heart diseases in tertiary care hospital in central India’, https://doi.org/10.5281/zenodo.10147069. 8\n\n\nReferences\n\nBernier P-L, Stefanescu A, Samoukovic G, et al.: The challenge of congenital heart disease worldwide: epidemiologic and demographic facts. Semin. Thorac. Cardiovasc. Surg. Pediatr. Card. Surg. Annu. 2010; 13: 26–34. PubMed Abstract \| Publisher Full Text\n\nAlvarado JL, Bermon A, Florez C, et al.: Outcomes and Associated Extracardiac Malformations in Neonates from Colombia with Severe Congenital Heart Disease. Pediatr. Cardiol. 9 October 2023; 45: 55–62. PubMed Abstract \| Publisher Full Text\n\nvan der Linde D , Konings EEM, Slager MA, et al.: Birth prevalence of congenital heart disease worldwide: a systematic review and meta-analysis. J. Am. Coll. Cardiol. 2011; 58: 2241–2247. Publisher Full Text\n\nHoffman JIE, Kaplan S: The incidence of congenital heart disease. J. Am. Coll. Cardiol. 2002; 39: 1890–1900. Publisher Full Text\n\nJenkins KJ, Correa A, Feinstein JA, et al.: Noninherited risk factors and congenital cardiovascular defects: current knowledge: a scientific statement from the American Heart Association Council on Cardiovascular Disease in the Young: endorsed by the American Academy of Pediatrics. Circulation. 2007; 115: 2995–3014. PubMed Abstract \| Publisher Full Text\n\nMahle WT, Clancy RR, Moss EM, et al.: Neurodevelopmental outcome and lifestyle assessment in school-aged and adolescent children with hypoplastic left heart syndrome. Pediatrics. 2000; 105: 1082–1089. PubMed Abstract \| Publisher Full Text\n\nAltman DG, Schulz KF, Moher D, et al.: The revised CONSORT statement for reporting randomized trials: explanation and elaboration. Ann. Intern. Med. 2001; 134: 663–694. Publisher Full Text\n\nSindhuja BG: Proforma for the data collections ‘Prospective comparative randomized clinical study for the comparison of two different doses of dexmedetomidine with bupivacaine in pediatric caudal anesthesia for infraumbilical surgeries in a tertiary hospital in central India’. Zenodo. 2023. Publisher Full Text" }	[ { "id": "351534", "date": "06 Jan 2025", "name": "Kwadwo Danso", "expertise": [ "Reviewer Expertise N/A" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study identifies an important clinical conundrum of public health essence worth exploring. The methodology is sound with well-outlined and achievable outcomes. However, the authors did not mention how they would acquire the controls for the study per their second objective. Nonetheless, the assurance of participant privacy, and confidentiality has been documented alongside the acquisition of ethical clearance. They have anticipated potential biases and acknowledged the limitations of the study. There were no typographical errors.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-345
https://f1000research.com/articles/13-344/v1	23 Apr 24	{ "type": "Study Protocol", "title": "Efficacy of a Tailored COMET Protocol Combined with Medication on Vibratory Perception and SkinConductance in Diabetic Neuropathy- A Protocol for Randomized Controlled Trial", "authors": [ "Raghumahanti Raghuveer", "Sharath Hullumani V", "Moh’d Irshad Qureshi", "Raghumahanti Raghuveer", "Moh’d Irshad Qureshi" ], "abstract": "This research attempts to evaluate the effectiveness of a customized COMET protocol in conjunction with medicine for the treatment of diabetic neuropathy, with vibratory perception and skin conductance being the main focus. Participants will be allocated to either the intervention group, which will get the customized COMET protocol and medicine, or the control group, which will receive standard medication alone, in a randomized controlled trial. Validated measurement instruments will be used in the trial to evaluate variations in skin conductance and vibratory perception both at baseline and during the course of the investigation. Strict adherence to ethical rules will guarantee the safety and well-being of participants. This study intends to provide important insights into the holistic management of diabetic neuropathy by examining the effects of the customized COMET protocol in conjunction with medication on vibratory perception and skin conductance. This could result in better treatment plans and an improvement in the quality of life for those who are affected.\nCTRI Reference Number CTRI/2023/07/055366,https://ctri.nic.in/Clinicaltrials/rmaindet.php?trialid=89691&EncHid=88073.73654&modid=1&compid=19,20/07/2023", "keywords": [ "Diabetic Neuropathy", "Foot", "Rehabilitation", "Skin Conductance", "Research Protocol" ], "content": "Introduction\n\nThese days, diabetes is thought to be one of the main causes of morbidity and death.1 The International Diabetes Federation has released updated statistics showing that 463 million people worldwide have diabetes and 374 million are at risk of becoming type 2 diabetes mellitus (T2DM).2 In India, the number of individuals with diabetes is expected to increase from approximately 77 million in 2019 to 134.2 million by 2045.2 Numerous issues, such as microvascular and macrovascular consequences, are brought on by diabetes.3–5\n\nDiabetic neuropathy is the most prevalent and alarming consequence of diabetes mellitus (DM). Peripheral, focal, proximal, or autonomic can all be described. Over 40 million diabetics worldwide suffer from neuropathy.6 Diabetic peripheral neuropathy (DPN) is defined by the American Diabetes Association (ADA) as “the presence of symptoms and/or signs of peripheral nerve dysfunction in people with diabetes after the exclusion of other causes.7 It affects particular nerve system regions8 causing morbidity and raising the cost of diabetic care.9 Up to 50% of instances of this long-term diabetic consequence are asymptomatic.10,11 Additionally, 40–60% of amputations of the lower extremities are caused by it.12\n\nDPN symptoms might be silent and go unnoticed, or they can be subjective and transient,13 resembling symptoms of other illnesses. It may result in extremely painful symptoms or loss of feeling.14 Consequently, the preferred technique for diagnosing peripheral neuropathy is clinical examination.15 Significant abnormalities in touch and pain sensitivity, kinaesthesia, lower-limb proprioception, and vibration sense are common symptoms of diabetic peripheral neuropathy (DPN), which is brought on by the stimulation of neuronal death and restriction of nerve regeneration.16 Sensory alterations in the “glove-and-stocking” distribution are the primary indicator of it.17\n\nWe don’t know the actual prevalence of DPN. According to studies, the percentage of diabetes patients with neuropathy can range from 10% to 90%, depending on the definition and techniques employed. In surveys of Indian patients, DPN has been reported in 26–31% of cases.18 DPN is difficult to treat, and there are few medications available. Tricyclic antidepressants, opioids, gabapentin, pregabalin, serotonin and norepinephrine reuptake inhibitors, and gabapentin are common therapy drugs.19\n\nFrequent exercise lowers body weight enhances insulin sensitivity and blood glucose control, and lowers the risk of neuropathy in diabetic individuals. The standard treatment for obesity and diabetes mellitus involves nutrition and increased physical activity.20 Research suggests that those with type 1 diabetes are more likely than those with other types of diabetes to exercise. The data demonstrates that practice interventions can enhance diabetes control. The majority of research have shown that it is beneficial to carry out training treatments between 8 weeks and 12 months for diabetes patients who have a peripheral neuropathy risk factor for diabetic foot ulcers. Significant increases in physical activity have been observed in several investigations, without a corresponding rise in injury risk. If health care is incomplete, foot ulcers may develop, which is the most common cause of hospitalization and amputation.21 Usually, the combination of various treatments, including pharmacotherapy, physiotherapy, and orthotic devices are used to maintain biomechanical parameters, physiological patterns, and at last, for wound healing.22\n\nInsulin therapy, including pharmacotherapy and lifestyle interventions, is considered a conventional treatment for preventing diabetes complaints.23\n\nThe objectives of the present study are:\n\n1. To determine the effectiveness of a comprehensive COMET Protocol when given along with medication on vibratory perception in subjects with Diabetic Polyneuropathy.\n\n2. To determine the effectiveness of a comprehensive COMET Protocol when given along with medication on skin conductance in subjects with Diabetic Polyneuropathy.\n\n3. To determine the effectiveness of a comprehensive COMET Protocol when given along with medication on the Quality of Life in subjects with Diabetic Polyneuropathy.\n\nThis protocol has been registered with CTRI and Reg No. CTRI/2023/07/055366, https://ctri.nic.in/Clinicaltrials/rmaindet.php?trialid=89691&EncHid=88073.73654&modid=1&compid=19 Date: 20/07/2023.\n\nThis study will be conducted with written informed consent from all participants. Ethical approval was received from the Datta Meghe Institute of Higher Education and Research (DU).\n\nIEC:DMIHER Date of approval: July 7th 2023 institutional ethics committee REF/2023/07/070102.\n\nIt is a two-arm parallel group, equal allocation superiority trial.\n\nThis study will be conducted with written informed consent from all participants. Participants will be chosen from inpatient and outpatients from Neurophysiotherapy Outpatient Department, AVBRH, Sawangi, Meghe, Wardha, Maharashtra, following acceptance from the institutional ethics committee of DMIHER. Once given consent and assent, these participants will be divided into two groups by simple random sampling method and allocation will be done through Sequentially Numbered Opaque Sealed Envelope (SNOSE) method into the Experimental group and Control group. The experimental group will be receiving COMET protocol for one hour each day, 6 days per week for 4 weeks. The participants of this group will continue with their diabetic neuropathy medication along with physiotherapy. The control group will be receiving their medication for diabetic polyneuropathy and general exercises will be taught which the participants will be continuing for a month.\n\n\n\n1. Those who were aged more than 30 years and diagnosed positive for type 2 diabetes for at least 1-year duration with random blood sugar >200 mg/dL or fasting blood sugar >126 mg/dL as per the Indian Council of Medical Research guidelines 2005.\n\n2. MNSI score ≥ 7 for History and ≥ 2.5 for Examination.\n\n\n\n1. Patients with Gestational Diabetes\n\n2. Patients diagnosed with Type-1 DM\n\n3. Patients with foot ulcers\n\n4. Patients who underwent amputation following DPN.\n\n5. History of surgical procedures secondary to DPN\n\n6. Patients with a history of Joint degenerative diseases\n\n7. Subjects falling under the absolute contraindication category for physiotherapy.\n\nData will be collected on the baseline as pre and post-data, followed by intervention for 4 weeks and post-intervention data on the last day of the 4th week is again recorded, CONSORT Flow chart is mentioned in Figure 1.\n\nGroup A: The experimental group will be receiving COMET protocol (Table 1), the Acronym\n\n1. COntrast Bath\n\n2. Mobility - Nerve Mobilization & Mobility Exercises\n\n3. E-Stim - Plantar Electrical Stimulation\n\n4. Therapeutic Foot Massage\n\n\n\n1. Position of the Patient: The patient is comfortably placed in a seated position on a chair with back support. The height of the chair must be sufficient to position the hips and knees at 90o.\n\n2. Instructions to the Patient: The patient is instructed to be as relaxed as possible and inform the therapist at once in case of any discomfort.\n\n3. Procedure:\n\ni. The contrast bath is applied either by a Contrast Bath Modality (CBM) or by using a bucket filled with warm or cold water sufficient to immerse the patient’s foot.\n\nii. A thermometer is used to record the water temperature throughout the intervention and a clock to measure the time duration.\n\niii. The patient is instructed to place his foot (one at a time) in the CBM/Bucket filled with warm water between 37o-43o for a duration of 4 minutes.\n\niv. After 4 minutes, the leg is lifted from the bucket and at once placed in a CBM/Bucket filled with cold water between 12o-15o for a duration of 1 minute.\n\nv. This process of alternating between warm water and cold water is repeated 4 times for a total duration of 20 minutes.\n\n4. Winding up of the procedure: Once the total immersion time of 20 minutes is complete, the patient is instructed to lift his leg from the bucket, and the skin is dried with a soft towel. The process is repeated for the contralateral foot.\n\n\n\n1. Position of the Patient: The patient is positioned in a relaxed supine lying position without any pillow under the head.\n\n2. Instructions to the Patient: The patient is instructed to be as relaxed as possible and inform the therapist at once in case of any discomfort.\n\n3. Nerve mobilization for Peroneal Nerve: Application of Proximal and Distal Sliders:\n\ni. With the patient in a supine, and the therapist in a walk stance on the side being treated, the therapist elevates the hip to 45o and the knee slightly flexed to allow the leg to be positioned horizontally.\n\nii. The therapist faces towards the foot and holds the knee between his forearm and trunk. The therapist's upper limb nearer to the patient will support the leg.\n\niii. The volar aspect of the therapist's forearm will be in contact with the posteromedial aspect of the patient's leg supporting it.\n\niv. The farther upper limb of the therapist places his palm on the dorsolateral aspect of the patient's forefoot such that the fingers overlap the toes, and the thumb is towards the dorso- medial surface.\n\nv. For the proximal slider, the therapist extends the knee on the flexed hip with the foot drawn into dorsiflexion and eversion.\n\nvi. For the distal slider, the therapist flexes the knee up to 90o on the flexed hip with the foot drawn into plantarflexion and inversion.\n\n4. Nerve mobilization for Posterior Tibial Nerve: Application of Proximal and Distal Sliders:\n\ni. With the patient in a supine, and the therapist in a walk stance on the side being treated, the therapist elevates the hip to 45o and the knee slightly flexed to allow the leg to be positioned horizontally.\n\nii. The therapist faces towards the foot and holds the knee between his forearm and trunk. The therapist's upper limb nearer to the patient will support the leg.\n\niii. The volar aspect of the therapist's forearm will be in contact with the posteromedial aspect of the patient's leg and the therapist's hand will caress the calcaneum of the patient.\n\niv. For the proximal slider, the therapist dorsiflexes the heel with his proximal hand by pushing it forward and dorsiflexes the forefoot and toes drawing them into eversion with his distal hand. This is done till resistance is encountered or symptoms elicited.\n\nv. This is followed by slowly extending the knee until further range is impossible or there is discomfort.\n\nvi. At this position, the pressure of dorsiflexion and eversion is slowly released with the knee still in the previous extended position. This will allow the nerve to migrate proximally.\n\nvii. For the distal slider, the therapist elevates the hip to 45o and the knee slightly flexed to allow the leg to be positioned horizontally.\n\nviii. The therapist dorsiflexes the heel with his proximal hand by pushing it forward and dorsiflexes the forefoot and toes drawing them into eversion with his distal hand. This is done till resistance is encountered or symptoms elicited.\n\n\n\n1. Position of the Patient: The patient is comfortably placed in a supine position with a pillow under the knee.\n\n2. Instructions to the Patient:\n\nThe patient is instructed to be as relaxed as possible and is informed that he will feel mild tingling in the sole where the electrode is placed. The patient is also instructed to inform the therapist immediately in case of discomfort.\n\n3. Procedure:\n\ni. The skin on the plantar surface of both feet is cleansed with cotton dipped in tap water and dried.\n\nii. A two-channel TENS machine is used with each channel of paired electrodes applied on each foot.\n\niii. The self-sticking adhesive electrodes are used, and each pair are placed with one electrode over the metatarsal heads in the middle of the forefoot and the other over the attachment of the plantar fascia in the middle of the junction between the mid-foot and hind foot.\n\niv. The machine is switched on, and the intensity is gradually increased till the patient informs a comfortable tingling sensation under the electrodes.\n\nv. The intensity is maintained at this level and the foot is stimulated for a duration of 20 minutes.\n\n4. Winding up of the procedure: Once the total stimulation time of 20 minutes is complete, the machine is switched off, the electrodes are removed, and the skin is inspected for any changes. If no changes are found, the skin is cleansed again with cotton dipped in tap water and dried. The patient is instructed to get up from a lying position whenever he/she is comfortable.\n\n\n\n1. Position of the Patient: The patient is comfortably placed in the prone position and the lower limb is exposed up to the inferior gluteal region.\n\n2. Instruction to the patient: The patient is instructed to be relaxed as much as possible and inform the therapist at once in case of any discomfort.\n\n3. The procedure of Massage:\n\ni. Massaging gel or coconut oil is used for massaging as it helps in moisturizing and lubrication.\n\nii. The massage begins with touching the heel of the foot to initiate contact.\n\niii. Effleurage strokes are used from the heel to the entire leg 3-5 times to spread the lubricant and warm the tissues.\n\niv. Petrissage manipulation including horizontal and vertical thumb and finger kneading, and static pressure are applied to the bottom of the feet starting with the base of the middle toe, moving one thumb width up towards the center of the foot, moving up towards the heel, spreading down towards the mid arches of the foot and ending at the base of the first and fifth toes.\n\nv. These are followed by effleurage strokes 3-5 times toward the popliteal lymph nodes.\n\nvi. Using both hands, hold the calcaneum between the thenar and hypothenar muscles and apply compression and distraction at the talocalcaneal joint.\n\nvii. This is followed by contacting the Achilles tendon by the ulnar side of both hands caressing it and sliding back and forth.\n\nviii. The calf muscle is reached with hands still in contact with the skin, and petrissage manipulations including thumb kneading, finger kneading, wringing, and picking up are applied to the calf muscles from distal to proximal till the knee joint line.\n\nix. Thumb kneading is done to the tender areas of the calf muscle between the heel and the knee joint.\n\nx. These manipulations are ended by effleuraging the entire foot, leg, and thigh 3-5 times.\n\n4. Winding of the Procedure: After completion of the massage, the patient is instructed to lie for a few minutes and get up whenever he/she is comfortable.\n\nGroup B The control group will be receiving their medication for diabetic polyneuropathy and general exercises will be taught which the participants will be continuing for a month.\n\n\n\nA. Vibratory Perception Threshold (VPT): it is an instrument which is used to measure the vibratory perception threshold.\n\nB. Galvanic Skin Conductance (GSC): It is an instrument which is used to measure the level of conductance across the skin.\n\nC. Michigan Neuropathy Screening Instrument (MNSI): An instrument to screen and diagnose diabetic patients with neuropathy.\n\nD. NeuroQoL questionnaire (NQOL): It is a specific validated neuropathy and foot ulcer QoL instrument which assesses diabetic neuropathy-related physical and emotional problems affecting daily life and well-being.\n\n\n\nRepresents the desired level of statistical significance\n\nZβ=0.84 Represents the desired power = 0.80 for 80%\n\nN = Minimum samples required for each group\n\nPrimary Variable = Perception of vibration sensitivity\n\nWhere,\n\n% of improvement in Perception of vibration sensitivity (Pre) in control group = P1 = (79.31%- 75.86%) = 3.45% (As per ref. article Krishna Dalal et al., Determination of efficacy of reflexology in managing patients with Diabetic Neuropathy; A Randomised Controlled Trial).\n\nConsidering 20% significant margin superiority of improvement for interventional group (comet protocol) = 23.45%\n\nMinimum sample size required\n\nPer group\n\nConsidering 10% drop out = 45 per group\n\nTotal samples required = 45 + 5 = 50 per group.\n\nAdverse events will be reported at each time. No adverse effects are anticipated.\n\n\nMethods\n\nData collection methods: The assessment and collection of outcomes will be done in the preintervention stage after assigning them to the intervention groups. Post- intervention data will be collected on the same day. This will be followed by the collection of post-intervention data after the completion of 4 weeks of intervention.\n\nData management: The collected information will be summarized by using frequency percentage for qualitative data and mean and standard deviation for quantitative data.\n\nStatistical methods: To find the effectiveness of COMET Protocol along with medication on Vibratory Perception Threshold (VPT), Galvanic Skin Conductance (GSC), Michigan Neuropathy Screening Instrument (MNSI) and NeuroQOL in subjects with Diabetic Polyneuropathy, paired t-test will be used for within-group comparison and unpaired t-test will be used for between-group comparisons. If the data is not following a normal distribution, the Wilcoxon sign rank test will be used for within-group comparisons and the Mann-Whitney U test will be used for between- group comparisons.\n\nA “p” value less than 0.05 will be considered significant. Outcome measures will be evaluated by using SPSS 21 software version.\n\nData monitoring: The data will be monitored by the Data Monitoring Committee of Ravi Nair Physiotherapy College.\n\nAny episode of the adverse events shall be reported to the Ethical Committee and the clinician in charge for assessing and managing the solicited and spontaneous adverse events and other unintended effects of trial interventions or trial conduct.\n\nConsent and assent: Participants who will be enrolled in the study will be made aware of the study and informed consent and assent will be obtained from each one of them.\n\nConfidentiality: Any information pertaining to the subjects participating in the study shall be maintained confidential. Any patient-related information will only be used with due permission from the subjects.\n\nDeclaration of interests: There are no financial or competing interests to mention.\n\nAccess to data: All the data collected during or after the study shall be stored and maintained by the study’s Principal Investigator. The PI will have access to the final trial dataset, and it will be shared with de-identification after receiving a formal request for research and publication purposes only.\n\nAncillary and post-trial care: Care shall be provided to the study subjects in case of events leading to harm from trial participation by the PI in accordance with the policy of Ravi Nair Physiotherapy College and DMIHER.\n\nDissemination policy: Any data collected during or after the study will only be used for academic and research-related purposes culminating in a publication in a reputed journal and to present in international or national journal.\n\n\nDiscussion\n\nWith a specific focus on vibratory perception and skin conductance as primary outcome measures, this proposed randomized controlled trial seeks to assess the effectiveness of a customized COMET protocol in conjunction with medication for the management of diabetic neuropathy. A thorough evaluation of participants’ baseline skin conductance and vibratory perception will be part of the procedure. After that, participants will be randomly assigned to either the intervention group, which will get the customized COMET protocol and the control group, which will receive standard medication alone. Using established measurement instruments, researchers will closely monitor changes in skin conductance and vibratory perception throughout the experiment to provide quantitative evidence on the efficacy of the combined intervention approach. The research will comply with strict ethical standards and give top priority to participant safety, guaranteeing that every participant will receive the necessary attention and supervision throughout the study. This trial has the potential to offer important insights into the comprehensive management of diabetic neuropathy by examining the effects of the customized COMET protocol in conjunction with medication on vibratory perception and skin conductance. Ultimately, this could improve the quality of life for those who suffer from this difficult condition.\n\nThis study protocol aims to produce credible evidence on the efficacy of the customized COMET protocol combined with medication in addressing vibratory perception and skin conductance in diabetic neuropathy through the use of a robust randomized controlled trial design and standardized assessment tools. The study will carefully gather and examine data pertaining to alterations in these physiological parameters, allowing for a thorough assessment of the influence of the intervention on peripheral nerve function and autonomic nervous system activity. The trial design places a strong emphasis on participant welfare and ethical considerations, making sure that participants receive the proper assistance and oversight during the study. Through a more thorough comprehension of the possible advantages of the customized COMET protocol when combined with medication, this study could influence clinical practice and help create efficient, individualized treatment plans for people with diabetic neuropathy, ultimately improving their general health and well-being.\n\nThis study will be conducted with written informed consent from all participants. Ethical approval was received from the Datta Meghe Institute of Higher Education and Research (DU)IEC:DMIHER Date of approval: July 7th 2023 institutional ethics committee REF/2023/07/070102.", "appendix": "Data availability\n\nNo data were associated with this article.\n\nZenodo: Spirit Checklist for Efficacy of a Tailored COMET Protocol Combined with Medication on Vibratory Perception and SkinConductance in Diabetic Neuropathy - A Protocol for Randomized Controlled Trial, DOI https://doi.org/10.5281/zenodo.10076923\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nWe would like to acknowledge Mr. Laxmikant Umate Sir, who has helped us in sample size calculation and data analysis planning.\n\n\nReferences\n\nZychowska M, Rojewska E, Przewlocka B, et al.: Mechanisms and pharmacology of diabetic neuropathy - experimental and clinical studies. Pharmacol. Rep. 2013; 65(6): 1601–1610. PubMed Abstract \| Publisher Full Text\n\nCollins SL, Moore RA, McQuayHJ WP: Antidepressants and anticonvulsants for diabetic neuropathy and postherpetic neuralgia: a quantitative systematic review. J. Pain Symptom Manag. 2000 Dec; 20(6): 449–458. PubMed Abstract \| Publisher Full Text\n\nHussain S, Habib A, Najmi AK: Anemia prevalence and its impact on health-related quality of life in Indian diabetic kidney disease patients: Evidence from a cross-sectional study. J. Evid. Based Med. 2019 Nov; 12(4): 243–252. PubMed Abstract \| Publisher Full Text\n\nGheith O, Farouk N, Nampoory N, et al.: Diabetic kidney disease: world wide difference of prevalence and risk factors. J. Nephropharmacol. 2015 Oct 9; 5(1): 49–56. PubMed Abstract \| Free Full Text\n\nAbbott CA, Malik RA, van Ross ER , et al.: Prevalence and characteristics of painful diabetic neuropathy in a large community-based diabetic population in the U.K. Diabetes Care. 2011 Oct; 34(10): 2220–2224. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPop-Busui R, Boulton AJ, Feldman EL, et al.: Diabetic Neuropathy: A Position Statement by the American Diabetes Association. Diabetes Care. 2017 Jan; 40(1): 136–154. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVinik AI, Nevoret ML, Casellini C, et al.: Diabetic neuropathy. Endocrinol. Metab. Clin. N. Am. 2013 Dec; 42(4): 747–787. PubMed Abstract \| Publisher Full Text\n\nDyck PJ, Kratz KM, Karnes JL, et al.: The prevalence by staged severity of various types of diabetic neuropathy, retinopathy, and nephropathy in a population-based cohort: the Rochester Diabetic Neuropathy Study. Neurology. 1993 Apr; 43(4): 817–824. Erratum in: Neurology 1993 Nov;43(11):2345. PubMed Abstract \| Publisher Full Text\n\nAslam A, Singh J, Rajbhandari S: Pathogenesis of painful diabetic neuropathy. Pain Res. Treat. 2014; 2014: 412041. Epub 2014 May 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConsensus statement: Report and recommendations of the San Antonio conference on diabetic neuropathy. American Diabetes Association American Academy of Neurology. Diabetes Care. 1988 Jul-Aug; 11(7): 592–597. PubMed Abstract \| Publisher Full Text\n\nBaxi H, Habib A, Hussain MS, et al.: Prevalence of peripheral neuropathy and associated pain in patients with diabetes mellitus: Evidence from a cross-sectional study. J. Diabetes Metab. Disord. 2020 Jul 31; 19(2): 1011–1017. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDros J, Wewerinke A, Bindels PJ, et al.: Accuracy of monofilament testing to diagnose peripheral neuropathy: a systematic review. Ann. Fam. Med. 2009 Nov-Dec; 7(6): 555–558. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang Z, Chen R, Zhang Y, et al.: Scoring systems to screen for diabetic peripheral neuropathy. Cochrane Database Syst. Rev. 2018 Jul 30; 2018(7): CD010974. Publisher Full Text \| Free Full Text\n\nBansal V, Kalita J, Misra UK: Diabetic neuropathy. Postgrad. Med. J. 2006 Feb; 82(964): 95–100. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYoo M, D’Silva LJ, Martin K, et al.: Pilot Study of Exercise Therapy on Painful Diabetic Peripheral Neuropathy. Pain Med. 2015 Aug; 16(8): 1482–9. Epub 2015 Mar 20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaul UK, Sinharay K, Bhattacharyya AK, et al.: Update in diabetic neuropathy with special reference to Indian scenario. J. Indian Med. Assoc. 2012 Sep; 110(9): 616–622. PubMed Abstract\n\nFrancia P, Gulisano M, Anichini R, et al.: Diabetic foot and exercise therapy: step by step the role of rigid posture and biomechanics treatment. Curr. Diabetes Rev. 2014 Mar; 10(2): 86–99. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCrews RT, Schneider KL, Yalla SV, et al.: Physiological and psychological challenges of increasing physical activity and exercise in patients at risk of diabetic foot ulcers: a critical review. Diabetes Metab. Res. Rev. 2016 Nov; 32(8): 791–804. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarbosa AP, Medina JL, Ramos EP, et al.: Prevalence and risk factors of clinical diabetic polyneuropathy in a Portuguese primary health care population. Diabetes Metab. 2001 Sep; 27(4 Pt 1): 496–502. PubMed Abstract\n\nSartor CD, Watari R, Pássaro AC, et al.: Effects of a combined strengthening, stretching and functional training program versus usual-care on gait biomechanics and foot function for diabetic neuropathy: a randomized controlled trial. BMC Musculoskelet. Disord. 2012 Mar 19; 13: 36. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDalal K, Maran VB, Pandey RM, et al.: Determination of efficacy of reflexology in managing patients with diabetic neuropathy: a randomized controlled clinical trial. Evid. Based Complement. Alternat. Med. 2014; 2014: 843036. Epub 2014 Jan 9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBird SJ, Brown MJ, Spino C, et al.: Value of repeated measures of nerve conduction and quantitative sensory testing in a diabetic neuropathy trial. Muscle Nerve. 2006 Aug; 34(2): 214–224. PubMed Abstract \| Publisher Full Text\n\nGao M, Yun X, Zhang T: VSA-3000: A Quantitative Vibration Sensation Testing Device for Patients With Central Nervous System Injury. Front. Neurol. 2020 Sep 8; 11: 936. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "300797", "date": "29 Jul 2024", "name": "Saldy Yusuf", "expertise": [ "Reviewer Expertise diabetic foot care" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Authors\nThe protocol is interesting, with aim to evaluate the effectiveness of COMET again three different intervention, however we note some issue need to clarify.\nFirst, the urgency and novelty of current study unclear. In the last paragraph of introduction, authors fail to explain research problems. There is missing explanation from problems to research question and study aims. Authors uses following sentences: 1. Frequent exercise lowers body weight enhances insulin sensitivity...... 2. Type 1 diabetes more likely than those .....to exercise... 3. Significant increases in physical activity.... Three aforementioned premises seems that authors tend to introduce effect of exercise, with totally different with study aims (medication, not exercise).\nProtocol: No information what is Comprehensive COMET protocol, whats different with others COMET study?\nTrial Design Intervention group: Medication + Physiotherapy Control group: Medication + General exercise Its unclear for reader, what is the content both Physiotherapy and general exercise. Please give brief explanation and justification, why experiments conducted one hour a day for four weeks? give relevant citation.\nInclusion Criteria MNSI is a complex assessment, who performed MNSI assessment, what is their competence?\nGroup A COMET Protocol, again is unclear, what is the consideration giving COMET intervention (Contracts Bath, Nerve mobilization and mobility exercise, Plantar electrical simulation, and therapeutic foot massage). The COMET is mismatch with Trial Design, and Study Aim.\nGroup B authors use NQOL, but in inclusion criteria authors uses MNSI. In study aim, QoL is the 3rd study aim, but is unclear why QoL only evaluate in control group solely.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "300800", "date": "16 Sep 2024", "name": "Manoj Manoharlal Abraham", "expertise": [ "Reviewer Expertise Exercise Sciences", "Physiotherapy", "Orthopedics", "Diabetes", "Manual therapy", "Sports injuries" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. Wonderful work done by the authors. Yet in the Introduction, there is no content about the Comprehensive COMET Protocol. Because only one part of the COMET, ie., mobility or exercises were explained, but not the other components. Also the importance of assessing Vibratory Perception, Skin conduction was not clearly mentioned. 2. More of inclusion criteria could be added which would improve the precision effect of the procedures. History on Diabets onset and duration could have been added. 3. Regarding the Protocol, I have a query on duration, as it is mentioned one hour per day, and the protocol has so many things to do. Like Contrast bath, Mobility (which included both Nerve mobilization and mobility exercises – be precise with technique), E-stim and Therapeutic foot massage. The split up which was given in the table 1, was not match with the total duration of one hour. 4. Can be accepted for indexing after it is completely done and making the availability of the data sets, as it is mentioned in the article as No data were associated.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-344
https://f1000research.com/articles/13-337/v1	23 Apr 24	{ "type": "Genome Note", "title": "Genomic and transcriptomic resources for the brown thornbill (Acanthiza pusilla) to support the conservation of a critically endangered subspecies", "authors": [ "Luke W. Silver", "Ross Crates", "Dejan Stojanovic", "Catherine M. Young", "Katherine Belov", "Katherine A. Farquharson", "Rob Heinsohn", "Carolyn J. Hogg", "Ross Crates", "Dejan Stojanovic", "Catherine M. Young", "Katherine Belov", "Katherine A. Farquharson", "Rob Heinsohn", "Carolyn J. Hogg" ], "abstract": "Abstract* The brown thornbill (Acanthiza pusilla) is a songbird endemic to eastern Australia with five recognised subspecies within the brown thornbill. The most notable is the King Island brown thornbill (Acanthiza pusilla magnirostris) of which there are less than 100 remaining and based on expert elicitation are the most likely Australian bird to become extinct in the next 20 years. We sequenced PacBio HiFi reads of the brown thornbill to generate a high-quality reference genome 1.25Gb in size and contig N50 of 20.1Mb. Additionally, we sequenced mRNA from three tissues to generate a global transcriptome to aid with genome annotation. The generation of a reference genome for the brown thornbill provides an important resource to align additional genomic data which will be produced in the near future.", "keywords": [ "Genome assembly", "reference genome", "transcriptome", "Aves", "mitogenome" ], "content": "Introduction\n\nThe brown thornbill (Acanthiza pusilla) is a small species of songbird within the Acanthizidae family endemic to eastern and south-eastern Australia, including Tasmania (Higgins & Peter, 2002). There are five subspecies recognised within the brown thornbill including the Critically Endangered King Island brown thornbill (Acanthiza pusilla magnirostris). This taxon is considered the most likely Australian bird to become extinct within the next 20 years, based on expert elicitation (Geyle et al., 2018). Whilst the nominate brown thornbill is of least conservation concern, there are thought to be fewer than 100 King Island brown thornbills occurring on King Island (area 1098 km2), in the Bass Strait (Bell, Webb, Holdsworth, & Baker, 2023). Whilst surveys are ongoing, the King Island brown thornbill is understood to be restricted to patches of mature eucalypt forest on King Island, where it primarily forages in the canopy and in the crevices of bark on tree trunks (Bell et al., 2023).\n\nThe generation of a reference genome and associated transcriptomic data is a vital for informing genetic management of the King Island subspecies and can be used to align genetic data that will be produced in the near future. The genome is also the first for the genus Acanthiza, contributing to global efforts to sequence life on Earth (Lewin et al., 2022).\n\nTo facilitate detailed genomic research on this species, we sequenced DNA with PacBio HiFi long reads to generate a high-quality reference assembly and sequenced RNA from three tissues to provide transcriptomic resources and assist in genome annotation for the brown thornbill.\n\n\nMethods\n\nA single wild male brown thornbill (B974_KIBT) from Tasmania was captured using a mist net and euthanised for genome and transcriptome generation under Australian National University Animal Experimental Ethics Committee program of wildlife authorisation approval number #A2021/33 (approval date (13/07/2021) and Tasmanian Scientific Permit #TFA23010. Every effort was made to reduce suffering of animals, including (i) collecting the minimum number of animals required for the study (one); (ii) pre-arranging animal euthanasia with a qualified veterinarian; (iii) collection of the animal from as close to the location of the veterinarian as practically possible to minimise transportation time; and (iv) transportation in a soft, dark material ‘bird bag’ to minimise stress during transportation. Tissue samples were dissected and flash frozen at -80°C or preserved in RNA later before being frozen at -80°C. High molecular weight (HMW) DNA was then extracted from kidney tissue using the Nanobind Tissue Big DNA Kit v1.0 (Circulomics). A Qubit fluorometer was used to assess the concentration of DNA with the Qubit dsDNA BR assay kit (Thermo Fisher Scientific). Total RNA was extracted from liver, brain and gonads using the RNeasy Tissue Kit (Qiagen) with RNAse-free DNAse I set (Qiagen). RNA quality was determined using the NanoDrop (Thermo Fisher Scientific) and RNA integrity (RIN) score determined using the Bioanalyzer RNA nano 6000 kit (Agilent 2100).\n\nHMW DNA was sent for Pacific Biosciences High Fidelity (PacBio HiFi) library preparation with the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and sequencing on one single molecule real-time (SMRT) cell of the PacBio Revio machine at the Australian Genome Research Facility (St Lucia, Australia). Total RNA from the liver, brain and gonads was sequenced as 150 bp paired-end (PE) reads using an Illumina Novaseq X with Illumina Stranded mRNA library preparation at the Ramaciotti Centre for Genomics (University of New South Wales, Kensington, Australia).\n\nThe genome assembly was conducted on Galaxy Australia (The Galaxy Community, 2022) public server usegalaxy.org.au (Afgan et al., 2016) running the Genome assembly with ‘hifiasm’ (RRID:SCR_021069) on Galaxy Australia workflow v2.1 (Price & Farquharson, 2022). Briefly, Picard (http://broad institute.github.io/picard) (Galaxy version 2.18.2.2; RRID:SCR_006525) SamToFastq, samtools (Danecek et al., 2021; Li et al., 2009) (Galaxy version 2.0.3; RRID:SCR_002105) flagstat and fastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) (Galaxy version 0.72; RRID:SCR_014583) was used to convert BAM files to FASTQ and quality check the reads for input to Hifiasm (Cheng, Concepcion, Feng, Zhang, & Li, 2021; Cheng et al., 2022). Hifiasm (Galaxy version 2.1) was run on Galaxy Australia to assembly the genome. Basic genome assembly statistics were calculated using the stats.sh script in BBMap v37.98 (sourceforge.net/projects/bbmap/) (RRID:SCR_016965). Genome completeness was determined using Benchmarking Universal Single-Copy Orthologues (BUSCO; RRID:SCR_015008) v5.4.6 (Simao, Waterhouse, Ioannidis, Kriventseva, & Zdobnov, 2015) with both the vertebrata_odb10 (n = 3354) and aves_odb10 (n= 8338) lineages on Galaxy Australia. Genome completeness and base accuracy was also determined Merqury v1.3 (RRID:SCR_022964) (Rhie, Walenz, Koren, & Phillippy, 2020), implemented in the Genome assessment post assembly workflow on Galaxy Australia (Price, 2023). Repetitive elements of the genome were identified, classified and masked on a Pawsey Supercomputing Centre Nimbus cloud machine (256GB RAM, 64 vCPU, 3 TB storage) by building a database using RepeatModeler v2.0.1 (RRID:SCR_015027) (Flynn et al., 2020); repeats were then masked using RepeatMasker v4.0.9 (RRID:SCR_012954) (Smit, Hubley, & Green, 2013-2015) with the -nolow parameter to avoid masking low complexity repeats.\n\nThe contig representing the mitochondrial genome was identified from the reference genome assembly using MitoHiFi v2 (Allio et al., 2020; Uliano-Silva et al., 2023) and visualised using Proksee (Grant et al., 2023). MitoHiFi identified the yellow thornbill (Acanthiza nana) as the most taxonomically closely related publicly available mitochondrial genome (KY994614.1), used to search for the brown thornbill mitochondrial genome.\n\nTranscriptome assembly was performed on the University of Sydney’s High Performance Computer, Artemis. Raw transcriptome reads were quality assessed pre- and post-trimming with FastQC v0.11.8 (RRID:SCR_014583). Trimmomatic v0.39 (RRID:SCR_011848) (Bolger, Lohse, & Usadel, 2014) with the parameters SLIDINGWINDOW:4:5, LEADING:5, TRAILING:5 and MINLEN:25 and ILLUMINACLIP:2:30:10 with the TruSeq3-PE adapters was used to quality trim reads. The repeat masked genome was indexed and trimmed reads aligned using the -dta parameter with hisat2 v2.1.0 (RRID:SCR_015530) (Kim, Paggi, Park, Bennett, & Salzberg, 2019). Resulting sam files with converted to bam format and sorted using samtools v1.9 (Danecek et al., 2021; Li et al., 2009). Stringtie v2.1.6 (RRID:SCR_016323) (Pertea et al., 2015) was used to generate a GTF for each transcriptome. Stringtie v2.1.6 with the -merge parameter merged transcripts into a global transcriptome retaining only transcripts with a fragments per kilobase of exon per million mapped fragments (FPKM) > 0.1 and length > 30. CPC2 v2019-11-19 (Kang et al., 2017) was used to predict coding potential and only transcripts predicted to be coding were retained. TransDecoder v2.0.1 (https://github.com/TransDecoder/TransDecoder) (RRID:SCR_017647) was used to predict open reading frames in the global transcriptome with a minimum transcript length of 20. Transcriptome completeness was assessed using BUSCO v5.4.6 (Simao et al., 2015) with the vertebrata_odb10 (n= 3354) and aves_odb10 (n = 8338) lineages on Galaxy Australia.\n\nGenome annotation was performed using FgenesH++ v7.2.2 (Softberry; RRID:SCR_018928 (Solovyev, Kosarev, Seledsov, & Vorobyev, 2006)) using the longest open reading frame as predicted from the global transcriptome, non-mammalian settings and optimised parameters supplied with the American crow (Corvus brachyrhynchos) gene finding matrix. BUSCO v5.4.6 (Simao et al., 2015) in protein mode was run on Galaxy Australia to assess the completeness of the annotation with the vertebrata_odb10 (n = 3354) and aves_odb10 (n = 8338) lineages. The ‘genestats’ script (https://github.com/darencard/GenomeAnnotation) was used to obtain the average number of exons and introns and the average exon and intron length.\n\n\nResults\n\nThe hifiasm assembly of the brown thornbill from PacBio HiFi data resulted in a genome 1.25Gb in size consisting of 1,000 contigs and sequenced to a depth of 43x. The longest contig in the assembly is 97.7 Mb and the assembly has an N50 of 20.1 Mb and L50 of 17 (Table 1). The genome is also highly complete with 96.9% complete Aves BUSCOs present in the assembly (Table 1). Merqury analysis also indicated a high-quality genome with QV > 59 and 87.1% complete k-mers. The mitochondrial genome is 16,862 bp and contains 37 genes including 22 tRNAs and 13 genes and 2 rRNAs (Figure 1). Repeat masking identified 19.06% of the genome as repeats (Table 2), which is in a similar range to other bird species (Zhang et al., 2014).\n\nAll individual tissues had alignments rates greater than 85% against the repeat masked reference genome (liver: 93.52%, brain: 91.75% and gonads: 89.24%). A total of 45,082 transcripts were predicted to have coding potential and 12,549 longest open reading frame transcripts were used as input for genome annotation with FgenesH. A total of 29,706 genes were predicted by the FgenesH annotation software, with the annotation containing 73.9% complete aves_obd10 BUSCOs (Table 3). There were an average number of 7.42 exons and 6.42 introns per gene (Table 3).\n\nBirds were sampled under Australian National University Animal Experimentation Ethics Committee program of wildlife authorisation approval number #A2021/33 (approval date 13/07/2021) and Tasmanian Scientific Permit #TFA23010.\n\n\nAuthor contribution\n\nLuke W. Silver\n\nRoles: Data curation, formal analysis, investigation, software, methodology, Writing -original draft Preparation\n\nRoss Crates\n\nRoles: Conceptualization, Funding acquisition, data collection, administration, writing-original draft\n\nDejan Stojanovic\n\nRoles: Data collection, Writing – Review & Editing\n\nCatherine M. Young\n\nRoles: Data collection, Writing – Review & Editing\n\nKatherine Belov\n\nRoles: Conceptualization, Funding Acquisition, Supervision, Writing – Review & Editing\n\nKatherine A. Farquharson\n\nRoles: Methodology, Supervision, Writing – Review & Editing\n\nRob Heinsohn\n\nRoles: Administration, Supervision, Writing – Review & Editing\n\nCarolyn J. Hogg\n\nRoles: Conceptualization, Funding Acquisition, Project Administration, Supervision, Writing – Review & Editing", "appendix": "Data availability\n\nThe raw PacBio HiFi and transcriptome data are publicly available through the Bioplatforms Australia Threatened Species Initiative: https://data.bioplatforms.com/organization/threatened-species . The assembled genome, global transcriptome and annotation generated in this study are available on Amazon Web Services Australasian Genomes Open Data Store: https://awgg-lab.github.io/australasiangenomes/genomes.html.\n\nRaw genome and transcriptome sequences are also available from:\n\nNCBI’s Short Read Archive (SRA): Raw RNA data for the generation of transcriptome. SRR26937195 (https://www.ncbi.nlm.nih.gov/biosample/38393458) (Silver et al., 2024)\n\nNCBI’s Short Read Archive (SRA): Raw RNA data for the generation of transcriptome. SRR26937196 (https://www.ncbi.nlm.nih.gov/biosample/38393457) (Silver et al., 2024)\n\nNCBI’s Short Read Archive (SRA): Raw RNA data for the generation of transcriptome. SRR26937197 (https://www.ncbi.nlm.nih.gov/biosample/38393456) (Silver et al., 2024)\n\nNCBI’s Short Read Archive (SRA): Raw DNA data for the generation of genome. SRR26937198 (https://www.ncbi.nlm.nih.gov/biosample/38393455) (Silver et al., 2024)\n\nThe data produced as part of this study are stored on NCBI under BioProject PRJNA1044448. Databases of molecular data on the NCBI Web site include such examples as nucleotide sequences (GenBank), protein sequences, macromolecular structures, molecular variation, gene expression, and mapping data. They are designed to provide and encourage access within the scientific community to sources of current and comprehensive information. Therefore, NCBI itself places no restrictions on the use or distribution of the data contained therein.\n\nFigshare: Checklist for ARRIVE.pdf for Genomic and transcriptomic resources for the brown thornbill (Acanthiza pusilla) to support the conservation of a critically endangered subspecies, https://doi.org/10.6084/m9.figshare.25396282.v1\n\n\nAcknowledgements\n\nThe authors would like to thank the Tasmanian Museum and Art Gallery (TMAG) for dissection, storage and shipping of the samples used to generate the genome and transcriptomes. Computational resources were provided by the Australian FGENESH++ Service provided by the Australian BioCommons and the Pawsey Supercomputing Research Centre with funding from the Australian Government and the Government of Western Australia; Galaxy Australia, a service provided by the Australian Biocommons and its partners; and the University of Sydney’s High Performance Computing facility Artemis provided by the Sydney Informatics Hub. The authors wish to acknowledge the use of the services and facilities of the Ramaciotti Centre for Genomics, UNSW and of the Australian Genome Research Facility.\n\n\nReferences\n\nAfgan E, Baker D, van den Beek M , et al.: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016; 44(W1): W3–W10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAllio R, Schomaker-Bastos A, Romiguier J, et al.: MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol. Ecol. Resour. 2020; 20(4): 892–905. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBell PJ, Webb MH, Holdsworth M, et al.: Defining and mapping habitat requirements to support the survival of King Island threatened birds.2023.\n\nBolger AM, Lohse M, Usadel B: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–2120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCheng H, Concepcion GT, Feng X, et al.: Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods. 2021; 18(2): 170–175. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCheng H, Jarvis ED, Fedrigo O, et al.: Haplotype-resolved assembly of diploid genomes without parental data. Nat. Biotechnol. 2022; 40(9): 1332–1335. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDanecek P, Bonfield JK, Liddle J, et al.: Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2): giab008. PubMed Abstract \| Publisher Full Text Reference Source\n\nFlynn JM, Hubley R, Goubert C, et al.: RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. USA. 2020; 117(17): 9451–9457. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGeyle HM, Woinarski JCZ, Baker GB, et al.: Quantifying extinction risk and forecasting the number of impending Australian bird and mammal extinctions. Pac. Conserv. Biol. 2018; 24(2): 157–167. Publisher Full Text\n\nGrant JR, Enns E, Marinier E, et al.: Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res. 2023; 51(W1): W484–w492. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHiggins PJ, Peter JM: Handbook of Australian, New Zealand and Antarctic birds. Volume 6: Pardalotes to spangled drongo. Higgins PJ, Peter JM, editors. Melbourne: Oxford University Press; 2002.\n\nKang YJ, Yang DC, Kong L, et al.: CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res. 2017; 45(W1): W12–W16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim D, Paggi JM, Park C, et al.: Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 2019; 37(8): 907–915. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLewin HA, Richards S, Lieberman Aiden E, et al.: The Earth BioGenome Project 2020: Starting the clock. Proc. Natl. Acad. Sci. 2022; 119(4): e2115635118. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi H, Handsaker B, Wysoker A, et al.: The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25(16): 2078–2079. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPertea M, Pertea GM, Antonescu CM, et al.: StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 2015; 33(3): 290-+. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrice G: Genome assessment post assembly. WorkflowHub. 2023; Publisher Full Text\n\nPrice G, Farquharson K: PacBio HiFi genome assembly using hifiasm v2.1. WorkflowHub. 2022. Publisher Full Text\n\nRhie A, Walenz BP, Koren S, et al.: Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020; 21(1): 245. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSilver L, Crates R, Stojanovic D, et al.: Acanthiza pusilla Genome sequencing and assembly.2024. Reference Source\n\nSimao FA, Waterhouse RM, Ioannidis P, et al.: BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19): 3210–3212. Publisher Full Text\n\nSmit A, Hubley R, Green P: RepeatMasker Open-4.0.2013-2015. Reference Source\n\nSolovyev V, Kosarev P, Seledsov I, et al.: Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 2006; 7(S1): S10–S1012. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThe Galaxy Community: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 2022; 50(W1): W345–W351. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUliano-Silva M, Ferreira JGRN, Krasheninnikova K, et al.: MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads. bioRxiv. 2023. 2022.2012.2023.521667. Publisher Full Text\n\nZhang G, Li C, Li Q, et al.: Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014; 346(6215): 1311–1320. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "297997", "date": "01 Aug 2024", "name": "Natalie Forsdick", "expertise": [ "Reviewer Expertise Genome assembly", "population genomics" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Genome Note 'Genomic and transcriptomic resources for the brown thornbill (Acanthiza pusilla) to support the conservation of a critically endangered subspecies' provides a clear and brief account of the genome assembly and annotation of this species, which will be used to inform subspecific conservation efforts in the future. The methods described are clear and follow regular conventions. Other than a few minor typographic suggestions (below), I have no further feedback.\nIntroduction paragraph 2: 'is a vital [tool]'. Also, would be nice to indicate how future genetic data will be used. RNAlater is one word. 'determined [using] Merqury' - also, was Merqury assessment done using the HiFi data as input?\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-337
https://f1000research.com/articles/13-335/v1	23 Apr 24	{ "type": "Research Article", "title": "Adverse effects of COVID-19 vaccines in university students", "authors": [ "Kanathip Jongmekwamsuk", "Sirashat Hanvivattanakul", "Jakapat Vanichanan", "Thana Khawcharoenporn", "Kanathip Jongmekwamsuk", "Sirashat Hanvivattanakul", "Jakapat Vanichanan" ], "abstract": "Background Existing data on adverse effects of coronavirus disease 2019 (COVID-19) vaccines among university students are limited. This study aimed to investigate the characteristics of adverse effects that may arise from administering COVID-19 vaccines to university students in Thailand.\n\nMethods An online survey study was conducted among students from 12 Health Sciences faculties, and from 16 non-Health Sciences faculties of two universities from October 2021 to January 2022 to assess types and adverse effects of COVID-19 vaccines received by the students.\n\nResults There were 1,439 participating students; 522 (36%) were from Health Sciences faculties, and 917 (64%) were from 16 non-Health Sciences faculties. The types of the first-dose vaccine received were inactivated (49%), viral vector (46%), and mRNA (5%), while the types of the second-dose vaccine received were viral vector (53%), inactivated (40%) and mRNA (7%). The first-dose vaccines’ most common adverse effects of inactivated, viral vector, and mRNA vaccines were muscle pain (47%, 82%, and 58%, respectively). The second-dose vaccines’ most common adverse effects were cough (47%) for inactivated vaccines and muscle pain (49% for viral vector vaccines and 56% for mRNA vaccines). Viral vector vaccines were more likely to cause fever, muscle pain, diarrhoea, headache, and rashes than the others. The mRNA vaccines caused injection site pain more than inactivated vaccines. The majority of adverse effects occurred 24-48 hours after vaccination (68%), were more severe with the first dose compared with the second dose, and resolved spontaneously without any treatment at a hospital.\n\nConclusions The adverse effects experienced by the students were various according to the types and number of doses of COVID-19 vaccines. The adverse effects were mostly non-severe and occurred less for the second dose compared with the first dose.", "keywords": [ "COVID-19", "vaccine", "adverse effects", "university students", "Thailand" ], "content": "Introduction\n\nThe coronavirus disease 2019 (COVID-19) pandemic is one of the greatest global threats, with manifestations of acute respiratory syndrome caused by the SARS-CoV-2 virus.1 This has led to hospitalizations and deaths since early 2020, with a mortality rate of 1% and a total of more than 6.8 million deaths as of 25 March 2023.2 Vaccination has proven to be an effective preventive measure against COVID-19, reducing its spread and severity.3 In Thailand, there are three major types of vaccine: (1) inactivated vaccines, including CoronaVac and BBIBP-CorV, (2) viral vector (VV) vaccine, including ChAdOx1 nCoV-19, and (3) mRNA vaccines, including BNT162b2 and mRNA-1273.4,5 In February 2021, CoronaVac was implemented as the first official COVID-19 vaccination regimen for populations at risk of COVID-19 and for healthcare workers. Subsequently, VV and mRNA vaccines became available. However, due to the limited supply of the vaccines, alternative primary vaccine regimens of heterologous COVID-19 vaccines including CoronaVac-ChAdOx1 nCoV-19, CoronaVac-BNT162b2, and ChAdOx1 nCoV-19-BNT162b2 have been used since late 2021.6–9 These heterologous COVID-19 vaccine regimens have gained significant interest among the Thai population because there is less evidence of serious adverse events and because they are more accessible.7,10\n\nWhile university students have less symptomatic COVID-19 infection than other populations, their social interaction increases the possibility of asymptomatic transmission, leading to higher rates of community infections.11,12 COVID-19 vaccination is essential to control the spread of the virus and achieve herd immunity. Especially for adolescents, the vaccines help prevent asymptomatic infection and therefore play an important role in disease control in the community.13,14 However, vaccine hesitancy among university students is a concerning issue, as it may lead to prolonged community transmission and increased chances of infection. Some students may be skeptical about the safety, efficacy, and adverse effects of the vaccine, which may discourage them from getting vaccinated.5,15,16\n\nThe adverse effects of COVID-19 vaccines may vary depending on the type of vaccine administered. Some of the most common adverse effects associated with COVID-19 vaccines include soreness or redness at the injection site, fever, headaches, fatigue, and muscle pain.17–19 In rare cases, more serious adverse effects, such as myopericarditis and thrombotic events, may occur in adolescents and young adults but usually with a favorable prognosis.20,21 While studies show that the overall adverse effects among the global population are mild and self-limited,22 there is limited research specifically focused on type, intensity, onset, difference between each dose, and natural history of the adverse effects among university students.\n\nThis study aimed to investigate the characteristics of adverse effects that may arise from administering COVID-19 vaccines to university students in Thailand. The results will provide valuable information and guide strategies to implement mass COVID-19 vaccination among university students.\n\n\nMethods\n\nThis study was conducted in accordance with the amended Declaration of Helsinki and was approved by the Ethics Committee of Thammasat University on August 3, 2021 (approval number 190/2564) and the Ethics Committee of Chulalongkorn University on September 27, 2021 (approval number 048/2021). Informed consent was obtained within the online questionnaire presented to participants at the onset of the study.\n\nA cross-sectional survey was conducted among university students from two large public universities in the Bangkok metropolitan area, from 1st October 2021 to 31st January 2022. All participants were aged 18 years and were studying in 12 Health Science (HS) faculties (Medicine, Dentistry, Allied Health Sciences, Pharmaceutical Science, Cardiothoracic Technology, Chinese Medicine, Veterinary Science, Psychology, Nursing, Thai Traditional Medicine, Public Health, and Sport and Exercise Science), 5 Science faculties (Science, Engineering, Sirindhorn International Institute of Technology, Architecture, and Science and Technology) and 11 Social Science faculties (Communication Art, Law, Economics, Accounting, Liberal Arts, Political Science, Arts, Fine Art, Social Work, Social Science and Humanity, and Education). The students from Science and Social Science faculties were categorized as Non-Health Sciences (NHS) students.\n\nAn online self-administered questionnaire was created on Google Forms. An informative statement prefaced the anonymous online survey, and completing the survey affirmed consent. Comprehensive details about the study were provided, after which participants expressed their consent by selecting a checkbox. This step affirmed their understanding of the study’s details and their agreement to provide information for research purposes. This method of obtaining informed consent was reviewed and approved by the Human Research Ethics Committee (Medicine) of Thammasat University and the Research Ethics Review Committee for Research Involving Human Subjects of Chulalongkorn University. The questionnaire collected data including demographic data, educational data, types of vaccine, number of doses, and type, severity, and management of adverse effects. Response to all questions in the survey was mandatory to minimize missing data. Reliability was assessed using internal consistency among 20 students determined with Cronbach’s alpha of 0.77. Changes to the content of the questionnaire, mainly to improve understanding of the survey questions, were made according to the pilot testing among these 20 students. Confidentiality and privacy of data were maintained during the whole study process. During the COVID-19 pandemic, the study questionnaire was introduced to students by the student affairs departments of each faculty of both universities through their social media, such as LINE Application, Facebook, and Instagram. Snowball sampling was further used for distribution among university students.\n\nIn terms of the privacy of the respondents in this research survey, there is no recording of data that identifies the respondent. The information obtained from the survey was accessible only by the investigators of this study. This study was reported based on STROBE cross-sectional reporting guidelines.23\n\nBased on the rates of AEs for the first dose of inactivated, VV and mRNA vaccines of 88%, 83%, and 83%, and for the second dose of inactivated, VV and mRNA vaccines of 72%, 99%, and 92%, with an acceptable margin of error of 10%, and the level of confidence of 95%, the minimum required sample size that received each dose and type of the vaccines are 41, 55, and 55 for the first dose and 78, 4, and 29 for the second dose. Statistical analyses were performed using the Software Package IBM SPSS Statistics Version 22.0 supplied by SPSS Inc (SPSS, Chicago, Illinois). Descriptive data were presented in number, median, and interquartile range (IQR). Categorical variables were analysed using the Chi-square test. Continuous variables were analysed using the Kruskal-Wallis test. P-value < 0.05 was considered statistically significant.\n\n\nResults\n\n* Comparison between the three groups.\n\n† Including Year 7 and graduate student.\n\nA total of 1728 university students participated in the study. Two hundred and eighty-eight participants were excluded because they received less than two doses of the vaccines. Of the remaining 1440 university students, 524 (36.4%) were from Health Science Faculties, 524 (36.4%) were from Social Science Faculties and 392 (27.2%) were from Science Faculties. The participants were predominately female (64.9%). Significantly higher proportions of students were from Social Science Faculties, were female, and were first-year students.\n\n* Comparison between the three groups.\n\n† Each student could report more than one adverse effect.\n\n‡ Including shivering, sleepiness, cubital swelling and pain, abnormal menstruation, increased appetite, acne, gastroesophageal reflux disease, chest pain, polyarthritis, hemiparesis, and dry mouth.\n\nOf the 1,440 students, 700 (48.6%) students received the inactivated vaccine, 669 (46.4%) students received the VV vaccine, and 71 (4.9%) students received the mRNA vaccine. 718 (49.9%) students reported having at least one adverse effect after receiving the vaccination. The students who received VV vaccines reported the highest rate (61.6%) of AEs. The most common AE of inactivated, VV, and mRNA vaccines was muscle pain (31.6%, 57.1%, and 42.3%, respectively). VV vaccine was reported to cause more muscle pain, fever, headaches, numbness, loss of appetite, fainting, vomiting, and diarrhea than the other two types. Both VV and mRNA vaccines were reported to cause more injection site pain than the inactivated vaccine. Most of the AEs occurred within the first two days (88.4%). A higher proportion of AEs were caused within 24 hours by the VV vaccine compared to the other two types.\n\n* Comparison between the three groups\n\n† Each student could report more than one adverse effect.\n\nOf the 1,440 students, 573 (39.8%) students received the inactivated vaccine, 756 (52.5%) students received the VV vaccine, and 111 (7.7%) students received the mRNA vaccine. 717 (49.8%) students reported having at least one adverse effect after receiving the vaccination. Muscle pain was the most common AE of inactivated, VV, and mRNA vaccines (23.2%, 30.7%, and 37.8%, respectively). The mRNA vaccine was reported to cause more muscle pain, fever, injection site pain, and loss of appetite than the other two types, while the VV vaccine was reported to cause more cough than the other two vaccines. Most AEs occurred between 24-48 hours and after 4 days. A higher proportion of AEs were caused by the mRNA vaccine between 24-48 hours than by the other two types. A higher proportion of AEs were caused by the VV vaccine after 4 days.\n\n* Comparison between the three groups.\n\nOf the 924 students who received the same type of vaccine for the first and second doses, 327 (35.3%) students received the inactivated vaccine, 549 (59.4%) students received the VV vaccine, and 48 (5.2%) students received mRNA vaccine. Most of the AEs (62.6%) resolved spontaneously without further treatment. Compared to the other two types of vaccine, a higher proportion of the AEs of the VV vaccine required symptomatic treatment. Most of the participants reported that the adverse effects of the first dose were more severe than those of the second dose. The AEs of VV vaccine were likely to be more severe in the first than the second dose, while the AEs of the first and second doses of inactivated vaccine were likely to be equally severe.\n\n\nDiscussion\n\nAdverse effects originate from natural reactions to exogenous substances, such as vaccines. When these substances are detected by innate immune lineages, specifically neutrophils and macrophages, cytokines are released to trigger an immune response. This can result in systemic adverse effects, such as fever, muscle pain, headache, and nausea.24 The introduction of an inactivated COVID-19 vaccine in a population aged over 18 years has shown a significant induction of T-cell response secreting IFN-gamma.25 This mechanism may explain why young adults are more likely to experience vaccine-related systemic adverse effects than other age groups, as they have lower spike-specific IFN-gamma+CD4+ T cells, leading to more widespread T-cell activation and cytokine secretion.26 In our study, we found high rates of adverse reactions among university students (49.9% and 49.8% for the first and second doses, respectively). These results were consistent with high prevalence of adverse effects after COVID-19 vaccination among young adults reported from previous studies.27–31\n\nRegarding the COVID-19 vaccines’ adverse effects, muscle pain, fever, and injection site pain were common among all three types of vaccines, which was similar to other studies.14,18,27–29,31–33 Injection site pain was common because of local responses induced by the injection and the high concentration of vaccine at the affected tissue.14,31 In contrast, muscle pain and fatigue are systemic reactions which commonly occur as a result of changes in pro-inflammatory cytokine levels in response to vaccine. These include a rise in interleukin-6 (IL-6) (causing fever) and increase in autoimmune activities that impair self-tolerance, disrupt the balance of muscle metabolism and cause cell damage and muscle pain.26,34\n\nThe frequency of each adverse effect varied based on the number of doses and the vaccine types. Overall, regardless of the dose, the group receiving the inactivated vaccines reported a lower prevalence of adverse effects compared to those receiving the VV and mRNA vaccines, which was similar to a report by Al Khames Aga et al.18 According to a review of COVID-19 vaccine effectiveness and adverse effects, inactivated vaccines elicit lower antibody responses compared to mRNA or viral vector vaccines because of their lower reactogenicity.35 The adverse effects of VV and mRNA vaccines can vary depending on the number of doses. In particular, VV vaccines had more adverse effects after the first dose compared to the second dose, while mRNA vaccines had more after the second dose compared to the first dose. These findings were consistent with those described in previous studies.19,30,36 Although the underlying mechanism of the different AE intensity between two doses is currently unknown, we hypothesize that it may be due to the body’s adaptation to the VV vaccine component leading to less adverse effect intensity in the second dose, while the increased immune response for the second dose of mRNA vaccine explains the more intense adverse effects in the second dose.\n\nSome students experienced minor adverse effects like loss of appetite, vomiting, and diarrhea after receiving one of the three vaccine types, which were also reported in some studies.18,27,32 Rare adverse events like thrombosis and myocarditis have been reported following VV and mRNA COVID-19 vaccination,27,37,38 but were not reported in this study. Gastrointestinal symptoms and other minor effects were not frequently reported in this study compared to other studies.28,33,39 The VV vaccine was reported by some of our study participants to have caused coughing in addition to other common adverse effects. This was possibly due to an immune response to the vaccine that led to respiratory tract inflammation and triggered the cough reflex arc.40 For the mRNA vaccines, the prevalence of minor adverse effects, such as loss of appetite, vomiting, diarrhea and rashes was higher after the second dose compared to the first dose. This finding was consistent with the result from a previous study and might be explained by the increased immunogenicity and reactogenicity induced by the second dose.32\n\nMost adverse effects from the first dose of the COVID-19 vaccines typically occurred within 48 hours. The onset of these side effects matched the reports of mRNA vaccines stating that systemic adverse effects are usually observed within the first or second day.31,36 However, our study showed that adverse effects from the second dose may be delayed and can occur up to 96 hours post vaccination. While some studies have compared the severity of effects after the first and second doses,18 few have discussed the management of adverse effects from COVID-19 vaccines. Our study found that symptomatic treatment was typically required for the adverse effects caused by the VV vaccine, which accounted for the highest proportion of such cases among the three major types of vaccines. This may be explained by the higher intensity of adverse effects experienced by students than with the other types of vaccines. However, overall adverse effects were non-severe, and only a small number of cases required hospital treatment. These findings are consistent with those reported in a previous study.27\n\nThere were recognizable limitations of this study. First, the single-center study may limit generalizability to other students in different settings. Second, because the survey was anonymous and self-administered, some questions may have been misunderstood. Third, the survey was conducted in a short period of time, and the respondents may have been affected by time limitations and by influences from recent social media and/or news. Lastly, there were inherent limitations, such as recall bias and confounding factors. Therefore, further research is necessary to determine the causal relationship between types and number of vaccine doses and adverse effects, especially among university students.\n\nIn conclusion, this study highlights the adverse effects that university students experienced after receiving the three major types of COVID-19 vaccines. Muscle pain, injection site pain, fever, headaches, and fatigue were commonly reported adverse effects while gastrointestinal symptoms and cough were reported less commonly. Overall, inactivated vaccines and the VV vaccine had the lowest and highest incidence of adverse effects, respectively. The majority of adverse effects occurred 24-48 hours after vaccination, were more severe with the first dose compared to the second dose, and resolved spontaneously without any treatment at a hospital. The study findings can be informative for university students and stakeholders in their institutions. Our findings can also help those involved in public health policies to improve vaccine acceptance and to improve management and monitoring of COVID-19 vaccines’ adverse effects among university students.", "appendix": "Data availability\n\nOpen Science Framework: Adverse effects of COVID-19 vaccines in university students. https://doi.org/10.17605/OSF.IO/Y92BZ. 41\n\nThis project contains the following underlying data:\n\n• Data file 1. Datasets.xlsx\n\nOpen Science Framework: Adverse effects of COVID-19 vaccines in university students. https://doi.org/10.17605/OSF.IO/Y92BZ. 41\n\nThis project contains the following extended data:\n\n• Data file 2. Questionnaire.pdf\n\nOpen Science Framework: STROBE checklist for ‘Adverse effects of COVID-19 vaccines in university students’. https://doi.org/10.17605/OSF.IO/Y92BZ. 41\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgement\n\nWe are grateful for the practical assistance from the Departments of Student Affairs from all faculties in the two universities for the distribution of the electronic research poster and the invitational messages for the online survey.\n\n\nReferences\n\nCDC: COVID-19 and Your Health. Centers for Disease Control and Prevention; February 11, 2020. Accessed March 29, 2023. Reference Source\n\nCOVID - Coronavirus Statistics: Worldometer. Accessed March 25, 2023. Reference Source\n\nZheng C, Shao W, Chen X, et al.: Real-world effectiveness of COVID-19 vaccines: a literature review and meta-analysis. Int J Infect Dis. 2022; 114: 252–260. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMinistry of Public Health of Thailand: COVID-19 Vaccination Infographic: Ministry of Public Health, Immunization Center. Accessed March 25, 2023. Reference Source\n\nMueangpoon K, Inchan C, Kaewmuneechoke P, et al.: Self-Reported COVID-19 Vaccine Hesitancy and Willingness to Pay: A Cross-Sectional Survey in Thailand. Vaccines. 2022; 10(4): 627. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSuphanchaimat R, Nittayasoot N, Jiraphongsa C, et al.: Real-World Effectiveness of Mix-and-Match Vaccine Regimens against SARS-CoV-2 Delta Variant in Thailand: A Nationwide Test-Negative Matched Case-Control Study. Vaccines. 2022; 10(7): 1080. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThepgumpanat P, Wongcha-um P: In first, Thailand to mix Sinovac, AstraZeneca vaccine doses. Reuters; July 12, 2021. Accessed March 25, 2023. Reference Source\n\nPairat K, Phaloprakarn C: Acceptance of COVID-19 vaccination during pregnancy among Thai pregnant women and their spouses: a prospective survey. Reprod Health. 2022; 19(1): 74. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThepgumpanat P, Setboonsarng C: Thailand cites positive results from Sinovac-AstraZeneca vaccine formula. Reuters; September 2, 2021. Accessed March 30, 2023. Reference Source\n\nWanlapakorn N, Suntronwong N, Phowatthanasathian H, et al.: Safety and immunogenicity of heterologous and homologous inactivated and adenoviral-vectored COVID-19 vaccine regimens in healthy adults: a prospective cohort study. Hum Vaccines Immunother. Published online February. 2022; 18: 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRussell FM, Greenwood B: Who should be prioritised for COVID-19 vaccination? Hum Vaccin Immunother. 2021; 17(5): 1317–1321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTavolacci MP, Dechelotte P, Ladner J: COVID-19 Vaccine Acceptance, Hesitancy, and Resistancy among University Students in France. Vaccines. 2021; 9(6): 654. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDagan N, Barda N, Barda N, et al.: BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Mass Vaccination Setting. N Engl J Med. 2021; 384(15): 1412–1423. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFrenck RW, Klein NP, Kitchin N, et al.: Safety, Immunogenicity, and Efficacy of the BNT162b2 Covid-19 Vaccine in Adolescents. N Engl J Med. 2021; 385(3): 239–250. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuto K, Yamamoto I, Nagasu M, et al.: Japanese citizens’ behavioral changes and preparedness against COVID-19: An online survey during the early phase of the pandemic. PLoS One. 2020; 15(6): e0234292. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReno C, Maietti E, Fantini MP, et al.: Enhancing COVID-19 Vaccines Acceptance: Results from a Survey on Vaccine Hesitancy in Northern Italy. Vaccine. 2021; 9(4): 378. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlmufty HB, Mohammed SA, Abdullah AM, et al.: Potential adverse effects of COVID19 vaccines among Iraqi population; a comparison between the three available vaccines in Iraq; a retrospective cross-sectional study. Diabetes Metab Syndr Clin Res Rev. 2021; 15(5): 102207. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAga QAAK, Aga QAAK, Alkhaffaf WH, et al.: Safety of COVID-19 vaccines. J Med Virol. 2021; 93(12): 6588–6594. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAndrzejczak-Grządko S, Czudy Z, Donderska M: Side effects after COVID-19 vaccinations among residents of Poland. Eur Rev Med Pharmacol Sci. 2021; 25(12): 4418–4421. PubMed Abstract \| Publisher Full Text\n\nOverview of EU/EEA country recommendations on COVID-19 vaccination with Vaxzevria, and a scoping review of evidence to guide decision-making.May 18, 2021. Accessed March 30, 2023. Reference Source\n\nYasuhara J, Masuda K, Aikawa T, et al.: Myopericarditis After COVID-19 mRNA Vaccination Among Adolescents and Young Adults: A Systematic Review and Meta-analysis. JAMA Pediatr. 2023; 177(1): 42–52. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBerg SK, Wallach-Kildemoes H, Rasmussen LR, et al.: Short- and Long-Term Self-Reported Symptoms in Adolescents Aged 12–19 Years after Vaccination against SARS-CoV-2 Compared to Adolescents Not Vaccinated—A Danish Retrospective Cohort Study. Vaccines. 2022; 10(11): 1863–1863. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nvon Elm E , Altman DG, Egger M, et al.: Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. BMJ. 2007; 335(7624): 806–808. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhu FC, Guan XH, Li YH, et al.: Immunogenicity and safety of a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years or older: a randomised, double-blind, placebo-controlled, phase 2 trial. Lancet. 2020; 396(10249): 479–488. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBueno SM, Abarca K, González PA, et al.: Safety and Immunogenicity of an Inactivated SARS-CoV-2 Vaccine in a Subgroup of Healthy Adults in Chile. Clin Infect Dis. 2022; 75(1): e792–e804. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChou J, Thomas PG, Randolph AG: Immunology of SARS-CoV-2 infection in children. Nat Immunol. 2022; 23(2): 177–185. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlghamdi AN, Alotaibi MI, Alqahtani ASA, et al.: BNT162b2 and ChAdOx1 SARS-CoV-2 Post-vaccination Side-Effects Among Saudi Vaccinees. Front Med China. 2021; 8: 760047. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHan BH, Song Y, Li C, et al.: Safety, tolerability, and immunogenicity of an inactivated SARS-CoV-2 vaccine (CoronaVac) in healthy children and adolescents: a double-blind, randomised, controlled, phase 1/2 clinical trial. Lancet Infect Dis. 2021; 21(12): 1645–1653. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRamasamy MN, Minassian AM, Ewer KJ, et al.: Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2/3 trial. Lancet. 2021; 396(10267): 1979–1993. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMenni C, Klaser K, May AM, et al.: Vaccine side-effects and SARS-CoV-2 infection after vaccination in users of the COVID Symptom Study app in the UK: a prospective observational study. Lancet Infect Dis. 2021; 21(7): 939–949. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPolack FP, Thomas SJ, et al.: Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N Engl J Med. 2020; 383(27): 2603–2615. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPormohammad A, Pormohammad A, Zarei M, et al.: Efficacy and Safety of COVID-19 Vaccines: A Systematic Review and Meta-Analysis of Randomized Clinical Trials. Vaccines. 2021; 9(5): 467–467. Publisher Full Text\n\nZhang Y, Zeng G, Pan H, et al.: Safety, tolerability, and immunogenicity of an inactivated SARS-CoV-2 vaccine in healthy adults aged 18-59 years: a randomised, double-blind, placebo-controlled, phase 1/2 clinical trial. Lancet Infect Dis. 2021; 21(2): 181–192. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHannah JR, Ali SS, Nagra D, et al.: Skeletal muscles and Covid-19: a systematic review of rhabdomyolysis and myositis in SARS-CoV-2 infection. Clin Exp Rheumatol. 2022; 40(2): 329–338. Publisher Full Text\n\nChi W-Y, Li Y, Huang H-C, et al.: COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection. J Biomed Sci. 2022; 29(1): 82. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlhazmi A, Alamer E, Daws D, et al.: Evaluation of Side Effects Associated with COVID-19 Vaccines in Saudi Arabia. Vaccine. 2021; 9(6): 674. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPavord S, Scully M, Hunt BJ, et al.: Clinical Features of Vaccine-Induced Immune Thrombocytopenia and Thrombosis. N Engl J Med. 2021; 385(18): 1680–1689. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGargano JW, Wallace M, Hadler SC, et al.: Use of mRNA COVID-19 Vaccine After Reports of Myocarditis Among Vaccine Recipients: Update from the Advisory Committee on Immunization Practices - United States, June 2021. Morb Mortal Wkly Rep. 2021; 70(27): 977–982. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXia S, Duan K, Zhang Y, et al.: Effect of an Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity Outcomes: Interim Analysis of 2 Randomized Clinical Trials. JAMA. 2020; 324(10): 951–960. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSong WJ, Hui CKM, Hull JH, et al.: Confronting COVID-19-associated cough and the post-COVID syndrome: role of viral neurotropism, neuroinflammation, and neuroimmune responses. Lancet Respir Med. 2021; 9(5): 533–544. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJongmekwamsuk K, Hanvivattanakul S, Vanichanan J, et al.: Adverse effects of COVID-19 vaccines in university students.2024. Publisher Full Text" }	[ { "id": "283016", "date": "18 Jun 2024", "name": "Nasikarn Angkasekwinai", "expertise": [ "Reviewer Expertise Infectious diseases" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study surveyed the adverse effects experienced by university students following COVID-19 vaccination from two public universities. The author presented the data in a concise and clear manner. However, there remains several concerns, as follows:\n1. When is the timing for conducting a survey after vaccination? The timing of survey is crucial in minimizing recall bias, which can distort the accuracy of self-reported data, leading to potential inaccuracies in their responses. Also, what is the number of respondents from each university?\n2. Are there any screening question to exclude respondents who have contracted COVID-19 shortly after vaccination? Because the symptoms that occur may be the result of infection, not from the vaccine as this study was conducted during a period of high prevalence of COVID-19 disease in the country.\n3. In the discussion, the author found that VV vaccines caused more AEs following the first dose compared to the second, which aligns with the presented data. However, the results for mRNA vaccines are less conclusive. We cannot say for certain that mRNA vaccines had more AEs after the second dose compared to the first dose (from Table 4).\n4. Since the study was conducted in multiple faculties, in which student groups, HS or NHS were the question formats tested to improve comprehension? Because students in HS and NHS may have different levels of background knowledge and familiarity with the question being asked. It's also interesting to know whether there are any differences in the study results between the different student groups?\n5. This study was multicenter study from two universities, not single-center study. However, the study may limit its generalizability to students in other educational settings.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-335
https://f1000research.com/articles/13-334/v1	23 Apr 24	{ "type": "Study Protocol", "title": "Study of inflammatory biomarkers in Chronic obstructive pulmonary disease (COPD) and their association with comorbidities", "authors": [ "AISHWARYA KEDAR", "Ulhas Jadhav", "Ulhas Jadhav" ], "abstract": "Background Chronic Obstructive Pulmonary Disease (COPD) is a prevalent respiratory condition associated with systemic inflammation and various comorbidities, significantly impacting patients’ health outcomes. This study investigates the relationships between inflammatory biomarkers in COPD and their associations with comorbidities. By focusing on specific biomarkers such as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-ALFA), and fibrinogen, we seek to find the complex interplay between systemic inflammation, COPD severity, and the prevalence of comorbidities. This research is critical for advancing our understanding of the systemic manifestations of COPD and informing targeted interventions for improved patient management.\n\nMethods This cross-sectional observational study will be conducted at AVBRH, a tertiary care hospital in central India, over two years (August 2022 to August 2024). A sample size of 90 COPD patients will be randomly selected based on inclusion and exclusion criteria. Diagnostic tests will be performed, including pulmonary function tests, chest X-rays, and biomarker assessments. Statistical analyses, encompassing chi-square tests, Pearson’s correlation coefficient, and logistic regression, will explore associations between inflammatory biomarkers, COPD severity, and comorbidities. The study design ensures rigorous data collection and adherence to ethical standards, with SPSS 27.0 utilized for statistical analyses.\n\nExpected Outcome Anticipated outcomes include a comprehensive understanding of how inflammatory biomarkers correlate with the severity of COPD and their associations with comorbidities. We expect to identify specific biomarkers that may serve as indicators of increased risk for certain comorbid conditions. The findings will contribute valuable insights into the systemic nature of COPD and inform healthcare strategies tailored to mitigate comorbidity-related risks in COPD patients. This research has the potential to enhance clinical decision-making, guide personalized treatment plans, and ultimately improve the overall management of individuals living with COPD.", "keywords": [ "Chronic Obstructive Pulmonary Disease (COPD)", "Inflammatory Biomarkers", "Comorbidities", "Systemic Inflammation", "Respiratory Medicine", "Cross-sectional Study" ], "content": "Introduction\n\nChronic Obstructive Pulmonary Disease (COPD) represents a significant global health challenge characterized by persistent respiratory symptoms and airflow limitation.1 Beyond its pulmonary manifestations, COPD is increasingly recognized as a systemic inflammatory disorder with a propensity for various comorbidities, including cardiovascular diseases, diabetes, and renal dysfunction.2,3 Identifying and characterizing inflammatory biomarkers associated with COPD may provide valuable insights into the complex interplay between pulmonary and systemic manifestations of the disease.\n\nPrevious studies have implicated biomarkers such as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-ALFA), and fibrinogen in systemic inflammation and their potential roles as indicators of disease severity and comorbidity risk in COPD.4–6 However, a comprehensive understanding of the relationships between these biomarkers, COPD severity, and comorbidities remains an area of ongoing investigation.\n\nThis study protocol outlines a cross-sectional and observational investigation to assess inflammatory biomarkers in COPD patients and their associations with comorbidities. The study aims to contribute to the existing knowledge base, informing future research and enhancing clinical strategies for the holistic management of COPD patients. By employing rigorous methodologies and statistical analyses, we anticipate elucidating key relationships that may guide targeted interventions and improve patient outcomes.\n\nThe primary aim of this study is to investigate inflammatory biomarkers in Chronic Obstructive Pulmonary Disease (COPD) and explore their associations with comorbidities.\n\n\n\n1. To Study Inflammatory Biomarkers in COPD: Measure levels of inflammatory biomarkers, including CRP (C-reactive protein), IL-6, TNF-ALFA, and fibrinogen, in patients diagnosed with COPD.\n\n2. To Investigate the Association with Comorbidities: Explore the prevalence of comorbidities such as heart diseases, anemia, chronic renal failure, and diabetes in COPD patients.\n\n3. To Correlate Biomarker Levels with COPD Severity: Examine the correlation between the levels of inflammatory biomarkers and the severity of COPD, assessed through pulmonary function tests and chest imaging.\n\n4. To Identify Other Observations: Investigate any additional observations or patterns that may emerge during the study, contributing to a comprehensive understanding of the relationship between COPD, inflammatory biomarkers, and comorbidities.\n\n\nMethods\n\nThis study will employ a cross-sectional and observational design to investigate the relationship between inflammatory biomarkers and COPD and their association with comorbidities. The cross-sectional design allows data collection at a single point, providing a snapshot of the relationship between variables.\n\nThe study population will consist of patients diagnosed with Chronic Obstructive Pulmonary Disease (COPD) who meet the inclusion criteria. Patients will be selected from the Respiratory Medicine department at AVBRH. Inclusion criteria encompass individuals diagnosed with COPD and those aged above 40 years. Exclusion criteria include patients unwilling to provide consent, non-cooperative patients, and those with connective tissue disorders such as rheumatoid arthritis or COPD asthma overlap.\n\nThe study will be conducted at AVBRH, a tertiary care hospital attached to Jawaharlal Nehru Medical College. AVBRH is situated in the rural area of Sawangi, Meghe, Wardha, in central India. This location provides a diverse and representative sample of patients with COPD in a real-world clinical setting. The choice of a rural area enhances the study’s external validity, capturing a population that may have different characteristics compared to urban populations.\n\n\n\n1. Diagnosis of COPD: Patients must have a confirmed diagnosis of Chronic Obstructive Pulmonary Disease (COPD) based on established criteria, including clinical symptoms, pulmonary function tests (spirometry), and chest X-rays.\n\n2. Age criteria: Participants must be aged 40 years or above. This age threshold is chosen to focus on the population commonly affected by COPD and its associated comorbidities.\n\n\n\n1. Consent and cooperation: Patients unwilling or unable to provide informed consent for participation in the study will be excluded. Additionally, individuals who exhibit non-cooperative behavior during the study procedures may be excluded to ensure data reliability.\n\n2. Connective tissue disorders: Patients with known connective tissue disorders, such as rheumatoid arthritis, will be excluded. These conditions may introduce confounding variables that could affect the interpretation of inflammatory biomarkers.\n\n3. COPD asthma overlap: Patients diagnosed with COPD asthma overlap will be excluded. This exclusion aims to maintain a homogeneous study population and focus specifically on COPD without the potential influence of overlapping conditions.\n\n\n\n1. Selection bias:\n\n• Potential issue: If the inclusion criteria are not strictly followed or certain groups of COPD patients are systematically excluded, it may introduce selection bias.\n\n• Mitigation: Ensuring rigorous adherence to inclusion and exclusion criteria during participant selection can minimize this bias. Random selection of patients can also help in reducing selection bias.\n\n2. Information bias:\n\n• Potential issue: Inaccuracies in data collection or measurement of biomarkers, comorbidities, or COPD severity may lead to information bias.\n\n• Mitigation: Standardizing data collection methods, employing validated measurement tools, and providing appropriate training to personnel can minimize information bias.\n\n3. Confounding bias:\n\n• Potential issue: Factors not considered in the study that may influence the relationship between inflammatory biomarkers and comorbidities, leading to confounding bias.\n\n• Mitigation: Controlling for potential confounding variables through study design, statistical methods, or matching can help minimize confounding bias.\n\n4. Observer bias:\n\n• Potential issue: The knowledge of the study hypothesis or the involvement of biased observers in data collection may introduce observer bias.\n\n• Mitigation: Blinding participants and researchers to the study hypothesis, especially during the outcomes assessment, can reduce observer bias.\n\nThe data collection process for this study on inflammatory biomarkers in Chronic Obstructive Pulmonary Disease (COPD) and their association with comorbidities will be conducted with meticulous attention to detail and adherence to standardized procedures. Participant recruitment will involve identifying eligible individuals from the Respiratory Medicine department at AVBRH based on stringent inclusion and exclusion criteria. Informed consent will be sought from each participant, ensuring they fully understand the study’s purpose, procedures, and potential implications.\n\nUpon obtaining consent, a baseline assessment will be conducted to gather demographic information and confirm the diagnosis of COPD through pulmonary function tests and chest X-rays. Diagnostic tests, including spirometry for lung function, chest X-rays for initial assessment, and HRCT of the thorax in cases of severe derangement, will be carried out to evaluate the respiratory status of participants comprehensively.\n\nThe biomarker testing phase will involve a series of laboratory tests. Blood samples will be collected for C-reactive protein (CRP) testing and the Westergren Katz tube test to measure Erythrocyte Sedimentation Rate (ESR). A complete blood count (CBC) will also be performed to assess leukocyte count and hemoglobin levels. Participants will undergo HbA1c testing to rule out diabetes. Cardiac evaluations, including echocardiogram and ECG, will be conducted to assess heart function. Furthermore, kidney function tests and measurements of inflammatory biomarkers such as Interleukin-6 (IL-6), Tumor Necrosis Factor-Alpha (TNF-ALFA), and fibrinogen will be performed.\n\nData management will be a critical aspect of the process, involving the design of a secure and structured database to store and manage collected data. Regular checks and validation procedures will ensure data integrity throughout the study. Statistical analysis will be conducted using the SPSS 27.0 version, employing appropriate methods such as chi-square tests and Pearson’s correlation coefficient to analyze the relationships between biomarkers, COPD severity, and comorbidities.\n\n\n\nWhere;\n\nZ is the level of significance at 5%, i.e., 95% confidence interval = 1.96\n\nP = Prevalence of COPD = 7.4% (Reference study7)\n\n80% of COPD patients had comorbidity: 7.4∗80100=5.92%\n\nd = Desired error of margin = 5% = 0.05\n\nn = 90 COPD patients needed in the study.\n\nThe study on inflammatory biomarkers in Chronic Obstructive Pulmonary Disease (COPD) and their association with comorbidities will rigorously utilize various statistical methods to analyze the relationships among key variables. The initial phase involves descriptive statistics, which will summarize the study population’s demographic details, COPD severity, and prevalence of comorbidities. Measures such as mean, median, standard deviation, and percentages will provide an overview of the characteristics of the participants.\n\nChi-square tests will be employed to analyze categorical variables, particularly assessing the presence or absence of comorbidities across different COPD severity groups. This statistical method aids in understanding the associations between inflammatory biomarkers and the occurrence of specific comorbidities. Pearson’s correlation coefficient will be used to explore the linear relationship between continuous variables, such as the levels of inflammatory biomarkers and the severity of COPD. The strength and direction of these correlations will be assessed, providing valuable insights into potential associations.\n\nMultivariate analysis, including multiple regression analysis, may be considered to simultaneously examine the independent contributions of various factors to the observed associations. This approach provides a more comprehensive understanding of the interplay between inflammatory biomarkers, COPD severity, and comorbidities. Comparative analysis will involve statistical tests, such as t-tests or analysis of variance (ANOVA) for continuous variables and chi-square tests for categorical variables, to compare biomarker levels between different groups, such as varying COPD severity categories or the presence/absence of specific comorbidities.\n\nFurthermore, logistic regression will be employed to model the likelihood of comorbidities based on factors such as inflammatory biomarker levels and COPD severity. This statistical method aids in identifying potential predictors of comorbidities within the study population. Subgroup analysis will be conducted to explore variations in relationships across different subgroups, such as age groups or gender, providing insights into potential effect modifiers.\n\nSurvival analysis techniques like Kaplan-Meier curves and Cox proportional hazards models may be considered in cases involving longitudinal data and time-to-event outcomes. These methods can provide valuable information on the occurrence of specific comorbidities over time. Sensitivity analysis will be conducted to assess the robustness of results, testing the impact of variations in key parameters or assumptions.\n\nThe statistical software chosen for these analyses is SPSS version 27.0 statistical tools,8 ensuring the accuracy and reliability of the results. Through the thoughtful application of these statistical methods, the study aims to unveil meaningful associations, correlations, and predictors related to inflammatory biomarkers, COPD severity, and comorbidities, contributing to a nuanced understanding of the intricate relationships within this complex medical landscape.\n\nThe Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol (Reference number: DMIHER (DU)/IEC/2022/119. Date: 21-07-2022). Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.\n\nDespite the careful planning and execution of the study on inflammatory biomarkers in Chronic Obstructive Pulmonary Disease (COPD) and their association with comorbidities, several limitations must be considered. While efficient for snapshot assessments, the cross-sectional design cannot establish causal relationships, warranting the need for longitudinal studies to explore temporal dynamics. Sampling bias is inherent due to the study’s reliance on a specific tertiary care hospital in a rural area, potentially limiting the generalizability of findings to diverse populations. The exclusion of individuals with connective tissue disorders and COPD asthma overlap might introduce selection bias, impacting the representation of specific subgroups within the COPD population. Additionally, self-reported data may introduce recall and social desirability biases, affecting the accuracy of information provided by participants. The focus on specific inflammatory biomarkers may limit the study’s comprehensiveness, as other relevant biomarkers may exist. Unmeasured confounders, external factors, and ethnic and cultural influences could further impact the study’s generalizability. Acknowledging these limitations is essential for a proper interpretation of results and highlight the need for cautious application to broader populations.\n\nAfter the completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has yet to start. After the publication of the protocol, we will start recruitment in the study.\n\n\nDiscussion\n\nThe observed correlations between inflammatory biomarkers, COPD severity, and comorbidities in this proposed study underscore the systemic nature of COPD, aligning with previous findings that have highlighted the intricate interplay between pulmonary and extra-pulmonary manifestations.1,2 The association of COPD with systemic inflammation has been consistently reported in the literature, with elevated levels of biomarkers such as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-ALFA), and fibrinogen linked to disease progression and severity.4–6 By examining these specific biomarkers, our study aims to provide a more nuanced understanding of the underlying inflammatory processes in COPD.\n\nIdentifying these biomarkers as potential indicators of comorbidity risk in COPD patients is consistent with existing evidence.4 Studies have reported a higher prevalence of comorbidities, including cardiovascular diseases, diabetes, and renal dysfunction, in individuals with COPD.9 By investigating the correlation between biomarker levels and the presence of comorbidities, our study seeks to contribute valuable insights into the pathophysiological mechanisms linking systemic inflammation and associated health complications in COPD patients.\n\nHowever, it is essential to acknowledge the limitations of this proposed study. The cross-sectional design restricts our ability to establish causation, and the selected sample, drawn from a specific tertiary care hospital in central India, may limit the generalizability of our findings to broader populations. The exclusion criteria, mainly the exclusion of individuals with connective tissue disorders and COPD asthma overlap, might introduce selection bias, influencing the representation of specific COPD subgroups.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nGlobal Initiative for Chronic Obstructive Lung Disease: Global Initiative for Chronic Obstructive Lung Disease - GOLD. Accessed: December 5, 2023. Reference Source\n\nAgustí A, Edwards LD, Rennard SI, et al.: Persistent systemic inflammation is associated with poor clinical outcomes in COPD: a novel phenotype. PLoS One. 2012; 7: e37483. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSin DD, Anthonisen NR, Soriano JB, et al.: Mortality in COPD: Role of comorbidities. Eur. Respir. J. 2006; 28: 1245–1257. Publisher Full Text\n\nDonaldson GC, Hurst JR, Smith CJ, et al.: Increased risk of myocardial infarction and stroke following exacerbation of COPD. Chest. 2010; 137: 1091–1097. PubMed Abstract \| Publisher Full Text\n\nGan WQ, Man SFP, Senthilselvan A, et al.: Association between chronic obstructive pulmonary disease and systemic inflammation: a systematic review and a meta-analysis. Thorax. 2004; 59: 574–580. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPinto-Plata VM, Müllerova H, Toso JF, et al.: C-reactive protein in patients with COPD, control smokers and non-smokers. Thorax. 2006; 61: 23–28. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDaniel RA, Aggarwal P, Kalaivani M, et al.: Prevalence of chronic obstructive pulmonary disease in India: A systematic review and meta-analysis. Lung India. 2021; 38: 506–513. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIBM SPSS Statistics: Accessed: February 21, 2024. Reference Source\n\nMannino DM, Thorn D, Swensen A, et al.: Prevalence and outcomes of diabetes, hypertension and cardiovascular disease in COPD. Eur. Respir. J. 2008; 32: 962–969. Publisher Full Text" }	[ { "id": "308276", "date": "14 Aug 2024", "name": "Prof RA Stockley", "expertise": [ "Reviewer Expertise Pathophysiology of COPD", "inflammation", "comorbidities and biomarkers" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe association and causation of comorbidities in COPD is both intriguing and complex. COPD is accepted as an inflammatory disease with a presumed neutrophilic background. CV disease,Type 2 diabetes,osteoporosis,gingivitis are all present with greater prevalence in COPD but the reason/s are difficult to dissect. All are features of aging . COPD CVD Osteoporosis and gingivitis are all associated with smoking and all have a presumed inflammatory Pathophysiology although with different putative specific cytokine profiles. This leads to the concepts that one leads to systemic overspill influencing the prevalence of the others or that they all have the same inflammatory background (features that are difficult to dissect! COPD alone has clinical and pathological features that vary including bronchitis, emphysema, small airways dysfunction, bronchiectasis with and without chronic airways colonisation apart from “severity” as defined by airflow obstruction. These features have variable outcomes and variable local and systemic inflammation. The inflammatory markers chosen also reflect obesity and are largely non specific.\nIt seems unclear why the power calculations indicate such a low data set. With all these variables and the confounding factors and low prevalence a much larger data set is required. If the outcome is to identify common pathophysiological processes a clearer selection of putative markers is needed. If the plan is to use biomarkers to determine the likelihood of co morbidity that is already a recognised clinical approach to COPD. Characterisation of the presence of comorbidities requires much clearer and detailed assessment. For instance CVD requires Q risk scores and vascular stiffness. Perhaps the first step is to define a Local COPD cohort in detail and define the prevalence of comorbidities in detail as well as putative confounders. Thereafter define the comorbidities with and without COPD and both generalised and specific biomarkers. This alone requires a major effort and cohort size.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-334
https://f1000research.com/articles/13-332/v1	23 Apr 24	{ "type": "Brief Report", "title": "Are Narrative CVs contributing towards shifting research culture? Workshop Report from the 2023 Recognition and Rewards Festival", "authors": [ "Noémie Aubert Bonn", "James Peter Morris", "Sean Sapcariu", "Karen Stroobants", "James Peter Morris", "Sean Sapcariu", "Karen Stroobants" ], "abstract": "Abstract*\nBackground Over the past decade, calls for research assessment reform have grown, led by initiatives such as the Declaration on Research Assessment (DORA) and the Leiden Manifesto, and, more recently, the Coalition for Advancing Research Assessment (CoARA). A key element being discussed as part of research assessment reform is a shift towards more qualitative assessments, focussed on the content of research and the broad skills and competencies of researchers, and the array of contributions they make to knowledge creation and innovation. Narrative CV formats have emerged as a good practice example for enabling qualitative assessments of research projects and researchers, and are becoming more widely piloted and implemented.\n\nMethods As part of the 2023 Dutch Recognition and Rewards Festival, the authors hosted a workshop to gather perspectives on Narrative CVs, including whether and how they may contribute to shifts in research culture that are needed to support research assessment reform.\n\nResults Participants, representing research organisations and the research community, discussed both beneficial and critical aspects of narrative-style CV implementations from their experiences. The effects observed since narrative CVs have been implemented were discussed, with perspectives provided on career prospects and the empowerment of the research community to direct change. Finally, the discussion turned to expectations for the future, with workshop participants calling for focus on the roles that narrative-style CVs can play in improving research careers, recognition of collaborative work, and equality, diversity, and inclusion. A short informal survey exploring levels of implementation of narrative CVs across different research organisations was run prior to the workshop, the results of which are also presented as part of this report.\n\nDiscussion The authors intend to expand this discussion to other scientific and policy conferences, and this report serves as a basis for a wider and deeper dialogue in the community.", "keywords": [ "Research Assessment", "Research Culture", "Qualitative Assessment", "Narrative CV", "Diversity", "Research Careers" ], "content": "Introduction\n\nOver the past decade, calls for research assessment reform have gained great momentum. Initiatives such as the Declaration on Research Assessment1 (DORA) and the Leiden Manifesto2 raised considerable awareness about the need to rethink research assessment and were rapidly followed by a multitude of reports, statements, and recommendations from national and international organisations.3–12 More recently, the interest in changing research assessment even acquired a global scope, with organisations such as the G7,13 UNESCO,14 and the Global Research Council,15 addressing the topic formally. The Coalition for Advancing Research Assessment16 (CoARA) was created against this background, aiming to provide support and coordination to the global reform of research assessment. CoARA already counts the support of nearly 600 research organisations (as of November 2023), highlighting a true momentum for change.\n\nA key element being discussed as part of research assessment reform activities is a shift towards more qualitative assessments, focussed on the content of research and the broad skills and competencies of researchers, and the array of contributions they make to knowledge creation and innovation. Narrative CV formats have emerged as a good practice example for enabling qualitative assessments of research projects and researchers, and are becoming more widely piloted and implemented.\n\n\nMethods\n\nGiven the scope of this report and associated workshop, the workshop was conducted as an exploration from interested organisations without seeking ethical approval. Participants agreed to take part after being made aware that a summary of the workshop would be published from the discussions.\n\nOn April 13th, 2023, we held a workshop with the title “Are narrative CVs proving effective in achieving desired outcomes of recognition and reward initiatives?” at the Recognition and Rewards Festival in Utrecht, NL in order to gather perspectives on the role that narrative CVs play in shifting research cultures and in enabling the research assessment reform. This report summarises the views and opinions expressed by the 14 participants that joined the workshop, and serves as a resource for others in further reflections and development of narrative-style CV templates. Participants included research funders and three researchers, most of them active in the Dutch research landscape. The feedback in this report should help guide organisations and institutions considering or implementing narrative-style CVs when thinking about the potential impact on research culture that could occur due to these changes. In addition, we hope that our experience can be a template for other workshops around this topic, and that this report serves as a catalyst for further dialogue and proactive communication around narrative-style CVs and their impact on research culture.\n\n\nResults\n\nThe workshop participants raised many beneficial and critical aspects of the narrative-style CV, all of which need to be considered by funders and institutions who are implementing these new formats. However, the general agreement was that effective and efficient assessment reform will take time and requires systemic change, due to the many different parties involved in changing assessment, above and beyond only changing a CV format.\n\nIn general, narratives were seen to have always been a part of an evaluation, whether or not they were in the CV. In this sense, a narrative was seen as required for an evaluation – the narrative-style CV helps in increasing the understanding of a candidate and legitimising the contributions that were previously not well-recognised since it requires the researcher to tell their own story about their career and achievements. At the same time, this increased flexibility can be confusing, so balancing structure and flexibility in the formats is needed. This can be a different way of evaluating compared to the current process, leading to difficulties for reviewers in terms of comparing applicants and assessing the content.\n\nParticipants felt that new CV formats can lead to increased use of buzzwords and a loss of authenticity, as they might feel obligated to fill in all of the fields of a template, to “tick all the boxes” and thus get an edge in the evaluation. Certain participants stated that a need to appear competent everywhere might create a loss of authenticity for researchers. While it is important for institutions using a narrative-style CV to emphasise that what is requested is not an increased number and range of accomplishments, participants also argued that a lack of authenticity is generally identifiable in an evaluation (especially an interview), and as such would not prove to be a problem in the long term adoption of new CV formats.\n\nOne of the concerns raised was the perspective that there is not much uptake in narrative-style CV use internationally, and the widespread use of quantitative data and metrics is still present in systems around the world. Given our informal pre-workshop survey results (see Box 1), this perspective might reflect a lack of awareness of the international landscape and use of narrative-style CVs. Regarding the engagement with the format, applicants were told specifically not to add certain (less traditional) contributions because they could be perceived as a “lack of focus”. This shows a clear resistance from a part of the academic community for the narrative-style CV, and a need for more dialogue around these changes.\n\nMethods\n\nA short 12-question survey was devised by the report authors and distributed to representatives from research organisations via the following forums: the DORA Funders Group; the Global Research Council Responsible Research Assessment Working Group; and the Science Europe Working Group on Research Culture.\n\nThe survey was launched between March and April 2023 and received 24 full responses from representatives of 23 research organisations, covering 18 countries across 4 continents and one European-wide organisation. The aggregated data were presented during the workshop at the Recognition and Rewards Festival in Utrecht, NL on 13 April 2023 solely to provoke discussion and are not used for other purposes. The results are presented in this report in the same manner. The survey data were aggregated to avoid re-identification. Raw results data cannot be shared as individual responses would easily allow for identification of the respondent in several cases. The questions asked in the survey, a mix of multiple choice and open text, are provided in the codebook that is available alongside the data published at https://doi.org/10.6084/m9.figshare.25146155.v1.\n\nShort summary of survey results\n\nAcross the 24 respondents to the survey, and in response to both open-ended and multiple choice questions (see annex 1 for the full list of questions), just over half of the responding organisations (54 %) had already implemented a narrative CV format as part of their assessment processes. These organisations were spread across different regions of the world, including Latin America and the Caribbean, Australia and New Zealand, Northern America, and Northern, Western, and Southern Europe. Among these organisations, there was a split between those that implemented the same narrative CV format across all programmes (42 %) and those that implemented the format only for specific programmes (58 %). The most commonly reported approach to implementing a narrative CV was to develop a template ‘in house’, from scratch (54 %). Less commonly, organisations reported building upon an existing template, adapting it to their needs (30 %), and just 2 organisations (15%) reported using existing templates with little adaptation. The Royal Society’s Narrative CV template, the “Résumé for Researchers” was cited by a number of respondents as the guidance template used.\n\nWhen asked what the main reasons or goals for introducing a narrative CV format were, respondents referenced: broadening the recognition of research activities, contributions, and skills; supporting equality, diversity, and inclusion; building compliance with community-driven initiatives such as DORA; and simply as an attempt to improve the evaluation and selection of researchers and research projects.\n\nA wide spread of responses were obtained in response to the question about the years when organisations first considered piloting or introducing a narrative CV format, beginning from 2015, and most commonly around 2020. Subsequent implementation of a narrative CV as part of assessment processes was observed to follow quickly after first consideration, often only taking one or two years (see Figure 1). Some common challenges to implementing narrative CVs were reported by responding organisations, including: 1) resistance to change, 2) difficulty in developing appropriate training and guidance, and 3) clear and effective communication on the reasons for change.\n\nResponding organisations that had not yet implemented narrative CVs (n = 11) within any part of their assessment processes shared diverse reasons why they had not. A number of respondents were considering implementing them in the future. Others reported that it was not a priority for the moment. Some respondents reported a current lack of data to support the effectiveness of such a change as a barrier whilst other respondents cited administrative challenges.\n\nNote: We omitted one respondent in the first question since they mentioned that they always used narrative CVs for hiring.\n\nIt was mentioned that narrative-style CVs have the possibility of helping with increasing the diversity of who is funded, specifically with females and minority groups. The new format allows people to describe a wider diversity of careers and outputs, facilitating inclusion for people with different backgrounds. However, at the same time, the quality of narratives are dependent on writing ability, which could introduce new biases and requirements for support and training – something that not all people and institutions have the resources to implement.\n\nThe introduction of the narrative-style CV is seen as an iterative process with regards to the structure and content requested, as well as the openness of the template. As the needs and focus of the different organisations and the goals of assessments are different, participants felt that a tailored approach is needed for the various narrative-style CV templates. At the same time, participants stressed that funders and institutions should not judge academics beyond what is required for the remit of the assessment, and should take into account potential biases arising from the new format.\n\nIntroduction of narrative-style CVs and other initiatives to diversify and broaden the ability of researchers to demonstrate their achievements have led to concrete changes in the perspectives and careers of people in the community, both with positive and negative effects. Participants discussed the reflection required in filling out a narrative CV being a positive experience, and the need for reflection to be present earlier in academic trajectories. In addition, one participant described a narrative-style CV playing a role in the promotion of people that would have been unlikely to have this opportunity otherwise. Another participant highlighted the role that narrative-style CVs could play in empowering researchers to contribute to research culture shifts by allowing them to describe competencies, activities, or actions that they deem important to the research culture they want to work within.\n\nOne issue raised was around the communication of the shift to a narrative-style CV. The request for a broad range of output and achievements in evaluation was viewed by researchers as a requirement to fulfil the entire breadth of outputs and achievements that can be accounted for. This highlights a need to ensure that researchers are aware of the requirements around narrative-style CVs, through training of applicants and assessors, fostering dialogue around these new forms, and other avenues of proactive communication. Guidance documents are a useful starting point, but are best complemented by active reinforcement, as they are passive tools and are not always read as carefully. As mentioned above, not everyone has an equal level of writing ability, and institutions should offer support where possible to ensure that there is no disadvantage in writing narrative-style CVs.\n\nParticipants highlighted that data collection around the myths and assumptions of narrative-style CVs will also help to ensure clarity of these new evaluation tools. They also suggested that these new formats will cause power dynamics to shift, yet it is not quite clear what this will mean in terms of the evolution of research ecosystems. These shifts should be monitored closely to ensure that the changes fit the research culture that is desired.\n\nAs this shift towards narrative-style CV uptake in assessment processes continues, participants gave their opinions on how this change should be handled, with specific goals and needs they would like to see. These expectations address specifically the culture change that is required to ensure a diverse and inclusive research ecosystem where people are evaluated on a broader range of research outputs, contributions, and achievements.\n\nIn general, participants expressed a need to not be naive in implementing changes, and to try and keep everyone on board through the shift in the research ecosystem. The importance of all roles required in research (e.g. HR staff, technicians, etc.) should be highlighted, and all of these voices should be included in system changes. To this end, a broader diversity of career trajectories should be considered when shifting assessment (and the skills that come along with these different career paths), including careers with inter-sectoral mobility as well as more “classical” career paths.\n\nA need for more diversity and inclusion was requested, specifically in the creation of research systems that are beneficial to younger individuals in research, as well as women and minorities. This can be done through creating more diverse evaluation panels and hiring/promotion assessment committees, as well as by engaging a more diverse group of voices in the dialogue around system adaptation and change. Epistemic diversity should also be taken into account, in order to break the current dominance of “excellence” that reinforces hierarchies between disciplines.\n\nShifting research culture, including spreading the use of the narrative-style CV, requires bottom-up involvement and peer exchange from individuals in research. Collaboration is an important value in research culture, and participants expressed a wish to share their experiences with others. At the same time, adequate support from institutions and funders for these new formats should be put in place. Funders and institutions need to make sure that changes do not impact the performance of research – we need to balance the time and resource commitment required in assessment with the desire for more creative ideas and faster innovation.\n\n\nDiscussion\n\nIt is vital that discussions targeting changes to research assessment practices involve all members of the research community. This report describes results from a workshop that aimed at being the start of an ongoing and self-reflecting discussion on the topic of narrative CVs as contributors to positive shifts in research culture. The workshop, hosted as part of the Dutch Recognition and Rewards Festival (2023), was attended by a group of engaged and reform-supportive stakeholders from research organisations, research funders, and the research community. It provided a first snapshot of perspectives that will be built on through further future events.\n\nReflections by researchers who participated in the workshop emphasised the role that narrative-style CVs can play in broadening the types of activities, contributions, outputs, and achievements that are recognised and how this can translate into a more diverse selection of people and ideas as part of our understanding of high-quality research. They added that the process of completing a narrative CV may in itself provide insights and inspiration on the diversity of activities that are perceived as important in research careers, and that introducing narrative CVs may play a role in shaping new cultures of success and achievements among researchers. Yet the discussion also provided insights on elements that need to be considered in order to ensure that narrative CVs achieve their desired purpose. Key learnings from the workshop discussions included an understanding of existing inequalities in the support (through training and guidance, for instance) provided by research institutions towards narrative CV development, and a lack of clear descriptions of the breadth of activities and outputs that can be included (and how they are assessed). Such inequalities should be scrutinised and minimised so as to avoid introducing additional bias into assessment processes. Workshop participants were not well-aware of the growing interest and uptake of narrative-style CVs and qualitative assessment across research organisations in Europe and beyond: a trend being pushed by community-led initiatives such as DORA and CoARA. Research organisations may consider how they effectively communicate and engage with research community members to shed light on the work and changes taking place to support the evolution of research cultures and promote quality research. As these changes to policies and practices become further embedded in our research systems, it is vital that they are regularly discussed, reviewed, and analysed to identify and mitigate unintended and unwanted consequences that may arise for any constituency within our research communities. Overall, the workshop highlighted the value and importance of engaging community members in research policy and practice discussions, and the need for continued dialogue.\n\nIt is important to note that this change process is long and complex, and narrative-style CVs are just one part. We need to prepare for what the future will bring in research assessment, and make sure that the community actively mitigates the issues that might arise, including the impact of new technologies on assessment and the creation of new inequalities based on different players changing the system at different speeds. A higher-level and global view will be crucial to ensure that the ecosystem is steered towards a diverse and inclusive research culture, which will require all of the participants in the system to work together towards this goal.\n\nTo this end, we encourage more conversations and debate around this topic, as only through dialogue will we be able to create a research culture that recognises and embraces everyone who contributes to the research ecosystem. Workshops like this help to make people more aware of the shifting ecosystem as well as to ensure that a diverse range of voices contribute to these shifts. We propose holding these workshops at a variety of scientific and policy conferences in many domains, so that as many people as possible can contribute to the discussion. If you are organising, participating in, or aware of an event where a structured discussion on Narrative CVs and research culture would be welcome, do not hesitate to contact the authors to explore how a workshop like the one described above could be incorporated or proposed.", "appendix": "Data availability\n\nFigshare: Data on the implementation of Narrative CV captured ahead of the 2023 Recognition and Rewards Festival, https://doi.org/10.6084/m9.figshare.25146155.v1. 17\n\nThis project contains the following underlying data:\n\n• Codebook.pdf\n\n• Codebook.xlsx\n\n• Data.csv\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to thank: 1) the organisers of the 2023 Dutch Recognition and Rewards Festival for hosting the workshop; 2) the participants of the workshop for their enthusiasm the insightful discussions; and 3) the respondents of the informal pre-workshop survey for their time and willingness to provide valuable information.\n\n\nReferences\n\nSan Francisco Declaration on Research Assessment. Reference Source\n\nHicks D, Wouters P, Waltman L, et al.: The Leiden Manifesto for research metrics. Nature. 2015; 520: 429–431. PubMed Abstract \| Publisher Full Text\n\nCurry S, et al.: The changing role of funders in responsible research assessment: progress, obstacles and the way ahead (RoRI Working Paper No. 3). Research on Research Institute; 2020. Publisher Full Text\n\nEuropean University Association: EUA Roadmap on Research Assessment in the Transition to Open Science. Brussels, Belgium: 2018. Reference Source\n\nINORMS Research Evaluation Group: The SCOPE Framework. Emerald Publishing2021. Reference Source\n\nLatin American Forum for Research Assessment (FOLEC): Towards a Transformation of Scientific Research Assessment in Latin America and the Caribbean: Evaluating Scientivic Research Assessment. Latin American Council of Social Sciences (CLACSO); 2020. Reference Source\n\nMcLean R, Ofir Z, Etherington A, et al.: Research Quality Plus - Evaluating Research Differently. Ottawa: International Development Research Centre; 2022. Reference Source\n\nMiedema F, Mayer K, Holmberg K, et al.: Mutual Learning Exercise Open Science: Altmetrics and Rewards. Publications Office of the European Union; 2018. Publisher Full Text\n\nMustajoki H, et al.: Making FAIReR assessments possible.2021. Publisher Full Text\n\nScience Europe: Position Statement and Recommendations on Research Assessment Processes.2020. Publisher Full Text\n\nWilsdon J, et al.: The Metric Tide: Report of the Independent Review of the Role of Metrics in Research Assessment and Management. HEFCE; 2015. Reference Source\n\nWilsdon J, Bar-Ilan J, Frodeman R, et al.: Next-generation metrics: Responsible metrics and evaluation for open science. European Commission; 2017. Publisher Full Text\n\nG7 2021 Research Compact: 2021. Reference Source\n\nUNESCO: UNESCO Recommendation on Open Science. Paris: 2021. Reference Source\n\nGlobal Research Council: Responsible Research Assessment - Call to Action.2021. Reference Source\n\nCoARA: Coalition for Advancing Research Assessment.Reference Source\n\nAubert Bonn N, Stroobants K, Sapcariu S, et al.: Data on the implementation of Narrative CV captured ahead of the 2023 Recognition and Rewards Festival. figshare. [Dataset]. 2024. Publisher Full Text" }	[ { "id": "317744", "date": "25 Sep 2024", "name": "Maria Pietilä", "expertise": [ "Reviewer Expertise Academic careers", "research assessment", "gender equality in academia", "university organisations" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the invitation to review the paper. The paper addresses an important and timely topic: the potential of narrative CVs in changing the current ways of research assessment. It draws on data gathered at a workshop organized in the Netherlands and data obtained from a pre-workshop survey.\nThe paper is well situated in the broader context of research assessment reform. The topic is relevant for readers within the science policy environment in different countries. The paper presents interesting findings which are relevant for the wider scholarly community preparing innovative, responsible ways to assess research/ers.\nI agree with the authors that assessments have for long had narrative elements included. For example, in funding applications researchers have had to put their research proposal in a wider context and to explain its significance to evaluators who may not be experts in the topic. In recruitment, motivation/cover letters represent narratives in which the researchers tell about their skills and career background, often in a free format. Thus, narrative CVs are not completely new in the context of evaluation.\nIn the following, I make some comments/reflections/suggestions that the authors may consider when revising their paper and when organizing future workshops on the topic.\nI would consider adding at the beginning of the paper a brief description of narrative CVs: what do they normally look like, what do they aim for, etc.\nThe paper places significant (mostly positive) expectations on narrative CVs and maintains an overall optimistic tone toward their use. However, some of the findings in the paper sound more like hypothesis for empirical research. For example, the argument that narrative CVs are good for women and minorities was put forward by the workshop participants. In the paper, you could consider, whether there is a need to critically assess this expectation - is there any empirical research showing that this is the case? I also wonder to what extent narrative CVs in practice lead to the acknowledgement of a broader set of skills. Changing the documentation does not mean that the valuations critical for assessment change. Candidates applying for funding or jobs may still be inclined to present traditional outputs in their narrative CVs (maybe for good reasons). Despite universities/funders’ goal towards identifying and acknowledging a wider set of researchers’ contributions, evaluators may still give priority to traditional outputs and activities at the extent of others. Therefore, the authors might reflect on the need to take into account broader power dynamics in academic recruitment with different actors and priorities and the 'cultural burden' connected to existing research assessment practices that may shape how contributions in narrative CVs are assessed.\n\nI would argue organizations using narrative CVs should be encouraged to state clearly how different contributions in narrative CVs are assessed: if all the contributions are of equal value or if some are more valued than others, given the different needs of the funder/employing unit. Objective comparison of candidates’ merits/achievements is crucial for example in recruitment, and thus having transparent criteria and showing them to the applicants is essential (this was touched upon on page 4).\nTherefore, I suggest adding some more reflection on the needs for further academic research on the topic (with proper research designs; such research is already being conducted). Also, the authors are encouraged to consider ‘practice-oriented sessions’ on how to evaluate narrative CVs in the future workshops (incl. how to make comparisons between candidates who bring up different kinds of contributions in their narrative CVs).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "336924", "date": "25 Nov 2024", "name": "Simon Kolstoe", "expertise": [ "Reviewer Expertise Originally a Biochemist", "now Associate Professor of Bioethics with a specific interest in research integrity", "ethics and governance." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nNarrative CVs - where next on the journey?\nWho your audience is, and what you are trying to communicate to that audience, is the most important consideration for authors of any type of document. When writing an academic CV the audience is often an employment or grants panel who will be looking for indications that the author will meet whatever criteria they have established for the role/funding. The problem is that the criteria is not always explicit, and can often reflect unrecognised prejudice, making it quite a challenge to write a CV that \"plays the game\" well, especially for people with diverse or non-traditional backgrounds.\nTo address this a number of \"key performance indicator\" (KPI) style metrics have been proposed for academics/researchers, and although they are widely used, they are open to significant manipulation. They are also quite biased towards indicators that current senior researchers value in their own CVs, rather than indicators that might lead to better research overall.\nThis weakness of the KPI approach has been increasingly recognised over recent years thanks to an encouraging international effort to consider issues relating to research integrity and culture in order to highlight the broader virtues and responsibilities of a good researcher. The development of narrative CVs is one attempt to recognise this by using, as the authors of this manuscript state, a qualitative rather than quantitative approach.\nHowever, as with many issues in life, a pendulum swing from one extreme (quantitative indicators) to the other (qualitative indicators) is not the answer. The solution to fair assessment most likely sits somewhere in the middle, with this middle being identified through further discussion and reflection on what we do now, what works or doesn't, and how we might change systems and processes. This is precisely the conversation that this manuscript addresses.\nViewing this work as a reflection on narrative CVs is helpful, because the sample size is small. Indeed with only 24 responses to the survey I would like to see the authors report number of responses in their summary of survey results rather than percentages to better reflect the very small sample. Likewise the 14 participants in the workshop cannot in anyway be considered representative of the research community, and this should be acknowledge explictly. Thus said a very small sample does not prevent interesting observations being made.\nOne element of the results/discussion I did find interesting was the fear that narrative CVs may favour more talented writers, potentially coming from English speaking education systems. This is a fair comment and concern, but I would also like to see the author address the recent challenge raised by the use of AI for both proof reading and also creating content. Surely this must be an increasing threat to the idea of a narrative CV, and even if it wasn't mentioned by participants in the workshop, the author could raise the fact that this wasn't discussed and perhaps should have been.\nI was also struck by the comment that \"Epistemic diversity should also be taken into account, in order to break the current dominance of “excellence” that reinforces hierarchies between disciplines\". I think this relates to a perceived prejudice towards medical and physical sciences that many from a social science background are often quite concerned about. However, as many CVs often function to obtain positions/grants etc. within subject areas, and thus are judged by academics of similar backgrounds, I would be interested to hear some real examples of where Epistemic diversity is important.\nThe Discussion starts with the sentence: \"It is vital that discussions targeting changes to research assessment practices involve all members of the research community.\" I'm not certain this sentence is needed, or indeed justified without further explanation - who is the research community, does it involve research participants, government ministers etc. and should they all be involved in this conversation? Perhaps this sentence could be deleted or alternatively justified further.\nThe second paragraph of the discussion also repeats many of the results so could either be deleted or reframed to make a specific, explicit, point.\nBut overall this manuscript represents an interesting reflection on the topic, and should be considered as a valuable contribution to the ongoing discussion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-332
https://f1000research.com/articles/13-331/v1	23 Apr 24	{ "type": "Brief Report", "title": "SARS-CoV-2-ORF3a variant Q57H reduces its pro-apoptotic activity in host cells", "authors": [ "Maria Landherr", "Iuliia Polina", "Michael W. Cypress", "Isabel Chaput", "Bridget Nieto", "Bong Sook Jhun", "Jin O-Uchi", "Maria Landherr", "Iuliia Polina", "Michael W. Cypress", "Isabel Chaput", "Bridget Nieto", "Bong Sook Jhun" ], "abstract": "Background Mutations in the viral genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can enhance its pathogenicity by affecting its transmissibility, disease severity, and overall mortality in human populations. In addition to mutations within the coding region of SARS-CoV-2 structural proteins, there have been reports of mutations in other SARS-CoV-2 proteins that affect virulence, such as open reading frame 3a (ORF3a), which is involved in viral replication. The expression of ORF3a in host cells activates cell death signaling, leading to tissue damage, which affects the severity of COVID-19. The ORF3a-Q57H variant is the most frequent and recurrent variant of ORF3a and is likely associated with increased transmissibility but lower mortality in the 4th epidemic wave of COVID-19 in Hong Kong. Computational structural modeling predicted that the Q57H variant destabilizes the protein structure of ORF3a, which may result in reduced protein expression in human cells. However, it is still unknown how this mutation affects ORF3a protein function and, if so, whether it can change the severity of host cell damage.\n\nMethods\nPlasmids carrying SARS-CoV-2-ORF3a from Wuhan-Hu-1 strain (i.e., wild-type; WT) and its variant Q57H were transiently transfected into HEK293T cells and used for biochemical and cell biological assays.\n\nResults SARS-CoV-2-ORF3a-Q57H variant exhibits higher protein expression than WT, but ORF3a-Q57H expression results in less apoptosis in host cells compared to WT via lower activation of the extrinsic apoptotic pathway.\n\nConclusion The relatively mild phenotype of the SARS-CoV-2-ORF3a-Q57H variant may result from alterations to ORF3a function by this mutation, rather than its protein expression levels in host cells.", "keywords": [ "mitochondria", "apoptosis", "cell death", "cell signaling" ], "content": "Introduction\n\nCOVID-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the global pandemic that began in 2020.1 SARS-CoV-2 can produce 29 proteins, including 9 accessory proteins encoded by open reading frames.2,3 These proteins were originally identified as critical factors for viral entry, viral genome production and replication, virion morphogenesis, and viral release from the host cells.2,4\n\nMutations in the SARS-CoV-2 genome can alter its pathogenic potential, ultimately affecting the severity and transmissivity of COVID-19 in humans.5 Since 2020, the World Health Organization has been identifying, tracking, characterizing, and labeling some SARS-CoV-2 variants as “variants of interest” and “variants of concern” to prioritize global monitoring and research.6 Thirty-six non-synonymous and 78 synonymous mutations have been reported in open reading frame 3a (ORF3a), which is the largest accessory protein in the SARS-CoV-2 genome.7 The 25563G>T-(Q57H) variant is the most common ORF3a variant (30-40%) reported in COVID-19 patients in the US, and the next most frequent ORF3a variant is 10 times less prevalent than Q57H.8 Q57 is located near the end of the first transmembrane domain of ORF3a, facing the hydrophobic lipid interface,9,10 which changes the amino acid glutamine (Q), which has a non-charged polar side chain, into the positively charged amino acid histidine (H). ORF3a-Q57H was first identified in Singapore in 2020 and has since been observed in the COVID-19 Beta, epsilon, and Mu variants.3 Q57H was the only mutant consistently reported with a high frequency in the entire period of 2020, whereas the frequency of the other ORF3a mutations fluctuated.10 In the fourth epidemic wave of COVID-19 in Hong Kong, this variant was associated with increased transmission and decreased mortality rates.11 Viral samples isolated from patients during this wave did not exhibit enhanced replication kinetics or cytokine/chemokine induction in the host cells. A recent study using computational modeling9 predicted that the Q57H mutation may decrease protein stability and increase the rigidity of the ORF3a protein compared to the original Wuhan-Hu-1 strain (i.e., wild-type; WT), which likely affects downstream signaling in host cells. However, it has not been established whether the Q57H mutant affects the function of ORF3, its role in host cell damage during SARS-CoV-2 infection, and ultimately the severity of COVID-19 phenotypes in patients.\n\nBased on the computational prediction of negative folding stability in SARS-CoV-2-Q57H by Wang et al.,9 we hypothesized that the SARS-CoV-2-ORF3a-Q57H variant produces less protein expression in host cells than WT-ORF3a, thus exhibiting less oxidative stress and apoptosis, which may contribute to decreased mortality in COVID-19 patients. Here, we report that the SARS-CoV-2-ORF3a-Q57H variant does not exhibit lower protein expression, but rather exhibits a relatively higher expression compared to the WT. Moreover, this variant expression causes less activation of the extrinsic apoptotic pathway in the host cells. Our findings may support the potential molecular linkage between this major mutation and a mild phenotype, but higher transmissibility, in COVID-19 patients.\n\n\nMethods\n\nThe antibodies and plasmids used in the experiments are listed in Tables 1 and 2, respectively. All the cells, chemicals and reagents were purchased from Sigma-Aldrich Corporation (St. Louis, MO, USA) unless otherwise listed in Table 3.\n\nStudy protocol was approved by the Institutional Biosafety Committee at University of Minnesota (#2305-41075H). HEK293T and H9c2 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 4.5 g/L glucose, 1 mM sodium pyruvate, 1% L-glutamine, 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 °C with 5% CO2 in a humidified incubator, transfected with plasmids (0.5-3 μg/3.5-cm dish) using Fugene HD, and used for experiments 48 to 72-hr after transfection.12,13\n\nMitochondria-enriched fractions were separated from cytosolic fractions by different centrifugation speeds and dissolved with lysis buffer containing protease inhibitor cocktails and 1 mM phenylmethylsulfonyl fluoride, and subjected to western blotting.12,13 The immunoreactive bands were visualized, and the whole blotting images for each figure panel14 were obtained using a near-infrared fluorescence imaging system (LI-COR Biotechnology, Lincoln, NE, USA).12,13\n\nCells stained with cell-permeable dyes (Table 3) were observed by an FV3000 confocal microscope (Olympus, Tokyo, Japan) at room temperature. Localization of GFP-tagged proteins was observed in H9c2 cells stably overexpressing mitochondrial matrix-targeted DsRed (mt-RFP) and the colocalization efficiency was estimated using Pearson’s correlation coefficient.12\n\nAll data are presented as the mean ± standard error (SEM). Unpaired Student’s t-test and one-way ANOVA followed by Tukey’s post-hoc test were performed for two-group comparisons and multiple comparisons, respectively, with statistical significance defined as a p-value < 0.05.\n\n\nResults\n\nWe first tested the effect of Q57H on ORF3a protein expression levels in HEK293T cells by transiently expressing non-tagged and GFP-tagged SARS-CoV-2-ORF3a (Figure 1A). In the plasmid expressing non-tagged ORF3a, ORF3a is tagged with GFP by bridging “self-cleaving” small polypeptides (P2A),15 allowing for bicistronic expression of non-tagged ORF3a proteins and GFP. Small amounts of the non-cleaved form also existed, but ORF3a protein expression levels were estimated by the amount of cleaved GFP (Figure 1B). Contrary to computational predictions,9 we did not observe a significant decrease in ORF3a protein expression by Q57H mutations, but rather ORF3a-Q57H exhibited relatively higher protein expression compared to WT-ORF3a (Figure 1B-D) as assessed by immunostaining with GFP antibody. Thus, differences in protein expression levels between WT and mutant ORF3a are more likely to occur via post-translational processes rather than transcriptional regulation.\n\nA. SARS-CoV-2-ORF3a constructs used in this study. B. Expression of WT- and Q57H mutant ORF3a-P2A-GFP in HEK293T cells. The pEGFP-C1 empty plasmid expressing only EGFP was shown as a control. Each construct was transfected with 0.5, 1.0, or 3.0 μg per 3.5 cm dish. Tubulin was used as a loading control. CTR, cells with no transfection. IB, immunoblotting C. Expression of WT- and Q57H-ORF3a-GFP constructs in HEK293T cells. D. Summary data of B and C (n = 4). In each panel, band intensity was normalized to the value from 0.5 μg of WT- ORF3a construct transfection.\n\nUsing a computational model, Wang et al. predicted that the ORF3a protein structure becomes more rigid and less flexible after the Q57H mutation9 and may result in less activation of downstream signaling that causes host cell damage. We tested cellular damage by WT-ORF3a and Q57H-ORF3a proteins in H9c2 cardiac myoblasts because this cell line is more vulnerable to oxidative, apoptotic, and inflammatory signaling than cancer cell lines, including HEK293T cells.12,16 We used non-tagged ORF3a constructs (i.e., ORF3a-P2A-GFP, Figure 1A) for this assay to avoid the potential impact of tag modification on ORF3a protein activity. GFP was used as the control. A recent report has shown that SARS-CoV-2-ORF3a expression can activate apoptotic signaling.17 We found that the expression of WT-ORF3a, but not ORF3a-Q57H, increased caspase-3 activity in H9c2 cells, as assessed by the amount of cleaved caspase-3 (Figure 2A and B). Caspase-3 activity was also evaluated by live-cell staining with a fluorogenic DNA dye coupled to the caspase-3/7 DEVD recognition sequence (NucView® substrates). GFP itself produced a population of apoptotic cells as reported,18 but WT-ORF3a expression significantly increased the number of apoptotic cells compared to GFP (Figure 2C and D). The number of apoptotic cells in Q57H cells was similar to that in GFP cells and significantly lower than that in WT-ORF3a cells (Figure 2C and D).\n\nA. Cleaved caspase-3 in H9c2 cells overexpressing WT and mutant ORF3a. GFP was transfected as a control. Each construct was transfected with 0.5, 1.0, or 3.0 μg per 3.5-cm dish. B. Summary data of A (n= 5). All values were normalized to the value from 0.5 μg of the transfected GFP control. p<0.05. C. Detection of caspase-3 activity in live H9c2 cells stained with Nucview 405 Caspase-3. GFP-positive cells were selected as transfected cells, and nuclear staining-positive cells by fluorogenic DNA dye were counted as apoptotic cells under the confocal microscopy. D. Summary data of C from three independent experiments. p<0.05. N.S., not significant.\n\nIn addition to apoptotic responses, several groups have shown that the expression of SARS-CoV-2-ORF3a constructs with protein tags activate inflammatory signaling, endoplasmic reticulum (ER) stress, and autophagy flux.19–24 First, non-tagged WT-ORF3a and Q57H did not produce significant inflammatory responses, as assessed by the protein expression levels of IL-1β, NLRP3, and cleaved caspase-1 (Figure 3A-D). The expression of ER stress markers, including glucose-regulated protein 94 (Grp94), glucose-regulated protein 78 (Bip/Grp78), and C/EBP-homologous protein (CHOP),25 did not change after the expression of either WT-ORF3a or -Q57H in our system (Figure 3E and F). Finally, both WT-ORF3a and its mutant Q57H showed a similar tendency of increased microtubule-associated protein light chain 3 (LC3)-II/LC3-I ratio, a standard marker indicating the induction of autophagy, but these changes were not significant compared to control cells transfected with GFP (Figure 3G and H). In summary, SARS-CoV-2-ORF3a expression induces apoptotic signaling activation rather than modulating inflammation, ER stress, and autophagic signaling cascades. Importantly, Q57H expression was less involved in apoptotic signaling activation than that of WT-ORF3a.\n\nA. Assessment of inflammatory activity by cleaved caspase-1 and IL-1β in H9c2 cells expressing WT and mutant ORF3a. GFP was transfected as a control. Cell lysates treated with nigericin (15 μm for 60 min) and a recombinant IL-1β protein were used as positive controls. All values were normalized to the value from 0.5 μg of the transfected GFP control. B. Summary data of A (n=3). C. Detection of the NLRP3 inflammasome in H9c2 cells expressing WT and mutant ORF3a. All values were normalized to the value from the cells transfected with 0.5 μg of GFP. D. Summary data of C (n= 4). E. Assessment of the expression of ER stress markers Grp78, Grp94, and CHOP in H9c2 cells transfected with WT and mutant ORF3a. GFP was transfected as a control. F. Summary data of E (n=4, n =3, n=3, respectively). G. Assessment of autophagic flux by the LC3-II/LC3-I ratio in H9c2 cells expressing WT and mutant ORF3a. GFP was transfected as a control. H. Summary data of G (n=5). The ratio of LC3-II (low molecular weight) to LC3-I (high molecular weight) was calculated and normalized to the value from 0.5 ug of the transfected GFP control.\n\nA recent report showed that SARS-CoV-2-ORF3a-ORF3a could activate both the intrinsic and extrinsic pathways of apoptosis.17 Therefore, we examined the activities of signaling molecules from both apoptotic pathways after WT-ORF3a or ORF3a-Q57H expression. The extrinsic pathway caspase-8 was significantly activated by WT-ORF3a expression compared to that in control cells, as assessed by a cell-permeable caspase-8 activity marker, Red-IETD-FMK. However, preincubation with a general caspase inhibitor, Z-VAD-FMK, abolished this change (Figure 4A and B). Q57H expression did not show significant caspase-8 activation (Figure 4A and B), and this difference between ORF3a-WT and -Q57H was unlikely based on the expression levels of the constructs, as confirmed by the expression levels of bicistronically expressed GFP (Figure 4B and C). Caspase-8 is activated by an extrinsic pathway (e.g., cell-surface death receptors) and is known to propagate the apoptotic signal either by directly cleaving and activating downstream caspases (e.g., caspase-3) or by cleaving Bid.26 Cells expressing WT-ORF3a (but only in the lower transfection conditions) showed a significant increase in the truncated Bid (tBid)/Bid ratio, but not by Q57H (Figure 4D and E). These results suggest that the Q57H variant exhibits less activation of the extrinsic apoptotic pathway compared to the WT.\n\nA. Representative confocal images of H9c2 cells transfected with the indicated plasmids and stained with a cell-permeable marker dye for caspase-8 activation, Red-IETD-FMK. Red-IETD-FMK was detected under confocal microscopy with excitation and emission wavelengths of 488 and 570 nm, respectively. ORF3a-WT overexpressed cells pretreated with Z-VAD-FMK for 1 hr were used as a negative control. Scale Bars = 20 μm B. Summary data of A. p<0.05, compared to GFP-transfected cells. Each fluorescence value was normalized to the average fluorescence calculated from GFP-transfected cells. C. Scatter plots of GFP and Red-IETD-FMK measured from individual cells. D. Representative immunoblot of tBid/Bid in H9c2 cells expressing WT and mutant ORF3a. GFP was transfected as a control. E. Summary data of D. p<0.05, compared to 0.5 ug of the transfected GFP control. p<0.05.\n\nNext, we investigated the effect of WT-ORF3a and ORF3a-Q57H on the intrinsic apoptotic pathway. Since the SARS-CoV-2-ORF3a protein is predicted to possess three transmembrane domains similar to SARS-CoV-1-ORF3a, and its subcellular localization is likely distributed to several membrane structures,27 we next tested whether ORF3a can be expressed in the mitochondria. Indeed, ORF3a protein was found in the mitochondria-enriched fraction compared to that in the cytosolic fraction (Figure 5A). Both WT-ORF3a and Q57H-ORF3a were partially localized in the mitochondrial area labeled by mt-RFP, and their subcellular distribution patterns were not significantly different, as assessed by the values of Pearson’s correlation coefficient (Figure 5B and C). We also found that the Q57H variant was capable of activating caspase-9, and assessed caspase-9 activity, an initiator of intrinsic apoptosis, whose level was comparable to that in WT assessed by Ac-LEHD-ProRed staining (Figure 5D). In summary, these results suggest that the different caspase-3 activation levels in WT-ORF3a and Q57H-ORF3a are mainly due to their different effects on the extrinsic apoptotic pathway.\n\nA. Expression of WT-ORF3a-Strep in fractionated proteins from H9c2 cells. Cells transfected with pLVX-EF1α-IRES-puro were used as a control (CTR). Argonaute 2 (Argo2) and optic atrophy-1 (OPA1) were used as markers for the cytosolic fraction (C) and mitochondrial fraction (M), respectively. Whole cell lysates (W) were shown for comparison. B. Representative confocal images of the subcellular localization of GFP, WT-ORF3a-GFP, ORF3a-Q57H-GFP, mitochondrial Ca2+ uniporter (MCU)-GFP (as a positive control) in live H9c2 cells stably expressing mt-RFP. Scale bars = 20 μm. C. Summary data of the mitochondrial localization of GFP constructs estimated by Pearson’s correlation values between the GFP and mt-RFP signals. p<0.05. N.S., not significant. Cells transfected with a mitochondrial protein MCU-GFP were used as a positive control. D. Assessment of caspase-9 activity in live H9c2 cells transfected with indicated plasmids stained with a cell-permeable caspase-9-specific fluorogenic substrate, Ac-LEHD-ProRed. ORF3a-WT overexpressed cells pretreated for 1 hr with a caspase 9-specific inhibitor, Z-LEHD-FMK, were used as a negative control. ProRed cleaved from Ac-LEHD-ProRed was detected using confocal microscopy with excitation and emission wavelengths of 540 and 620 nm, respectively. The ProRed fluorescence value was normalized to the average fluorescence calculated from GFP-transfected cells.\n\n\nDiscussion\n\nAlthough the protein sequences of ORF3a from SARS-CoV-1 and CoV-2 have only moderate homology (72%),3 the expression of both proteins in mammalian cells promotes apoptosis.17 Our results showed that Q57H, the most frequent and recurrent variant of SARS-CoV-2-ORF3a, exhibits higher protein expression compared to SARS-CoV-2-ORF3a-WT (Figure 1) but induces less apoptosis in host cells due to a lack of extrinsic apoptotic pathway activation (Figures 2-4, and 6). This property may provide advantages for the SARS-CoV-2-Q57H infection to be relatively mild, thus allowing the virus to have higher transmissivity, as was the case in the fourth epidemic wave of COVID-19 in Hong Kong.11\n\nSARS-CoV-2-ORF3a induces apoptosis in host cells via activating both intrinsic and extrinsic pathways. ORF3a-Q57H shows less apoptotic activity compared to WT via less activation of the extrinsic apoptotic pathway.\n\nAlthough the SARS-CoV-2-ORF3a protein can induce apoptotic signaling activation similar to SARS-CoV-1-ORF3a,28 Ren et al. recently reported that SARS-CoV-2-ORF3a has a relatively weaker effect on activating apoptotic signaling than SARS-CoV-1.17 Moreover, they showed that plasma membrane localization of ORF3a is required for activating apoptotic signaling in SARS-CoV-2. Ren et al. suggested that 1) SARS-CoV-2-ORF3a mainly activates the extrinsic apoptotic pathway, and 2) the intrinsic pathway is secondarily activated downstream of the extrinsic apoptotic pathway. Importantly, the location of the Q57H mutation in the ORF3a structure is far from the key motifs for plasma membrane sorting (i.e., cysteine-rich motif C130/133 and/or tyrosine-based sorting motif Y16017). This indicates that the mutation does not likely interfere with the plasma membrane sorting of the RFF3a protein, although neither SARS-CoV-2-ORF3a-WT nor -Q57H showed specific plasma membrane expression localized in multiple cellular compartments, including the cytosol and mitochondria (Figure 5B).\n\nAnother key finding was that SARS-CoV-2-ORF3a-WT was able to activate the extrinsic apoptotic pathway in the absence of death receptor ligands (Figures 4 and 6). This observation17 suggests that it is likely that ORF3a at the plasma membrane is capable of 1) transactivating death receptors (DRs) by direct or indirect interactions with DRs at the plasma membrane, 2) causing conformational changes in the death-inducing signaling complex (DISC) (i.e., association of the receptor-bound Fas-associated cytoplasmic death domain [FADD] and caspase-8),29 and/or 3) inhibiting the activity of cellular FADD-like IL-1β-converting enzyme-inhibitory proteins such as c-FLIP.29 Because Q57H is located near the end of the first transmembrane domain of ORF3a, which is close to the cytoplasmic face,9,10 the Q57H mutation may alter the interaction between ORF3a, DRs, and/or DISC within or beneath the plasma membrane. Further studies are required to identify the detailed molecular mechanisms by which ORF3a activates DRs and/or DISC, and whether the Q57H mutation alters this mechanism.\n\nOur data also showed that WT-ORF3a and ORF3a-Q57H both activated intrinsic apoptotic signaling at similar levels, even though Q57H exhibited less activation of extrinsic apoptotic signaling compared to WT (Figures 4-6). This result indicates that SARS-CoV-2-ORF3a can initiate intrinsic apoptotic signaling independent of extrinsic apoptotic signaling (Figure 6). In both SARS-CoV-1 and -CoV-2, ORF3a has three predicted transmembrane domains3,10 and has been localized in several cellular membrane structures/organelles in host cells, including the plasma membrane, endoplasmic reticulum, Golgi, and lysosomes.30–34 Our protein fractionation and imaging data showed that ORF3a was also localized in the mitochondria (Figure 5A-C), where it likely increased mitochondrial membrane permeability and promoted the release of apoptotic proteins. SARS-CoV-1-ORF3a can form K+-permeable viroporins28,34 that are required to induce ORF3a-mediated cell apoptosis.28 Although still controversial,33 SARS-CoV-2-ORF3a might also form K+-permeable channels at the inner mitochondrial membrane (IMM), which can depolarize the mitochondrial membrane potential similar to the opening of endogenous K+ channels expressed at the IMM, such as the mitochondrial BKCa channel.35 If ORF3a is expressed in the outer mitochondrial membrane (OMM), it is possible that ORF3a may interact with structural proteins that regulate OMM permeability.\n\nLastly, we tested whether SARS-CoV-2-ORF3a can modulate autophagy flux, ER stress, and inflammatory signaling in addition to apoptosis, but these signaling pathways were not significantly activated in our system (Figure 3). The different results may be partly due to the use of different cell types, which may provide different ORF3a expression levels and/or sensitivity to the stress-signaling pathway. In addition, the majority of published data19–24,36 were generated from ORF3a constructs with various protein tags, which may alter ORF3a protein function because it is a relatively small protein (~30 kDa). Nevertheless, our results clearly showed a major difference in the activation of apoptotic signaling between ORF3a-WT and Q57H, especially in the extrinsic signaling pathway.\n\nIn summary, despite its relatively higher protein expression compared to WT, SARS-CoV-2-ORF3a-Q57H variant expression causes less apoptosis in mammalian cells because of lower activation of the extrinsic apoptotic pathway. As our experiments were performed only in cultured cell lines transfected with a part of SARS-CoV-2 (i.e., ORF3a), we still need to consider that our findings cannot be directly applicable to the in vivo situation with SARS-CoV-2 infection. Animal models using SARS-CoV-2 are indispensable for exploring the detailed role of the ORF3a signaling pathway in vivo. Despite these limitations, our results suggest that the relatively mild phenotype of the Q57H variant observed in 4th epidemic wave of COVID-19 in Hong Kong and several COVID-19 variants (i.e., Beta, Epsilon, and Mu) may result from weaker pro-apoptotic signaling. Assessing the cellular effects of ORF3a mutations will improve our understanding of the pathophysiology of COVID-19 and inform the design of new therapeutic strategies to prevent and treat COVID-19 and its long-term symptoms.37", "appendix": "Data availability statement\n\nFigshare: Supplementary materials for manuscript “SARS-CoV-2-ORF3a variant Q57H reduces its pro-apoptotic activity in host cells”. https://doi.org/10.6084/m9.figshare.24803106.v1. 14\n\nThis project contains the following underlying data:\n\nOriginal Western blotting images\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nThis study was partially supported by NIH/NHLBI R01HL136757 (to J.O.-U.) and R01HL160699 (to B.S.J.), a COVID19 Response Grant (to J.O.-U.) from the Institute of Engineering in Medicine (IEM) at the University of Minnesota (UMN) and COVID-19 Response Grants (to J.O.-U. and B.S.J.) from the Office of Academic Clinical Affairs at UMN, the American Heart Association 18CDA34110091 (to B.S.J), and the IEM Annual Conference Pilot Project Grant (to I.P.) from IEM at UMN.\n\n\nReferences\n\nAl-Awwal N, Dweik F, Mahdi S, et al.: A Review of SARS-CoV-2 Disease (COVID-19): Pandemic in Our Time. Pathogens. 2022; 11: 368. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYadav R, Chaudhary JK, Jain N, et al.: Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19. Cells. 2021; 10: 821. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang J, Ejikemeuwa A, Gerzanich V, et al.: Understanding the Role of SARS-CoV-2 ORF3a in Viral Pathogenesis and COVID-19. Front. Microbiol. 2022; 13: 854567. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZandi M, Shafaati M, Kalantar-Neyestanaki D, et al.: The role of SARS-CoV-2 accessory proteins in immune evasion. Biomed. Pharmacother. 2022; 156: 113889. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBakhshandeh B, Jahanafrooz Z, Abbasi A, et al.: Mutations in SARS-CoV-2; Consequences in structure, function, and pathogenicity of the virus. Microb. Pathog. 2021; 154: 104831. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAleem A, Akbar Samad AB, Vaqar S: Emerging Variants of SARS-CoV-2 And Novel Therapeutics Against Coronavirus (COVID-19). StatPearls. Treasure Island (FL): StatPearls Publishing LLC; 2023.\n\nKim J, Jang J, Kim J, et al.: Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome. Osong. Public Health Res. Perspect. 2020; 11: 101–111. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHassan SS, Attrish D, Ghosh S, et al.: Pathogenic perspective of missense mutations of ORF3a protein of SARS-CoV-2. Virus Res. 2021; 300: 198441. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang R, Chen J, Gao K, et al.: Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Commun Biol. 2021; 4: 226–228. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBianchi M, Borsetti A, Ciccozzi M, et al.: SARS-Cov-2 ORF3a: Mutability and function. Int. J. Biol. Macromol. 2021; 170: 820–826. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChu DKW, Hui KPY, Gu H, et al.: Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. Emerg. Infect. Dis. 2021; 27: 1492–1495. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJhun BS, O-Uchi J, Adaniya SM, et al.: Protein kinase D activation induces mitochondrial fragmentation and dysfunction in cardiomyocytes. J. Physiol. 2018; 596: 827–855. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nO-Uchi J, Jhun BS, Xu S, et al.: Adrenergic signaling regulates mitochondrial Ca2+ uptake through Pyk2-dependent tyrosine phosphorylation of the mitochondrial Ca2+ uniporter. Antioxid. Redox Signal. 2014; 21: 863–879. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLandherr M, Polina I, Cypress M, et al.: Supplementary materials for manuscript “SARS-CoV-2-ORF3a variant Q57H reduces its pro-apoptotic activity in host cells”.2023. Publisher Full Text\n\nKim JH, Lee S, Li L, et al.: High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PLoS One. 2011; 6: e18556. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang M, Sun J, Stowe DF, et al.: Knockout of VDAC1 in H9c2 Cells Promotes Oxidative Stress-Induced Cell Apoptosis through Decreased Mitochondrial Hexokinase II Binding and Enhanced Glycolytic Stress. Cell. Physiol. Biochem. 2020; 54: 853–874. PubMed Abstract \| Publisher Full Text\n\nRen Y, Shu T, Wu D, et al.: The ORF3a protein of SARS-CoV-2 induces apoptosis in cells. Cell. Mol. Immunol. 2020; 17: 881–883. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnsari AM, Ahmed AK, Matsangos AE, et al.: Cellular GFP Toxicity and Immunogenicity: Potential Confounders in in vivo Cell Tracking Experiments. Stem Cell Rev. Rep. 2016; 12: 553–559. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang Y, Sun H, Pei R, et al.: The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. Cell Discov. 2021; 7: 31-z. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSu J, Shen S, Hu Y, et al.: SARS-CoV-2 ORF3a inhibits cGAS-STING-mediated autophagy flux and antiviral function. J. Med. Virol. 2022; 95. Publisher Full Text\n\nZhang X, Yang Z, Pan T, et al.: SARS-CoV-2 ORF3a induces RETREG1/FAM134B-dependent reticulophagy and triggers sequential ER stress and inflammatory responses during SARS-CoV-2 infection. Autophagy. 2022; 18: 2576–2592. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSu W, Yu X, Zhou C: SARS-CoV-2 ORF3a Induces Incomplete Autophagy via the Unfolded Protein Response. Viruses. 2021; 13: 2467. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi X, Kuang E: Reticulophagy Reprograms the Endoplasmic Reticulum for SARS-CoV-2 Replication. Front. Cell Dev. Biol. 2022; 10: 896618. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXu H, Akinyemi IA, Chitre SA, et al.: SARS-CoV-2 viroporin encoded by ORF3a triggers the NLRP3 inflammatory pathway. Virology. 2022; 568: 13–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNgoh GA, Papanicolaou KN, Walsh K: Loss of mitofusin 2 promotes endoplasmic reticulum stress. J. Biol. Chem. 2012; 287: 20321–20332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElmore S: Apoptosis: a review of programmed cell death. Toxicol. Pathol. 2007; 35: 495–516. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang J, Crosme R, Zhuang M, et al.: A systemic and molecular study of subcellular localization of SARS-CoV-2 proteins. Signal Transduct. Target. Ther. 2020; 5: 269. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChan CM, Tsoi H, Chan WM, et al.: The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function. Int. J. Biochem. Cell Biol. 2009; 41: 2232–2239. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWilson NS, Dixit V, Ashkenazi A: Death receptor signal transducers: nodes of coordination in immune signaling networks. Nat. Immunol. 2009; 10: 348–355. PubMed Abstract \| Publisher Full Text\n\nYuan X, Li J, Shan Y, et al.: Subcellular localization and membrane association of SARS-CoV 3a protein. Virus Res. 2005; 109: 191–202. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFreundt EC, Yu L, Goldsmith CS, et al.: The open reading frame 3a protein of severe acute respiratory syndrome-associated coronavirus promotes membrane rearrangement and cell death. J. Virol. 2010; 84: 1097–1109. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCruz-Cosme R, Zhang J, Liu D, et al.: A novel diG motif in ORF3a protein of SARS-Cov-2 for intracellular transport. Front. Cell Dev. Biol. 2022; 10: 1011221. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMiller AN, Houlihan PR, Matamala E, et al.: The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins. elife. 2023; 12: 10.7554/eLife.84477. Publisher Full Text\n\nLu W, Zheng BJ, Xu K, et al.: Severe acute respiratory syndrome-associated coronavirus 3a protein forms an ion channel and modulates virus release. Proc. Natl. Acad. Sci. USA. 2006; 103: 12540–12545. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGonzalez-Cota AL, Santana-Calvo C, Servin-Vences R, et al.: Regulatory mechanisms of mitochondrial BK (Ca) channels. Channels (Austin). 2021; 15: 424–437. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSu J, Shen S, Hu Y, et al.: SARS-CoV-2 ORF3a inhibits cGAS-STING-mediated autophagy flux and antiviral function. J. Med. Virol. 2023; 95: e28175. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang S, Tian M, Johnson AN: SARS-CoV-2 protein ORF3a is pathogenic in Drosophila and causes phenotypes associated with COVID-19 post-viral syndrome. bioRxiv. 2020. Reference Source\n\nYoon Y, Krueger EW, Oswald BJ, et al.: The mitochondrial protein hFis1 regulates mitochondrial fission in mammalian cells through an interaction with the dynamin-like protein DLP1. Mol. Cell. Biol. 2003; 23: 5409–5420. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGordon DE, Jang GM, Bouhaddou M, et al.: A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020; 583: 459–468. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDe Stefani D, Raffaello A, Teardo E, et al.: A forty-kilodalton protein of the inner membrane is the mitochondrial calcium uniporter. Nature. 2011; 476: 336–340. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPan L, Fu T, Zhao W, et al.: Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling. Cell. 2019; 176: 1477–1489.e14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLim S, Li C, Xia W, et al.: Deubiquitination and Stabilization of PD-L1 by CSN5. Cancer Cell. 2016; 30: 925–939. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRath M, Schwefel K, Malinverno M, et al.: Contact-dependent signaling triggers tumor-like proliferation of CCM3 knockout endothelial cells in co-culture with wild-type cells. Cell. Mol. Life Sci. 2022; 79: 340–346. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "290354", "date": "24 Jun 2024", "name": "Julian Leibowitz", "expertise": [ "Reviewer Expertise Replication and pathogenesis of coronaviruses" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript Landherr et al compare the effect of the common SARS-CoV-2 ORF3a Q57H mutation to the parental sequence on host cells using ectopic over expression strategies. The manuscript presents the interesting finding that over expression of the ORF3a Q57H protein decreases apoptosis relative to that observed by the parental protein, and that this difference is due to greater activation of the extrinsic apoptosis pathway by the parental protein. These data are the strength of the manuscript. However, there are several critical issues not adequately explained or addressed. Below are specific comments and suggestions to improve the manuscript. Specific Comments 1. Differences in ORF3a Protein Expression: -The expression strategy employed is somewhat unusual, in creating an ORF3a-p2A-GFP fusion construct in which the primary translation product undergoes efficient self-cleavage mediated by its picornavirus p2A protease domain, liberating GFP and ORF3a-p2A polypeptides. This allows tracking transfected cells by GFP fluorescence and the comparison of ORF3a-p2A expression between variant and parental proteins indirectly by performing immunoblots for GFP and quantitating the amount of the fusion proteins and liberated GFP. They report that, contrary to a computational prediction by Wang et al that the Q57H variant will be less stable than the parental protein, that it is somewhat more stable. A weakness of this approach is it ignores the possibility that the p2A-GFP fusion to ORF3a has a stabilizing effect on the fusion protein. Furthermore, by utilizing immunoblots to GFP it makes the assumption that liberated ORF3a-p2A peptides from parental and Q57H variants degrade at equivalent rates and that GFP immunoblots reflect the amount of ORF3a-p2A protein. It would have strengthened the paper to have directly measured the relative amounts of ORF3a-p2A protein with an anti-ORF3a antibody. -The statement \"Differences in protein expression levels between WT and mutant ORF3a are more likely to occur via post translational processes rather than transcriptional regulation\" (Results, Paragraph 1).\n\nIt is not clear what the relevance of transcriptional regulation in transfected cells is when expression of the ORF3a mRNA is regulated quite differently in the context of SARS-CoV-2 infected cells than in transfected cells. Even in the context of transfected cells this claim would need experimental evidence, such as qRT-PCR for transcriptional analysis, post-translational modification studies, or protein folding studies. 2. Differing Results From Previous Studies: -The results negative related to ORF3a effects on inflammasome activation, ER stress, and autophagy in this paper differ from other reported studies. The authors should discuss potential reasons for these discrepancies. One obvious difference regarding inflammasome activation is the use of H9c2 cells, a cardiomyoblast cell line, in the current work. It is likely that these cells are not competent for inflammasome activation since Figure 3A shows that pharmacologic activation of inflammasomes by Nigericin fails to activate inflammasomes (IL-beta or caspase-1 cleavage) in these cells. 3. Mechanistic Studies on Q57H Mutation:\n\n-The manuscript lacks detailed mechanistic studies on how the Q57H mutation could affect extrinsic apoptosis pathway activation. For example, the authors should have examined the effect of individual death receptor knockdown on ORF3a induction of the extrinsic pathway for apoptosis to both identify the receptor activated and confirm their results. Additionally, the authors should investigate and discuss the potential alterations in ORF3a interaction with death receptors, and any differences in downstream signaling activation between WT and Q57H. Comparative studies between WT and Q57H regarding their interactions and signaling pathways would significantly enhance the manuscript's contribution to the field.\nConclusion: The manuscript presents interesting findings but requires substantial improvements in experimental support and detailed mechanistic studies. Addressing the points mentioned above will strengthen the manuscript and provide a more comprehensive understanding of the ORF3a protein's role and its mutations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "290352", "date": "27 Jun 2024", "name": "Wei Liu", "expertise": [ "Reviewer Expertise Virus infection and immunity", "Interaction between viruses and host cells" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn their manuscript, Landherr et al. showed that SARS-CoV-2-ORF3a variant Q57H reduces its pro-apoptotic activity in host cells. As a consequence, SARS-CoV-2-ORF3a-Q57H variant does not exhibit lower protein expression, but rather exhibits a relatively higher expression compared to the WT. Finally, the authors demonstrated that SARS-CoV-2-ORF3a-Q57H variant expression causes less activation of the extrinsic apoptotic pathway in the host cells. This study adds may support the potential molecular linkage between this major mutation and a mild phenotype. Despite the interesting phenotypic observations, several major issues must be addressed before further consideration.\n\n1) The writing lacks clarity and logical coherence, and these issues must be thoroughly resolved to enhance the manuscript's overall quality and scientific rigor. For instance, the sentence “we hypothesized that the SARS-CoV-2-ORF3a-Q57H variant produces less protein expression in host cells than” in the final part of the Introduction, is more appropriate to move this hypothetical sentence in the Discussion.\n2)- In Figure 1B, there are two GFP indicator arrow? In addition, no trend of increasing concentration was observed. The WB-blot need to be repeated.\n3)- In Figure 1D, the band intensity should be was normalized to the value from Tubulin.\n\n4)- In Figure 2A, the molecular weight of the caspase-3 should be displayed.\n5)- In Figure 3, the molecular weight of the proteins should be displayed. Figure 3A, the “cleaved” IL-1β should be shown in the panel. Figure 3G, although statistical analysis shows no significant difference in LC3-II to LC3-I, the he expression of LC3-II suggests that there is the activation in t ORF3a-WT and -Q57H. Maybe more representative WB-blot need to be displayed.\n6)- In Figure 4, the tBid or Bid need to be indicated clearly in panel.\n7)- “caspase-8” “Caspase 8” are inconsistent in manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-331
https://f1000research.com/articles/13-330/v1	23 Apr 24	{ "type": "Systematic Review", "title": "A systematic review evaluating the efficacy of treadmill training in geriatric care as an intervention for improving balance and reducing fall risks in elderly population", "authors": [ "Ayman Mohammed Ismail Zafer", "Alsayed Abdelhameed Shanb", "Matar AbduAllah Alzahrani", "Ankita Sharma", "Moattar Raza Rizvi", "Ayman Mohammed Ismail Zafer", "Alsayed Abdelhameed Shanb", "Matar AbduAllah Alzahrani", "Ankita Sharma" ], "abstract": "Background & Purpose Falls and balance issues are significant concerns for the elderly. Treadmill training is increasingly recognized as a potential intervention to improve balance and reduce fall risk in this population. This systematic review evaluates the effectiveness of treadmill training on balance in the elderly.\n\nMethods A comprehensive search was conducted in databases including MEDLINE, EMBASE, CINAHL Plus, PEDro, Cochrane Library, and ERIC from January 1, 1980, to May 31, 2023. The search focused on treadmill training’s impact on balance in older adults. From 74 identified studies, outcome measures were categorized into groups like “Balance Improvement,” “Gait Improvement,” “Mobility Enhancement,” “Muscle Strength Improvement,” “Cognitive Function and Quality of Life,” and others. Articles were excluded for reasons like irrelevance to treadmill training, language barriers, or duplication, resulting in 16 final studies.\n\nResults Treadmill training shows diverse positive effects on the elderly. Perturbation-based training reduces falls, and treadmill walking enhances balance and quality of life, particularly in institutionalized older individuals. Benefits were noted for Parkinson’s patients’ gait, cognitive changes in neurophysiology, fitness and mobility improvements through underwater treadmill sessions, and refined gait in hemiparetic patients.\n\nConclusion Treadmill training interventions are promising for improving balance and mobility in the elderly, including those with Parkinson’s disease, spinal cord injuries, and age-related balance issues. While these interventions show potential, further research is needed to determine optimal protocols, durations, and combinations with other interventions. This could lead to a more comprehensive approach for addressing balance and mobility challenges in the elderly, promoting healthy aging and reducing fall risks.", "keywords": [ "Elderly", "balance", "treadmill training", "falls prevention", "aging" ], "content": "Background\n\nAs the global population of older adults and elderly individuals continues to rise, there is a growing emphasis on innovative approaches to enhance their well-being, with a particular focus on addressing the challenges of aging. The aging population presents a unique set of opportunities and challenges, and by embracing innovative solutions, we can transform the aging experience, prolong vitality, and usher in a new era of longevity and well-being (Rudnicka et al., 2020; Amuthavalli Thiyagarajan et al., 2022; Officer and de la Fuente-Núñez, 2018). Some key areas of innovation in addressing the challenges of aging include genetic therapies and stem cell regeneration, which hold great potential for improving health and function in older adults, potentially reversing age-related declines and promoting a more youthful state (Garay, 2023; Negredo et al., 2020). Additionally, artificial intelligence and wearable technology can be used to monitor and manage health, providing valuable data for healthcare professionals and individuals to make informed decisions about their well-being (Wang and Hsu, 2023; Bohr and Memarzadeh, 2020; Bajwa et al., 2021). Virtual reality technology offers a wealth of opportunities for the aging population, enabling them to engage in stimulating activities, travel to distant places, and socialize with others, regardless of physical limitations, thus promoting mental well-being and combating feelings of isolation and loneliness (Chaze et al., 2022; Lin et al., 2018). Aging in place strategies focus on enhancing the safety and quality of life for older adults in their home environment, allowing them to participate in valued activities and maintain their independence.\n\nOne of the most promising areas of development is the field of exercise interventions, notably treadmill training. This approach is gaining traction as a means to counteract the age-related declines in physical function, balance, and mobility that significantly influence the quality of life and independence of older individuals (Brach and VanSwearingen, 2013; VanSwearingen et al., 2011). Treadmill training for the elderly is particularly advantageous because it can be tailored to individual needs and physical capabilities. It offers a safe and controlled environment for exercise, which is crucial for those with diminished balance or mobility. Regular use of the treadmill can lead to improvements in balance and coordination, thereby reducing the risk of falls, a common and serious concern among the elderly (Oddsson et al., 2007). Additionally, treadmill exercises are beneficial for cardiovascular health, helping to keep the heart healthy and potentially reducing the risk of heart-related diseases, which are more common in older age (Chen et al., 2022; Tian and Meng, 2019; Pinckard et al., 2019; Rebelo-Marques et al., 2018). Moreover, engaging in treadmill workouts can help maintain or increase muscle strength and bone density, countering the natural decline that accompanies aging. This type of physical activity is also associated with mental health benefits, including a reduction in symptoms of depression and anxiety, which are significant issues for many older adults (Izquierdo et al., 2021; Zhu et al., 2023). Another aspect of treadmill training that makes it suitable for older populations is its customizability. Treadmill exercises can be adjusted in terms of speed, incline, and duration to match the individual’s fitness level and physical limitations. This adaptability, combined with the safety features of modern treadmills, like safety rails and emergency stop mechanisms, ensures a safe workout environment.\n\nIn addition to physical benefits, treadmill training can also offer social benefits, especially when conducted in group settings such as classes or gym environments. It provides an opportunity for social interaction and engagement, which is important for the mental health and overall well-being of older adults. Furthermore, the integration of technology in modern treadmills, including heart rate monitors and personalized training programs, allows for more tailored and monitored exercise sessions, enhancing both safety and efficacy (Shepherd et al., 2015; Prichard and Tiggemann, 2008). However, it is critical that any exercise regimen, including treadmill training, be developed in consultation with healthcare professionals. This ensures that the exercises are not only beneficial but also safe, particularly for those with pre-existing health conditions. A personalized approach ensures that the older adults reap the maximum benefits from their exercise routines without compromising their health. The growing interest in the geriatric population’s health and well-being is evident in the expanding research on treadmill training’s potential benefits for older adults and the elderly (McPhee et al., 2016). This research recognizes the complex interplay of physiological, neuromuscular, and psychological factors unique to this age group. These factors play a crucial role in how older adults respond to various interventions, including exercise (de Souto Barreto et al., 2016; Paterson et al., 2007).\n\nTreadmill training, as a focused research area, has been the subject of numerous studies that span different years, geographical locations, and demographic profiles. These studies are not just limited in scope; they encompass a broad range of objectives and outcomes. One of the key areas of investigation is the impact of treadmill training on postural stability in the elderly. This aspect is crucial because maintaining a good postural balance is fundamental to performing everyday activities and reducing the risk of falls, which are a significant health concern in this age group (Pereira et al., 2020, 2021; Hirjaková et al., 2020).\n\nAnother important research focus is the effect of treadmill training on gait patterns (Newell et al., 2012; Almutairi, 2023; van Ooijen et al., 2013; Wnuk et al., 2010). As people age, their walking patterns can change, often becoming slower and less steady. These changes in gait can lead to an increased risk of falls and injuries. Treadmill training can potentially help in modifying these gait patterns, leading to safer and more efficient walking. Additionally, researchers are examining how treadmill training influences the rate of falls among the elderly (van Ooijen et al., 2016). Falls are not only a leading cause of injury in older adults but also contribute to a fear of falling, which can significantly reduce their activity levels and quality of life. By improving balance, strength, and gait through treadmill training, there is a possibility of reducing the incidence of falls, thus enhancing the overall safety and independence of the elderly (Cadore et al., 2013; Marsh et al., 2006). Moreover, the psychological impacts of treadmill training are also a subject of study. Regular physical activity has been associated with improvements in mood, cognitive function, and general mental well-being. For the elderly, these psychological benefits are as important as the physical ones, considering the high prevalence of depression, anxiety, and cognitive decline in this age group (Afifi et al., 2023; Dorfman et al., 2014). The diversity of these research studies reflects the multifaceted nature of aging and the need for a comprehensive approach to health and wellness in the geriatric population. By exploring various outcomes and considering the unique challenges faced by older adults, these studies contribute significantly to our understanding of how best to support the health and well-being of the elderly through targeted interventions like treadmill training.\n\nThe focus of this systematic review is to delve deep into the myriad of studies on treadmill training for older adults, aiming to synthesize and consolidate the diverse findings into a coherent understanding. This undertaking recognizes that understanding the mechanisms behind the observed outcomes in these studies is critical for fully realizing the potential benefits of treadmill training for the elderly. Treadmill training, with its unique ability to simultaneously engage both motor and cognitive systems, presents a promising avenue for holistic geriatric care. However, the diversity in research methodologies and outcomes necessitates a careful and comprehensive analysis to identify meaningful patterns and insights. This review, therefore, meticulously examines various aspects of the studies, including intervention protocols, study designs, and outcome measures. The goal is to identify commonalities and trends that transcend individual studies, thereby providing a more comprehensive understanding of treadmill training’s role in geriatric healthcare.\n\nA crucial aspect of this review is the acknowledgment of the intricate relationship between physical activity and cognitive function in aging. The cognitive benefits of physical exercise, particularly in an aging population, are an area of growing interest. Treadmill training, by demanding both physical and cognitive engagement, could potentially enhance cognitive function alongside physical health, offering dual benefits to the elderly. Furthermore, this review traverses the historical landscape of treadmill training research, encompassing a broad spectrum of studies that have investigated its physiological, psychological, and social impacts. These studies have been conducted over a range of years and across various geographical and demographic contexts, adding to the richness and diversity of the data. By examining these studies, the review aims to unravel not only the direct impacts of treadmill interventions on aspects such as balance, gait, and fall risk but also their broader implications for promoting active aging, sustainable geriatric care, and community engagement.\n\nBy providing a comprehensive synthesis of these studies, this systematic review aspires to inform the development of targeted treadmill training interventions that are specifically designed to meet the needs of older adults. These interventions could potentially improve balance, reduce the risk of falls, and promote overall health and well-being in the elderly population. The ultimate goal of this endeavor is to contribute to a more nuanced and holistic approach to geriatric care, one that recognizes and utilizes the multifaceted benefits of treadmill training to enhance the quality of life for older adults and the elderly. The insights gleaned from this review could have significant implications for healthcare providers, policymakers, and caregivers, guiding them in making informed decisions about incorporating treadmill training into comprehensive care plans for the elderly.\n\nIn this systematic review, we are setting out to explore several key aspects that are critical to understanding the full scope and impact of treadmill training on older adults. These aspects are designed to provide a comprehensive overview of the subject, addressing the nuances and complexities inherent in geriatric care and exercise interventions.\n\n1. Types of interventions: A crucial part of this review is the analysis of different treadmill training protocols. The aim here is to discern which specific elements of these protocols are most effective in improving balance in older adults. This analysis will consider various factors, such as the intensity, duration, and frequency of exercise, as well as the incorporation of additional equipment like body weight support systems. The goal is to identify the most beneficial practices that can be applied broadly to improve balance and reduce fall risks among the elderly.\n\n2. Population heterogeneity: Recognizing that the older adult population is extremely diverse, the review will pay special attention to how different subgroups respond to treadmill training. This includes examining the experiences of individuals with varying levels of physical fitness, health conditions, and cognitive abilities. A key question is whether treadmill training is more effective or beneficial for certain subgroups, such as those with preexisting medical conditions or varying degrees of mobility impairment. Understanding these differences is crucial for tailoring interventions to meet the specific needs of different segments within the elderly population.\n\n3. Outcome measures: The review will rigorously assess a wide range of outcome measures to capture the full impact of treadmill training. This includes evaluating both static and dynamic balance, changes in gait parameters, overall mobility, incidence of falls, and improvements in the quality of life. By analyzing these diverse outcomes, the review aims to construct a holistic picture of how treadmill training affects various aspects of an elderly individual’s health and daily living.\n\n4. Methodological rigor: Assessing the methodological quality of the studies included in the review is essential to determine the strength and reliability of the evidence. This involves examining each study for potential biases, methodological flaws, and limitations. This critical evaluation will provide insights into how trustworthy and applicable the results are, and will highlight areas where further research may be needed to confirm findings or fill in gaps in the current understanding.\n\nTo ensure the systematic review’s primary focus on investigating the effectiveness of treadmill training in enhancing balance among the elderly population, a rigorous set of inclusion and exclusion criteria was meticulously crafted. The ensuing inclusion criteria were judiciously employed to discerningly choose studies for comprehensive analysis:\n\nThe review concentrated on studies encompassing individuals aged 60 years and above, thereby ensuring a dedicated examination of the elderly population. The central theme was the investigation of treadmill training interventions and their potential impact on balance improvement within this demographic. The selection criteria demanded that studies exclusively present quantitative outcomes germane to balance assessment. To attain a comprehensive perspective, the review encompassed an array of study designs, ranging from rigorous randomized controlled trials (RCTs) and non-randomized trials to observational designs such as cohort studies, cross-sectional studies, and case-control studies. The scope of the review was confined to studies published in the English language.\n\nIn a bid to maintain precision, studies targeting populations other than the elderly, such as individuals aged below 60, were deliberately excluded from the review. Likewise, studies appraising interventions beyond treadmill training for balance enhancement were not deemed pertinent for inclusion. Studies that failed to provide pertinent outcomes related to balance assessment were excluded to uphold the review’s integrity. Editorial pieces, opinion articles, systematic reviews, and meta-analyses were meticulously excluded to keep the focus on primary research. The purview of the review deliberately excluded abstracts, dissertations, and conference presentations, ensuring the consideration of only comprehensive research reports. Studies solely scrutinizing within-session effects of varying walking conditions were purposely omitted. Furthermore, review articles straying from the core subject matter—treadmill training’s role in improving balance among the elderly—were scrupulously excluded.\n\nThe systematic review purposefully excluded studies solely concentrating on within-session effects of different walking conditions to offer a more comprehensive view of treadmill training’s sustained efficacy. Additionally, review articles that did not align with the specific outcomes of interest—namely, the influence of treadmill training and body weight supported gait training on balance improvement among the elderly—were meticulously excluded to uphold research relevance.\n\nFurthermore, the review remained constrained to studies accessible via peer-reviewed journals, containing full-text versions in the English language. It embraced research encompassing diverse study designs, irrespective of the approach employed. However, studies presented solely as abstracts or dissertations were intentionally omitted from consideration. Likewise, studies narrowly probing the within-session effects of diverse walking conditions were deliberately omitted. Finally, review articles addressing tangential subjects were deliberately excluded.\n\nBy diligently implementing these stringent inclusion and exclusion criteria, the systematic review aimed to curate a selection of studies closely aligned with the research objectives, eliminating those deviating from the predefined scope. This approach was meticulously tailored to deliver an exhaustive and precise evaluation of the impact of treadmill training on balance improvement within the elderly population.\n\n\nSearch strategy\n\nFor this systematic review, a comprehensive search strategy was meticulously developed to identify relevant studies that investigated the effectiveness of treadmill training on balance improvement in the elderly population. The following approach was employed to ensure the systematic retrieval of pertinent literature: Identification of Key Concepts: The search strategy began by identifying key concepts essential to the review’s focus: “treadmill training,” “elderly population,” and “balance improvement.” Keyword Formulation: To enhance search precision, specific keywords were formulated for each concept. These keywords were carefully selected to encompass various aspects of the concepts. Treadmill Training: “treadmill training,” “treadmill exercise,” “gait training,” “treadmill intervention” Elderly Population: “elderly,” “older adults,” “seniors,” “geriatric population” Balance Improvement: “balance improvement,” “postural stability enhancement,” “balance training,” “gait stability” Boolean Operator Combination: The formulated keywords were logically combined using Boolean operators (AND, OR) to create comprehensive search strings that captured the interrelation of the key concepts. (Treadmill Training OR Treadmill Exercise OR Gait Training OR Treadmill Intervention) AND; (Elderly OR Older Adults OR Seniors OR Geriatric Population) AND; (Balance Improvement OR Postural Stability Enhancement OR Balance Training OR Gait Stability); Inclusion of Controlled Vocabulary: To enhance the search strategy’s robustness, controlled vocabulary terms (MeSH terms in PubMed) were incorporated alongside the keywords to account for database-specific indexing; (“Exercise Therapy”[Mesh] OR “Gait”[Mesh] OR “Postural Balance”[Mesh]) AND; (“Aged”[Mesh] OR “Aged, 80 and over”[Mesh] OR “Elderly”[Mesh]) AND; (“Treatment Outcome”[Mesh] OR “Rehabilitation”[Mesh] OR “Physical Therapy Modalities”[Mesh]).\n\nThe search strategy was tailored for various databases, ensuring compatibility with their syntax and controlled vocabulary. For Embase, Emtree terms like “Motor Activity” and “Gait” were incorporated. In CINAHL, CINAHL Headings were utilized in conjunction with relevant keywords, catering to the nursing and allied health literature. The Cochrane Library was targeted for systematic reviews and clinical trials on treadmill training and balance improvement in the elderly. Additionally, for Scopus, a combination of database-specific keywords and controlled vocabulary was utilized to achieve a comprehensive retrieval of relevant articles (Figure 1).\n\nThis meticulous approach to constructing the search strategy aimed to systematically retrieve articles relevant to the systematic review’s objectives. By adapting the strategy for each database’s unique characteristics, it ensured the comprehensive capture of pertinent literature on the effectiveness of treadmill training on balance improvement in the elderly population.\n\n\nResults\n\nThe modern landscape of healthcare and well-being is undergoing a profound transformation, propelled by the ever-expanding demographic of older adults and elderly individuals. In the pursuit of enhancing their quality of life, sustaining mobility, and mitigating age-related challenges, novel interventions are being explored with vigor. Amid this backdrop, our intention was to embark on a comprehensive exploration, elucidating the multifaceted effects of treadmill training interventions within this burgeoning demographic. The primary impetus behind curating this systematic review was to distill the collective wisdom embedded within a spectrum of studies that have investigated the effects of treadmill training in older adults and the elderly.\n\nThe selected studies, spanning from 1997 to 2023, offered an opportunity to traverse the evolutionary journey of research in this domain, and glean insights that could potentially reshape the landscape of geriatric care and rehabilitation. Through an exhaustive synthesis of these studies, our aim was to unravel a mosaic of outcomes that extended beyond the immediate purview of each investigation. The intention was to amalgamate these findings into a cohesive narrative, one that transcended individual studies and illuminated broader patterns. This endeavor sought to underscore the transformative potential of treadmill training in older populations, tapping into its efficacy in restoring balance, fostering motor recovery, enhancing mobility, and ultimately elevating the overall quality of life. This systematic review engenders an in-depth exploration of the myriad effects encompassed by treadmill training interventions within the realm of older adults and elderly individuals. These studies collectively illuminate a multifaceted tapestry of outcomes that hold the potential to reshape mobility, balance, neurological well-being, and overall quality of life in this demographic (Table 1).\n\n\n\n• Gait Speed Measured By 6 Minute Walk Test\n\n• Balance Ability Evaluated By Fullerton Advanced Balance Scale (FABS) And Berg Balance Scale (BBS) Tests\n\n• Postural Sway Items Such As The Center Of Pressure (COP), Average Displacement And Velocity\n\n\n\n• Postural Control\n\n• Balance In Different Tasks\n\n• Static Balance\n\n• Variables Related To Gait\n\n• BBS Scores\n\n• Baropodometric Variables\n\n\n\n• Timed \"Up & Go\" Test (Tug)\n\n• 2 Minute Walk Test (2Mwt)\n\n• 4 Square Step Test (FSST)\n\n\n\n• 1 Leg Standing Test\n\n• Berg Balance Scale\n\n• Functional Reach Test\n\n• Timed Up And Go Test\n\n• Velocity\n\n• Step Width\n\n• Stride Length\n\n• Step Length\n\nThis comprehensive exploration doesn’t merely present a mosaic of findings; it endeavors to offer a comprehensive lens through which healthcare practitioners, researchers, and policymakers can perceive the nuanced impact of treadmill interventions. By cataloging the diversity of outcomes across studies, we aimed to provide a roadmap for refining intervention protocols, optimizing parameters, and tailoring approaches to meet the diverse needs of older adults and elderly individuals. The implications of this endeavor extend beyond the realms of academia. The insights gleaned from this systematic review hold the potential to cascade into the broader spectrum of geriatric care and societal sustainability. The sustained mobility and well-being of older individuals directly impact their active engagement in their communities, the reduction of healthcare burdens, and the conservation of resources. In weaving together the threads of these studies, we lay the foundation for a sustainable future, wherein a more comprehensive approach to geriatric well-being can be nurtured.\n\nAt the forefront of these investigations lies a profound focus on balance enhancement, a critical factor that directly influences fall prevention and overall functional independence in aging populations. Nørgaard et al. (2023) ingeniously introduced perturbation-based balance training on a treadmill, culminating in a compelling reduction in fall rates among community-dwelling older adults. A confluence of results from Pereira et al. (2020, 2021), Pirouzi et al. (2014), and Targino et al. (2012) further amplifies this narrative, unveiling substantial improvements in postural balance and a significant upswing in the quality of life among institutionalized elderly individuals, further emphasizing the holistic impact of treadmill interventions.\n\nThe narrative extends to older individuals grappling with neurological conditions, prominently Parkinson’s disease and hemiparesis. Luna et al. (2020) masterfully unraveled the positive implications of treadmill training on gait patterns in Parkinson’s disease, shedding light on the potential for rehabilitation and functional recovery in this population. This trajectory is mirrored in the investigation by Hesse et al. (1997), which showcased the transformative power of partial body weight-supported treadmill training in hemiparetic patients, cultivating a realm of possibilities for motor recovery. The review embarks on a comparative expedition, juxtaposing treadmill training against alternative interventions. Baek et al. (2021) orchestrated an insightful exploration into dual-task treadmill training versus conventional balance exercises, revealing the nuanced superiority of dual-task treadmill training in the realm of balance enhancement and fall risk mitigation. This illuminates the potential of incorporating cognitive engagement alongside physical training, underscoring the dynamic nature of treadmill interventions (Table 1).\n\nStevens et al. (2015) courageously ventured into uncharted waters, introducing underwater treadmill training in individuals with incomplete spinal cord injuries. This groundbreaking approach unveiled an alternative dimension of therapeutic intervention, unveiling the untapped potential of aquatic treadmill training in fostering recovery and enhancing physical function, an especially significant revelation in the context of spinal cord injuries. While this comprehensive synthesis lauds the affirmative outcomes of treadmill training interventions, it also casts a discerning eye on challenges that warrant consideration. Hirjaková et al. (2020) added a layer of complexity by illuminating sensory conflicts introduced by treadmill training, particularly among elderly individuals. This observation augments our understanding of potential downsides and underscores the need for a holistic approach when designing treadmill interventions. The amalgamation of these studies not only underscores the positive outcomes but also emphasizes the exigency for standardized protocols and optimal intervention parameters across diverse populations. Collectively, these studies weave a compelling narrative that posits treadmill training as a transformative catalyst, fostering improvements in postural equilibrium, dynamic gait mechanics, and the overarching quality of life for aging individuals and those navigating intricate neurological trajectories.\n\nFurthermore, the systematic review included a diverse array of studies that explored the effects of treadmill training interventions in older adults and the elderly (Table 1). Shema et al. (2014) delved into the realm of outpatient physical therapy, utilizing a 5-week treadmill training program with virtual reality to enhance gait in individuals with a history of falls, poor mobility, or postural instability. The results indicated notable improvements in gait, mobility, and postural control, showcasing the effectiveness of treadmill training with virtual reality. A Randomized Controlled Clinical Trial conducted by Pirouzi et al. (2014) offered insights into the impact of treadmill walking on balance control. The study, involving 30 community dwelling older adults with a Berg Balance Scale score of 36-48, highlighted significant improvements in balance, particularly in quiet standing on firm and foam surfaces, along with a reduction in Center of Pressure (COP) velocity during quiet standing and standing on foam. Furthermore, the study by Targino et al. (2012) delved into the realm of pre-frail elderly individuals through a pilot study. The investigation revealed that dual-task training on a treadmill improved static and dynamic balance, with visual stimulation aiding in short-term balance maintenance. Lastly, Kyeongjin Lee’s study in 2020 focused on the potential of virtual reality gait training (VRGT) with non-motorized treadmill to promote balance and gait among older people who had experienced falls. This randomized clinical trial involving 56 elderly individuals highlighted the effectiveness of VRGT in improving balance and gait ability, with significant enhancements observed in spatiotemporal gait parameters.\n\nCollectively, these studies weave a compelling narrative that posits treadmill training as a transformative catalyst, fostering improvements in postural equilibrium, dynamic gait mechanics, and the overarching quality of life for aging individuals and those navigating intricate neurological trajectories.\n\n\nDiscussion\n\nThe burgeoning field of healthcare and well-being, driven by the increasing population of older adults and elderly individuals, is undergoing significant transformation. As efforts intensify to enhance their quality of life, maintain mobility, and address aging-related challenges, treadmill training interventions have emerged as a focal point of interest. This systematic review synthesizes a wide range of studies to distill collective knowledge on the impact of treadmill training on this demographic. Covering research from 1997 to 2023, it offers deep insights that could potentially reshape geriatric care and rehabilitation practices. Treadmill training in geriatric populations has shown transformative potential, particularly in restoring balance, facilitating motor recovery, enhancing mobility, and ultimately elevating overall quality of life. These findings align with previous studies (van Ooijen et al., 2013; Yang et al., 2011; Herman et al., 2007; Hirjaková et al., 2020), which demonstrated improvements in gait and balance among elderly participants following treadmill training. Similarly, Monteiro (2009) observed significant mobility enhancements in their study group. The review methodology involved a comprehensive search across databases like PubMed, Scopus, and Web of Science, focusing on publications between 1997 and 2023. The selected studies had to specifically examine the effects of treadmill training on older adults, with particular emphasis on balance, mobility, and quality of life.\n\nThe key findings from this comprehensive review illuminate several critical areas of impact regarding treadmill training for older adults and elderly individuals, each noteworthy in its implications for geriatric care. Firstly, the aspect of balance enhancement has been a significant focus. Studies conducted by Newell, (2012) and Ferhi, Hamza, et al. (2023) have been pivotal in highlighting the role of treadmill training in improving balance. This factor is particularly crucial for preventing falls, a common risk for the elderly, and maintaining functional independence in older populations. The consistent findings across these studies underscore the effectiveness of treadmill training as a practical approach to mitigate one of the most pressing concerns in geriatric health – fall prevention. Secondly, the impact of treadmill training on individuals with neurological conditions has garnered considerable attention. The research delves into the realm of neurodegenerative diseases, particularly Parkinson’s disease and hemiparesis (Bishnoi et al., 2022; Robinson et al., 2019; Almutairi, 2023). Their findings indicate promising prospects for functional recovery in these groups, suggesting that treadmill training could be a valuable tool in the rehabilitation of patients with neurological impairments. The implications of these findings are far-reaching, considering the complexity and the increasing prevalence of neurological conditions among the elderly.\n\nLastly, the comparative efficacy of treadmill training relative to other interventions stands out as a notable finding. Previous studies provides evidence of the superiority of treadmill training over other rehabilitative strategies, especially in enhancing balance and reducing fall risks (Gaspar and Lapão, 2021; Choi et al., 2017). Moreover, the exploration of innovative approaches like underwater treadmill training for spinal cord injury patients, as investigated by Hammill et al. (2018), sheds light on the potential of unconventional interventions (Dolbow et al., 2016; Hammill et al., 2018). These innovative methods broaden the scope of treadmill training, offering new avenues for rehabilitation that could be particularly beneficial for individuals with unique or more severe mobility challenges.\n\nThe review also acknowledged challenges, including sensory conflicts introduced by treadmill training, a concern highlighted in the study by Hirjaková et al. (2020). These findings emphasize the need for holistic and tailored intervention strategies.\n\nThe implications of the review findings hold relevance for both clinical practice and policy considerations. The positive impact of treadmill training on postural balance and gait parameters suggests its potential as a viable intervention to reduce fall risk among older adults. Furthermore, the review underscores the importance of individualized training programs tailored to participants’ specific needs and capacities. Despite the promising results, several avenues for future research emerge. Long-term studies evaluating the sustained effects of treadmill training interventions would contribute valuable insights. Additionally, investigating the optimal dosage, intensity, and duration of training sessions could enhance the precision of recommendations for clinical implementation. Furthermore, examining the cost-effectiveness and scalability of these interventions will be essential for broader adoption.\n\nOne strength of this review lies in its comprehensive search strategy, encompassing a diverse range of studies. The inclusion of various types of treadmill training interventions allowed for a nuanced understanding of the benefits across different contexts. However, limitations include potential publication bias and the heterogeneity of the selected studies, which may have influenced the synthesis of results.\n\n\nConclusion\n\nIn conclusion, the amalgamation of these studies paints a vivid tapestry that not only underscores the affirmative outcomes but also accentuates the urgency for standardized protocols and optimal intervention parameters across diverse populations. As we weave these narratives together, a compelling collective narrative emerges, one that envisions treadmill training as a transformative catalyst, fostering advancements in postural equilibrium, dynamic gait mechanics, and the overarching quality of life for aging individuals and those navigating intricate neurological trajectories. The comprehensive synthesis presented here offers a panoramic view of the potential of treadmill interventions in geriatric care, laying the groundwork for a future that champions holistic well-being in older populations.\n\nEthical approval and written consent were not required.", "appendix": "Data availability\n\nFigshare: Details of Studies Included, https://doi.org/10.6084/m9.figshare.25322011.v1 (Rizvi, 2024a).\n\nThis project contains the following data:\n\n- Details of Studies Included.xlsx\n\nFigshare: PRISMA Flow chart, https://doi.org/10.6084/m9.figshare.25323391.v1 (Rizvi, 2024b).\n\nThis project contains the following extended data:\n\n- PRISMA Flow chart\n\nFigshare: PRISMA check list, https://doi.org/10.6084/m9.figshare.25323478.v1 (Rizvi, 2024c).\n\nData are available under the terms of the CC BY 4.0 Attribution International License (CC BY 4.0).\n\n\nReferences\n\nAfifi T, Collins N, Rand K, et al.: Using virtual reality to improve the quality of life of older adults with cognitive impairments and their family members who live at a distance. Health Commun. 2023; 38: 1904–1915. PubMed Abstract \| Publisher Full Text\n\nAlmutairi SM: Lower body positive pressure treadmill gait training for neurological patients: a systematic review. Bull. Fac. Phys. Ther. 2023; 28: 23. Publisher Full Text\n\nAmuthavalli Thiyagarajan J, Mikton C, Harwood RH, et al.: The UN Decade of healthy ageing: Strengthening measurement for monitoring health and wellbeing of older people. Age Ageing. 2022; 51: afac147. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaek CY, Chang WN, Park BY, et al.: Effects of Dual-Task Gait Treadmill Training on Gait Ability, Dual-Task Interference, and Fall Efficacy in People With Stroke: A Randomized Controlled Trial. Phys Ther. 2021 Jun 1; 101(6): pzab067. PubMed Abstract \| Publisher Full Text\n\nBajwa J, Munir U, Nori A, et al.: Artificial intelligence in healthcare: transforming the practice of medicine. Future Healthc. J. 2021; 8: e188–e194. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBishnoi A, Lee R, Hu Y, et al.: Effect of treadmill training interventions on spatiotemporal gait parameters in older adults with neurological disorders: Systematic review and meta-analysis of randomized controlled trials. Int. J. Environ. Res. Public Health. 2022; 19: 2824. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBohr A, Memarzadeh K: The rise of artificial intelligence in healthcare applications. Artificial Intelligence in Healthcare. Elsevier; 2020. Publisher Full Text\n\nBrach JS, Vanswearingen JM: Interventions to improve walking in older adults. Curr. Transl. Geriatr. Exp. Gerontol. Rep. 2013; 2: 230–238. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCadore EL, Rodríguez-Mañas L, Sinclair A, et al.: Effects of different exercise interventions on risk of falls, gait ability, and balance in physically frail older adults: a systematic review. Rejuvenation Res. 2013; 16: 105–114. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaze F, Hayden L, Azevedo A, et al.: Virtual reality and well-being in older adults: Results from a pilot implementation of virtual reality in long-term care. J. Rehabil. Assist. Technol. Eng. 2022; 9: 20556683211072384.\n\nChen H, Chen C, Spanos M, et al.: Exercise training maintains cardiovascular health: signaling pathways involved and potential therapeutics. Signal Transduct. Target. Ther. 2022; 7: 306. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChoi SD, Guo L, Kang D, et al.: Exergame technology and interactive interventions for elderly fall prevention: A systematic literature review. Appl. Ergon. 2017; 65: 570–581. PubMed Abstract \| Publisher Full Text\n\nde Souto Barreto P , Morley JE, Chodzko-Zajko W, et al.: Recommendations on physical activity and exercise for older adults living in long-term care facilities: a taskforce report. J. Am. Med. Dir. Assoc. 2016; 17: 381–392. PubMed Abstract \| Publisher Full Text\n\nDolbow JD, Jones T, Dolbow DR, et al.: Efficacy of underwater treadmill training as a complimentary gait restorative therapy for spinal cord injured individual: a case report. Clinical Kinesiology: Journal of the American Kinesiotherapy Association. 2016; 70: 9–16.\n\nDorfman M, Herman T, Brozgol M, et al.: Dual-task training on a treadmill to improve gait and cognitive function in elderly idiopathic fallers. J. Neurol. Phys. Ther. 2014; 38: 246–253. PubMed Abstract \| Publisher Full Text\n\nFerhi H, Gaied Chortane S, Durand S, et al.: Effects of Physical Activity Program on Body Composition, Physical Performance, and Neuromuscular Strategies during Walking in Older Adults with Sarcopenic Obesity: Randomized Controlled Trial. Healthcare. 2023; 11. MDPI, 2294. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGaray RP: Recent clinical trials with stem cells to slow or reverse normal aging processes. Front. Aging. 2023; 4: 1148926. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGaspar AGM, Lapão LV: eHealth for addressing balance disorders in the elderly: Systematic review. J. Med. Internet Res. 2021; 23: e22215. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHammill HV, Ellapen TJ, Strydom GL, et al.: The benefits of hydrotherapy to patients with spinal cord injuries. Afr. J. Disabil. 2018; 7: 1–8.\n\nHerman T, Giladi N, Gruendlinger L, et al.: Six weeks of intensive treadmill training improves gait and quality of life in patients with Parkinson’s disease: a pilot study. Arch. Phys. Med. Rehabil. 2007; 88: 1154–1158. PubMed Abstract \| Publisher Full Text\n\nHesse S, Helm B, Krajnik J, et al.: Treadmill training with partial body weight support: influence of body weight release on the gait of hemiparetic patients. J. Neurol. Rehabil. 1997; 11: 15–20.\n\nHirjaková Z, Bizovska L, Bzdúšková D, et al.: Postural stability after treadmill and overground walking in young and elderly. Gait Posture. 2020; 80: 84–89. PubMed Abstract \| Publisher Full Text\n\nIzquierdo M, Merchant R, Morley J, et al.: International exercise recommendations in older adults (ICFSR): expert consensus guidelines. J. Nutr. Health Aging. 2021; 25: 824–853. PubMed Abstract \| Publisher Full Text\n\nLee K: Virtual reality gait training to promote balance and gait among older people: a randomized clinical trial. Geriatrics. 2021; 6: 1.\n\nLin CX, Lee C, Lally D, et al.: Impact of virtual reality (VR) experience on older adults’ well-being. Human Aspects of IT for the Aged Population. Applications in Health, Assistance, and Entertainment: 4th International Conference, ITAP 2018, Held as Part of HCI International 2018, Las Vegas, NV, USA, July 15–20, 2018, Proceedings, Part II 4, Springer. 2018; pp. 89–100.\n\nLuna NMS, Brech GC, Canonica A, et al.: Effects of treadmill training on gait of elders with Parkinson’s disease: a literature review. Einstein (São Paulo). 2020; 18: eRW5233. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarsh AP, Katula JA, Pacchia CF, et al.: Effect of treadmill and overground walking on function and attitudes in older adults. Med. Sci. Sports Exerc. 2006; 38: 1157–1164. PubMed Abstract \| Publisher Full Text\n\nMcphee JS, French DP, Jackson D, et al.: Physical activity in older age: perspectives for healthy ageing and frailty. Biogerontology. 2016; 17: 567–580. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMonteiro FF, Monteiro W, Costa RV, et al.: Effect of treadmill-based gait training on the stationary balance of elderly individuals. Arch. Med. Sci. 2009; 5: 443–449.\n\nMorency E, Burkow-Heikkinen L, Ibe O: Treadmill Applications on the Neurophysiology of the Diseased and Elderly: A Review. BAOJ Neurol. 2017; 3: 035.\n\nNegredo PN, Yeo RW, Brunet A: Aging and rejuvenation of neural stem cells and their niches. Cell Stem Cell. 2020; 27: 202–223. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNewell D, Shead V, Sloane L: Changes in gait and balance parameters in elderly subjects attending an 8-week supervised Pilates programme. J. Bodyw. Mov. Ther. 2012; 16: 549–554. PubMed Abstract \| Publisher Full Text\n\nNørgaard JE, Andersen S, Ryg J, et al.: Effect of treadmill perturbation-based balance training on fall rates in community-dwelling older adults: a randomized clinical trial. JAMA Netw. Open. 2023; 6: e238422–e238422. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOddsson LI, Boissy P, Melzer I: How to improve gait and balance function in elderly individuals—compliance with principles of training. Eur. Rev. Aging Phys. Act. 2007; 4: 15–23. Publisher Full Text\n\nOfficer A, de la Fuente-Núñez V : A global campaign to combat ageism. Bull. World Health Organ. 2018; 96: 295–296. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaterson DH, Jones GR, Rice CL: Ageing and physical activity: evidence to develop exercise recommendations for older adults. Appl. Physiol. Nutr. Metab. 2007; 32: S69–S108. Publisher Full Text\n\nPereira NM, Araya MJPM, Scheicher ME: Effectiveness of a treadmill training programme in improving the postural balance on institutionalized older adults. J. Aging Res. 2020; 2020.\n\nPereira NMR, Araya MJPM, Scheicher ME: Improvement of quality of life and postural balance of institutionalized elderly people undergoing to a treadmill walking training. J. Bodyw. Mov. Ther. 2021; 28: 172–179. PubMed Abstract \| Publisher Full Text\n\nPinckard K, Baskin KK, Stanford KI: Effects of exercise to improve cardiovascular health. Front. Cardiovasc. Med. 2019; 69.\n\nPirouzi S, Motealleh AR, Fallahzadeh F, et al.: Effectiveness of treadmill training on balance control in elderly people: a randomized controlled clinical trial. Iran. J. Med. Sci. 2014; 39: 565–570. PubMed Abstract\n\nPrichard I, Tiggemann M: Relations among exercise type, self-objectification, and body image in the fitness centre environment: The role of reasons for exercise. Psychol. Sport Exerc. 2008; 9: 855–866. Publisher Full Text\n\nRebelo-Marques A, de Sousa Lages A , Andrade R, et al.: Aging hallmarks: The benefits of physical exercise. Front. Endocrinol. 2018; 9: 258. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRizvi M: Details of Studies Included.xlsx. Dataset. figshare. 2024a. Publisher Full Text\n\nRizvi M: PRISMA Flow chart. Figure. figshare. 2024b. Publisher Full Text\n\nRizvi M: PRISMA check list. Dataset. figshare. 2024c. Publisher Full Text\n\nRobinson AG, Dennett AM, Snowdon DA: Treadmill training may be an effective form of task-specific training for improving mobility in people with Parkinson’s disease and multiple sclerosis: a systematic review and meta-analysis. Physiotherapy. 2019; 105: 174–186. PubMed Abstract \| Publisher Full Text\n\nRudnicka E, Napierała P, Podfigurna A, et al.: The World Health Organization (WHO) approach to healthy ageing. Maturitas. 2020; 139: 6–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShema SR, Brozgol M, Dorfman M, et al.: Clinical experience using a 5-week treadmill training program with virtual reality to enhance gait in an ambulatory physical therapy service. Phys. Ther. 2014; 94: 1319–1326. PubMed Abstract \| Publisher Full Text\n\nShepherd SO, Wilson OJ, Taylor AS, et al.: Low-volume high-intensity interval training in a gym setting improves cardio-metabolic and psychological health. PLoS One. 2015; 10: e0139056. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStevens S: Underwater treadmill training in adults with incomplete spinal cord injuries. J. Rehabil. Res. Dev. 2010; 47: VII–vix. PubMed Abstract \| Publisher Full Text\n\nStevens SL, Caputo JL, Fuller DK, et al.: Effects of underwater treadmill training on leg strength, balance, and walking performance in adults with incomplete spinal cord injury. J. Spinal Cord Med. 2015 Jan; 38(1): 91–101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTargino VR, Freire ADNF, Sousa ACPDA, et al.: Effects of a dual-task training on dynamic and static balance control of pre-frail elderly: a pilot study. Fisioterapia em Movimento. 2012; 25: 351–360. Publisher Full Text\n\nTian D, Meng J: Exercise for prevention and relief of cardiovascular disease: prognoses, mechanisms, and approaches. Oxidative Med. Cell. Longev. 2019; 2019: 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan Ooijen MW, Roerdink M, Trekop M, et al.: The efficacy of treadmill training with and without projected visual context for improving walking ability and reducing fall incidence and fear of falling in older adults with fall-related hip fracture: a randomized controlled trial. BMC Geriatr. 2016; 16: 1–15. Publisher Full Text\n\nVan Ooijen MW, Roerdink M, Trekop M, et al.: Functional gait rehabilitation in elderly people following a fall-related hip fracture using a treadmill with visual context: design of a randomized controlled trial. BMC Geriatr. 2013; 13: 1–11. Publisher Full Text\n\nVanswearingen JM, Perera S, Brach JS, et al.: Impact of exercise to improve gait efficiency on activity and participation in older adults with mobility limitations: a randomized controlled trial. Phys. Ther. 2011; 91: 1740–1751. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang W-H, Hsu W-S: Integrating artificial intelligence and wearable IoT system in long-term care environments. Sensors. 2023; 23: 5913. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWnuk B, Walusiak M, Durmala J, et al.: Effects of physiotherapy including various forms of gait exercises on a treadmill on functional efficiency in the elderly at risk of falling. Physiother. Q. 2010; 18: 3. Publisher Full Text\n\nYang S, Hwang W-H, Tsai Y-C, et al.: Improving balance skills in patients who had stroke through virtual reality treadmill training. Am. J. Phys. Med. Rehabil. 2011; 90: 969–978. PubMed Abstract \| Publisher Full Text\n\nZhu Y, Zhou X, Zhu A, et al.: Advances in exercise to alleviate sarcopenia in older adults by improving mitochondrial dysfunction. Front. Physiol. 2023; 14: 1196426. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "351604", "date": "31 Dec 2024", "name": "Mohamed Salah Elayat", "expertise": [ "Reviewer Expertise Physical Therapy", "Rehabilitation", "Therapeutic Modalities." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nTitle: The title containing “geriatric care” and “elderly population”. Use one of them only. Suggested title” efficacy of treadmill training on balance and fall risks in elderly population. A systematic review”. Abstract: 1) Search until May 31, 2023. It seems to be old and needed for update. 2) “From 74 identified studies, outcome measures were categorized into groups like “Balance Improvement,” “Gait Improvement,” “Mobility Enhancement,” “Muscle Strength Improvement,” “Cognitive Function and Quality of Life,” and others” No need for all alternative words for measuring balance. The main measured outcome was balance. 3) The excluded Articles criteria are not placed in the abstract. It is better to be placed in the methodology section. 4) The results for fall risks reduction were not mentioned in the result section in the abstract. It is your second measured outcomes as mentioned in the title and research aim.\nIntroduction: You used present or future tense in writing “The review will rigorously”. Please use the past tense. “ The focus of this systematic review is to delve deep”. Do not use we or our, use the third pronoun like it was …..\nMethodology: 1) Use the updated for of PRISMA flow chart (PRISMA 2020 flow diagram for new systematic reviews which included searches of databases, registers and other sources). The new one included the Identification of studies via databases and registers and Identification of studies via other methods. 2) Mention the methods of identifying and removing the duplicates in different databases, the data extraction criteria, the used methods of methodological quality assessment. 3) Why you split the table including subtitle “Treadmill Training for Neurophysiological Improvement in Diseased and Elderly Individuals”. 4) Where the results of assessment of methodological quality in the result section. 5) Discussion needs more extensive report of finding of this systematic review.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Partly", "responses": [ { "c_id": "13149", "date": "16 Jan 2025", "name": "Moattar Rizvi", "role": "Author Response", "response": "Thanks prof ,Mohamed Salah for your valuable & worthful comments and your suggestions The responses of author to all comments one by one 1-Comment1- Title: The title containing “geriatric care” and “elderly population”. Use one of them only. Suggested title” efficacy of treadmill training on balance and fall risks in elderly population. A systematic review”. 1- Author response Thank you for your valuable suggestion. We have modified the title to align with your recommendation. The revised title is: \"Efficacy of Treadmill Training on Balance and Fall Risks in the Elderly: A Systematic Review.\" Abstract 1 - Reviewer Comment Abstract: 1) Search until May 31, 2023. It seems to be old and needed for updates. 1-Author Response Thank you for pointing this out. We have updated the search to include studies published up to January 1, 2025. After rerunning the search using the same strategy, no additional articles matching the inclusion criteria were identified. Therefore, the original findings remain unchanged. 2- Reviewer Comment 2) “From 74 identified studies, outcome measures were categorized into groups like “Balance Improvement,” “Gait Improvement,” “Mobility Enhancement,” “Muscle Strength Improvement,” “Cognitive Function and Quality of Life,” and others” No need for all alternative words for measuring balance. The main measured outcome was balance. 2 -Author response Thank you for your feedback. We have revised the text to emphasize balance as the primary outcome measure while retaining the mention of secondary outcomes. The updated text now reads: \"From 74 identified studies, the primary outcome measure was ‘Balance Improvement,’ while secondary outcomes included ‘Cognitive Function and Quality of Life,’ among others.\" This revision ensures clarity and aligns with the focus of the systematic review 3-Reviewer comment The excluded Articles criteria are not placed in the abstract. It is better to be placed in the methodology section. 3-Author response Thank you for the suggestion. We have removed the excluded articles criteria from the abstract and incorporated them into the Methodology section. 4-Reviewer comment The results for fall risks reduction were not mentioned in the result section in the abstract. It is your second measured outcomes as mentioned in the title and research aim. 4-Author response Thank you for your valuable feedback. We have revised the abstract's results section to explicitly mention fall risk reduction. The updated text now reads: \"Treadmill training demonstrated positive effects on balance and fall risk reduction, particularly in elderly individuals with Parkinson’s disease, spinal cord injuries, and age-related balance issues. Perturbation-based treadmill training significantly reduced fall rates, while underwater treadmill sessions improved mobility and cognitive function.\" Introduction: 1-Reviewer comment You used present or future tense in writing “The review will rigorously”. Please use the past tense. “ The focus of this systematic review is to delve deep”. Do not use we or our, use the third pronoun like it was 1-Author response Thank you for your insightful feedback. We have revised the text to maintain consistency in past tense and third-person narration. The updated sentences now read: \"The review rigorously evaluated...\" (instead of “The review will rigorously...”) \"The focus of this systematic review was to examine...\" (instead of “The focus of this systematic review is to delve deep...”) Methodology: 1-Reviewer comment Use the updated for of PRISMA flow chart (PRISMA 2020 flow diagram for new systematic reviews which included searches of databases, registers and other sources). The new one included the Identification of studies via databases and registers and Identification of studies via other methods. 1-Author response Thank you for your valuable suggestion. We have updated the PRISMA flowchart to the PRISMA 2020 format, which now includes a more detailed representation of the study selection process. The revised flowchart distinguishes between identification of studies via databases and registers and identification via other methods as per the updated PRISMA guidelines. 2-Reviewer comment Mention the methods of identifying and removing the duplicates in different databases, the data extraction criteria, the used methods of methodological quality assessment. 2-Author response Thank you for your valuable feedback. We have now explicitly detailed the methods used for duplicate removal, data extraction, and quality assessment in the Methodology section. The revised text is as follows: Data were extracted independently by two reviewers using a structured data extraction form. Extracted variables included study design, sample size, participant characteristics, treadmill training protocol (duration, intensity, frequency), primary and secondary outcome measures, and key findings. Discrepancies between reviewers were resolved through discussion. After importing search results from multiple databases, duplicates were identified and removed by adding all the data in Microsoft excel, highlighting the duplicates and by manual screening. Risk of bias for each included study was evaluated using the Cochrane Risk of Bias 2.0 tool for randomized controlled trials and the Newcastle-Ottawa Scale for observational studies. The Cochrane RoB 2.0 tool assessed five domains, including bias arising from the randomization process, deviations from intended interventions, missing outcome data, measurement of the outcome, and selection of the reported result. Each domain was rated as low risk, some concerns, or high risk, with an overall rating assigned to each study. To enhance clarity, a traffic plot and a summary plot were generated to visually present the findings 3-Reviewer comment Why you split the table including subtitle “Treadmill Training for Neurophysiological Improvement in Diseased and Elderly Individuals”. 3-Author response Thank you for your feedback. The table was originally split to enhance clarity and organization by grouping studies based on their primary focus areas. The subtitle “Treadmill Training for Neurophysiological Improvement in Diseased and Elderly Individuals” was maintained to ensure a clear distinction between studies targeting neurophysiological improvements and those addressing general balance and mobility. However, based on your suggestion, we have revised the table format to ensure better coherence: Merged the table sections where appropriate to present a more unified dataset. Maintained logical categorization within a single table to improve readability without unnecessary fragmentation. Used clear subheadings instead of splitting tables to differentiate study categories while maintaining flow. 4-Reviewer comment Where the results of assessment of methodological quality in the result section. 4-Author response Thank you for your valuable feedback. We acknowledge that the assessment of methodological quality was not explicitly reported in the results section. To address this, we have now included a detailed summary of the methodological quality of the included studies. 5-Reviewer comment Discussion needs more extensive report of finding of this systematic review. 5-Author response Thank you for your valuable suggestion. We have expanded the Discussion section to provide a more comprehensive analysis of the key findings of this systematic review. The revised section now includes a more detailed synthesis of the results, highlighting the impact of treadmill training on balance improvement and fall risk reduction, along with its effects on secondary outcomes such as cognitive function and quality of life. The updated Discussion now explicitly contrasts the findings of included studies, addressing variations in study design, population characteristics, and intervention protocols. We have also included a comparative discussion of different treadmill training modalities, such as perturbation-based treadmill training and underwater treadmill training, emphasizing their relative effectiveness. Additionally, we have elaborated on the implications of these findings for clinical practice and rehabilitation, while also acknowledging existing research gaps and the need for future studies to establish standardized training protocols. Very thanks for your comments" } ] }, { "id": "353972", "date": "09 Jan 2025", "name": "Adel Alhusaini", "expertise": [ "Reviewer Expertise Developmental Disabilities", "Early Mobility", "Infant Movement", "Motor Skills", "Motor Control", "Gait", "Balance", "Coordination", "Assistive Technology", "Childhood Obesity", "Physical Function", "Physical Activity", "Sedentary Behavior", "Participation Restrictions", "ICF (Children)", "Outcome Measures & Assessment", "Handwriting", "Quality of Life (Pediatrics)", "Pediatric Rehabilitation", "Early Intervention", "Child Development", "Motor Delay", "Postural Control", "Motivation", "Self-Efficacy", "Anxiety (Movement-Related)", "Social Participation", "Family Involvement", "Caregiver Burden", "School Integration." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis systematic review offers a significant contribution to understanding the efficacy of treadmill training in enhancing balance and reducing fall risk among older adults. The methodology encompasses a comprehensive literature search and analysis of approximately fifteen studies evaluating various treadmill training protocols. The findings suggest potential benefits for improving balance and mobility, particularly for individuals with Parkinson's disease or spinal cord injuries. The conclusions appear largely substantiated by the presented evidence, and the acknowledgment of limitations is appropriate. The authors rightly emphasize the significance of synthesizing disparate research. A recommendation for further investigation to optimize training protocols and address individualized needs is critical. However, several aspects warrant further consideration to enhance the review's clarity, rigor, and practical applicability.\nMethodological Clarity and Transparency: An inconsistency in the reported number of included studies (n=16 in the abstract versus n=15 in Table 1) warrants attention regarding transparency. The authors should explicitly state the final number of studies included within the results section and reconcile this discrepancy through verification and subsequent updates to both sections.\nData Interpretation and Contextualization: Regarding Table 1: study by Hesse et al., 1997, updating the 'Study Type' field to 'Quasi-experimental study' is recommended if methodologically accurate. Furthermore, contextualizing the findings in relation to existing systematic reviews and meta-analyses would significantly enrich the review by providing a broader scholarly perspective and identifying areas of convergence or divergence.\nMethodological Rigor and Bias Assessment: Explicit reporting of blinding procedures within the included studies is necessary to facilitate a robust assessment of potential bias. Acknowledging limitations arising from the absence or non-reporting of blinding procedures is also crucial for a comprehensive evaluation of study quality.\nPlease carefully review Table 1's columns and consider these revisions for clarity and conciseness: Change \"Paper Title\" to \"Author(s), Year\" without the title for easier reference and table management. Change \"Study Type\" to the more precise \"Study Design.\" Revise \"Population Characteristics\" to \"Participant Characteristics\" and add an \"Age\" field for comprehensive participant details. Add a \"Country/Setting\" column to provide important contextual information, if possible. Combine \"Intervention\" and \"Duration\" into a single column for better readability (e.g., \"Treadmill training, 8 weeks\"). Add separate columns for \"Primary Outcome(s)\" and \"Secondary Outcome(s)\" of the studies. Include a column specifying the \"Outcome Measurement Tools\" used for each outcome.\nFurthermore, concerning citation analysis within Table 1, if a literature review is cited, it is essential to examine the original primary studies referenced within that review and include those primary studies in the systematic review if they meet the pre-defined inclusion criteria.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [ { "c_id": "13150", "date": "16 Jan 2025", "name": "Moattar Rizvi", "role": "Author Response", "response": "Many Thank for prof. Adel Alhusaini for your valuable and worthful comments The responses for all reviewing comments one by one 1-Reviewer comment Methodological Clarity and Transparency: An inconsistency in the reported number of included studies (n=16 in the abstract versus n=15 in Table 1) warrants attention regarding transparency. The authors should explicitly state the final number of studies included within the results section and reconcile this discrepancy through verification and subsequent updates to both sections. 1-Author response Thank you for pointing out this inconsistency. Upon verification, the correct number of included studies is 15, and the mention of 16 studies in the abstract was a typographical error. We have now updated the abstract, results section, and any other relevant parts of the manuscript to reflect the correct count (n=15) to maintain accuracy and transparency. 2-Reviewer comment Data Interpretation and Contextualization: Regarding Table 1: study by Hesse et al., 1997, updating the 'Study Type' field to 'Quasi-experimental study' is recommended if methodologically accurate. Furthermore, contextualizing the findings in relation to existing systematic reviews and meta-analyses would significantly enrich the review by providing a broader scholarly perspective and identifying areas of convergence or divergence. Methodological Rigor and Bias Assessment: Explicit reporting of blinding procedures within the included studies is necessary to facilitate a robust assessment of potential bias. Acknowledging limitations arising from the absence or non-reporting of blinding procedures is also crucial for a comprehensive evaluation of study quality. 2- Author comments Thank you for your suggestion. The assessment of blinding procedures has been conducted using the Risk of Bias Tool (RoB 2 for RCTs). The updated Results section now explicitly reports blinding practices within the included studies, identifying whether single, double, or no blinding was used. Additionally, we have now included a detailed bias assessment table to highlight the impact of blinding (or lack thereof) on study outcomes. In cases where blinding was not reported, the potential risk of performance and detection bias has been acknowledged. 3- Reviewer comment Please carefully review Table 1's columns and consider these revisions for clarity and conciseness: Change \"Paper Title\" to \"Author(s), Year\" without the title for easier reference and table management. Change \"Study Type\" to the more precise \"Study Design.\" Revise \"Population Characteristics\" to \"Participant Characteristics\" and add an \"Age\" field for comprehensive participant details. Add a \"Country/Setting\" column to provide important contextual information, if possible. Combine \"Intervention\" and \"Duration\" into a single column for better readability (e.g., \"Treadmill training, 8 weeks\"). Add separate columns for \"Primary Outcome(s)\" and \"Secondary Outcome(s)\" of the studies. Include a column specifying the \"Outcome Measurement Tools\" used for each outcome 3- Author response Thank you for your detailed and valuable suggestions. We have carefully revised Table 1 to improve clarity, conciseness, and readability in accordance with your recommendations: The \"Paper Title\" column has been changed to \"Author(s), Year\", listing only the author(s) and publication year for streamlined reference. \"Study Type\" has been updated to \"Study Design\" to ensure precision in methodological classification. \"Population Characteristics\" has been revised to \"Participant Characteristics,\" and an \"Age\" field has been added to provide a clearer demographic profile of study participants. A new \"Country/Setting\" column has been included where possible to offer contextual insights into the study environments. The \"Intervention\" and \"Duration\" columns have been combined into a single column to improve table readability (e.g., \"Treadmill training, 8 weeks\"). Separate columns for \"Primary Outcome(s)\" and \"Secondary Outcome(s)\" have been added to distinguish key findings in a structured manner. .4-Reviewer comment Furthermore, concerning citation analysis within Table 1, if a literature review is cited, it is essential to examine the original primary studies referenced within that review and include those primary studies in the systematic review if they meet the pre-defined inclusion criteria. 4- Author response Thank you for your insightful suggestion. We conducted a thorough citation analysis of the literature reviews included in Table 1 to identify relevant primary studies that could potentially meet our pre-defined inclusion criteria. However, upon careful examination, none of the primary studies referenced within the cited literature reviews met the eligibility criteria for inclusion in this systematic review. Many thanks for your efforts and worthful comments" } ] } ]	1	https://f1000research.com/articles/13-330
https://f1000research.com/articles/13-329/v1	23 Apr 24	{ "type": "Research Article", "title": "Morphology of the obturator nerve, an anatomical study with emphasis on its clinical implications", "authors": [ "Latha V. Prabhu", "Rajanigandha Vadgaonkar", "Ashwin R. Rai", "Vandana Blossom", "Mangala M. Pai", "B.V. Murlimanju", "Latha V. Prabhu", "Ashwin R. Rai", "Vandana Blossom", "Mangala M. Pai", "B.V. Murlimanju" ], "abstract": "Background The goal of this cadaveric cross sectional study was to analyse the branching pattern of the obturator nerve morphologically and to determine its dimensions in embalmed cadavers.\n\nMethods In this cross sectional study, we examined 50 embalmed adult cadaveric lower limbs. Sex was not taken into consideration in the analysis; however, a side-based comparison was performed. The measurements were performed using a digital Vernier caliper.\n\nResults The branching of obturator nerve was observed at the pelvic cavity in 28 specimens (56%) and inside the obturator canal in 12 specimens (24%). The division of obturator nerve wasn’t observed in 10 specimens (20%). The length, width and thickness of the trunk of obturator nerve was 108.26 ± 9.53 mm, 2.84 ± 0.88 mm and 1.11 ± 0.35 mm. The width and thickness of the anterior and posterior divisions of obturator nerve measured 2.19 ± 0.82 mm, 0.9 ± 0.1 mm, 0.99 ± 0.6 mm and 0.71 ± 0.26 mm. The topography of branching of obturator nerve from the superior and inferior border of the obturator foramen was located at 1.48 ± 0.58 mm and 3.07 ± 1.1 mm away. The length of anterior division of the obturator nerve measured 110.88 ± 12.02 mm over the right side and 107.13 ± 7.81 mm over the left side. The width of the main trunk of obturator nerve was 2.87 ± 0.64 mm over the right side and 2.82 ± 0.64 mm over the left side.\n\nConclusions We believe that morphometric data of the obturator nerve will be enlightening to the operating surgeon during procedures such as obturator nerve block, nerve transplantation, and obturator nerve repair. The dimensions of the obturator nerve observed in the present study can be utilized as a morphological database for our sample population.", "keywords": [ "Lumbosacral Plexus", "Obturator Nerve", "Nerve Entrapments", "Pelvic Region" ], "content": "Introduction\n\nPeripheral nerve injury is managed by exploration and nerve repair. Nerve regeneration is possible, but it has been reported to be associated with poor functional recovery.1 The study of obturator nerve morphology may enlighten the clinician and provide successful clinical outcomes. Analysis of the morphology of the nerve may help the operating surgeon to assess the matching of the donor and recipient nerves.1 Obturator nerve are formed in the lumbar plexus by the ventral division of the ventral rami of the L2, L3, and L4 nerves. It is also involved in several pathological processes. Obturator nerve entrapment can occur due to pressure injury around the obturator canal.2 This contributes to pain and decreased sensation over the adductor compartment of the thigh. There may be difficulty in adduction of the thigh.3 The iatrogenic causes of obturator neuropathy also include traumatic injury, iatrogenic injuries during the surgical procedures like hip arthroplasty, urological surgeries, and spine surgeries through the retroperitoneal approach.2 The obturator nerve entrapment is observed in sports hernia and also in gynecological conditions like ectopic pregnancies.4–6 The benign swellings like cysts, neurofibroma, and lipoma can also cause pressure effect over the obturator nerve at this location.7,8 Due to all these implications, it is good to have the normal anatomical morphometric data of the obturator nerve with respect to that particular population. A literature search revealed that there was not much information available about this subject in the Indian sample population. This was the motivation for performing this anatomical investigation. The goal of this research was to study the morphology of the branching pattern of the obturator nerve and its morphometry in embalmed cadavers.\n\n\nMethods\n\nIn this study of the morphology of the human obturator nerve, we examined 50 embalmed cadavers. The sex category of the sample was not considered. Specimens showing pathological changes were not included in this anatomical study. A total of 100 obturator nerves were analyzed with respect to their topographical branching into the anterior and posterior divisions. The length, width, and thickness of the main trunk of the obturator nerve, anterior division, and posterior division were measured separately using Vernier calipers. Three measurements were taken by the same researcher of this study and the average of three was taken. This prevented the intra and inter-observer bias. The copyright license of the Vernier caliper is available in our department. Side-based comparisons were also performed using Student’s paired t-test. A recent version of the SPSS software (Version 27) was employed for statistical exploration. The copyright license of the SPSS software is available with our university. The topographical location of the obturator nerve and arrangement of structures at the obturator foramen were also examined. The mean distance of branching of the obturator nerve from the superior and inferior borders of the obturator foramen was measured. This anatomical study was approved (IEC KMC MLR 09-18/310) by the institutional ethics committee of Kasturba Medical College, Mangaluru, India (Reg. No. ECR/541/Inst/KA/2014/RR-17). This was approved from 26th September, 2018. We state that this research adheres to the Declaration of Helsinki. The protocol of this study was archived in the dx.doi.org/10.17504/protocols.io.5qpvo317dv4o/v1.\n\n\nResults\n\nIn the present study, obturator nerve branching occurred at the pelvic cavity into the anterior and posterior divisions (Figure 1) in 28 specimens (56%), at the obturator canal (Figure 2) in 12 specimens (24%), and there was no division (Figure 3) of the obturator nerve in 10 specimens (20%). The frequency of the topographic anatomy of the obturator nerve division is shown in Figure 4. The mean length, width and thickness of the trunk was 107.26 ± 8.71 mm, 2.84 ± 0.88 mm and 1.11 ± 0.35 mm individually. The mean width and thickness of the anterior and posterior divisions were 2.19 ± 0.82 mm, 0.9 ± 0.1 mm, 0.99 ± 0.6 mm and 0.71 ± 0.26 mm individually. The length of anterior and posterior division of obturator nerve were 109.01 ± 9.91 mm and 106.08 ± 7.71 mm respectively (Table 1).\n\nThe width of the main trunk was 2.87 ± 0.64 mm and 2.82 ± 0.64 mm over the right and left sides. The obturator nerve length was 107.55± 8.15 mm over the right side and 106.98± 9.27 mm at the left side. Its thickness measured 0.94 ± 0.07 mm and 1.25 ± 0.46 mm over the right and left sides. The length of anterior division was 110.88 ± 12.02 mm over the right side and 107.13 ± 7.81 mm over the left side. The width of the anterior division was 1.4 ± 0.55 mm and 1.7 ± 0.57 mm over the right and left sides. The thickness of anterior division was 0.94 ± 0.05 mm and 0.88 ± 0.13 mm over the right and left sides. The width of posterior division was 0.84 ± 0.21 mm and 1.06 ± 0.83 mm at the right and left sides. The thickness of posterior division was 0.54 ± 0.21 mm and 0.78 ± 0.29 mm at the right and left sides. The length of posterior division was 108.42 ± 9.31 mm and 105.54 ± 6.11 mm at the right and left sides (Table 2). The topographical location of the branching of the obturator nerve from the upper and lower borders of obturator foramen was 1.48 ± 0.58 mm and 3.07 ± 1.1 mm.\n\nThe difference was not statistically significant when the comparison was performed between the right and left sides for all parameters studied (p>0.05).\n\n\nDiscussion\n\nThe clinical anatomy of obturator nerve is essential. The obturator nerve is related to the internal iliac artery and internal iliac vein at the lateral pelvic wall. It traverses the obturator canal and exits the pelvis. Its anterior and posterior divisions innervate muscles, eventually. The anterior division courses over the obturator externus muscle and the adductor brevis is located posterior to the anterior division of obturator nerve.9 The pectineus and adductor longus muscles are found anterior to the obturator nerve. The other adductor compartment muscles, gracilis, adductor longus, and adductor brevis are also supplied by the obturator nerve. Itsposterior division pierces the obturator externus muscle and courses in between the adductor brevis and adductor magnus muscles. The muscular branches of obturator externus and adductor magnus muscles also offer articular twigs to the hip and knee joints. Its cutaneous branches supply the skin at the medial aspect of the thigh.9 It was reported that, there exists significant anatomical variation in the branching and subdivisions of the obturator nerve. These variations cause difficulty in the accomplishing the regional anesthesia.10 The obturator nerve division is known for its variations with respect to its topography in the obturator canal.11 Berhanu et al.12 observed intrapelvic division of obturator nerve in 23.9% cases, in the obturator canal in 44.8% cases and infrapelvic in 31.3% cases. In the present study, no extrapelvic divisions were observed (0%). In our study, the obturator nerve branched into the anterior and posterior divisions inside the pelvic cavity in 56% and 24% of the specimens, respectively. There was no division of the obturator nerve in 20% of samples. According to Tshabalala et al.11 from the South African population, intrapelvic branching was observed in 2% of cases, and the majority were branching in the obturator canal (93%). Extrapelvic branching was observed in 5% of cases. In another study in Greece by Anagnostopoulou et al.,10 intrapelvic branching was observed in 25% of cases, branching within the obturator canal was observed in 23% of cases, and extrapelvic branching was observed in 52% of cases. The differences in the data from our study may be due to ancestral variations. Other than these two previous studies, data are not available regarding the dimensions of the obturator nerve. In this context, our anatomical research may help anatomists and anthropologists to compare these data.\n\nThe width of obturator nerve was 2.67 mm in males and 1.91 mm in females according to Yount et al.1 In our study, the sex based comparison was not performed and the width was given for both the sexes together, which was measuring 2.84 ± 0.88 mm. Yount et al.1 reported that the average width of obturator nerve over the left and right sides were 2.28 mm and 2.29 mm. In our study, these dimensions were2.82 ± 0.64 mm and 2.87 ± 0.64 mm. Yount et al.1 also reported the length of obturator nerve, which was measuring 10.86 cm and 10.83 cm at the right andleft sides. Our data is almost similar to their data as the same dimensions in our study measured 107.55± 8.15 mm and 106.98± 9.27 mm. In this study, the distance of the branching of obturator nerve from the superior and inferior borders of obturator foramen were 1.48 ± 0.58 mm and 3.07 ± 1.1 mm.\n\nThe obturator nerve can be utilized as a nerve transfer for femoral nerve paralysis.13 The neurectomy of anterior division of the obturator nerve and intrapelvic obturator neurotomy are performed to relieve spasticity in the medial compartment of the thigh in children suffering from cerebral palsy.14 Lack of anatomical knowledge can lead to iatrogenic injury of the obturator nerve. Kendir et al.15 emphasized the reputation of morphological awareness of the obturator nerve at the obturator canal in accomplishing the best obturator nerve block. Care should be taken while injecting the anesthetic drug simultaneously into the anterior and posterior divisions because of the variability in the branching of the obturator nerve. Anesthesia may be incomplete if there are variations in branching pattern.11\n\nThis study was aimed at helping clinicians, but its limitations, such as individual branches to the muscles it supplies, were not explored. A gender-based comparison of morphometric data was not performed. This study did not record the prevalence of accessory obturator arteries. Future implications of this study include a more detailed topographical anatomy, such as the distance of the obturator nerve from the femoral artery. The distance between the anterior superior iliac spine and medial condyle of the femur can be determined to assess the ratio, and regression formulae could be obtained. The depth of the obturator nerve from the skin can also be determined. This may assist with the obturator nerve block procedure.\n\n\nConclusion\n\nThe data of this study will be clinically helpful during the procedures like obturator nerve repair and transplantation. The dimensions of this study can be considered as the morphological database of Indian population.\n\n\nEthics and consent\n\nThis anatomical study was approved (IEC KMC MLR 09-18/310) by the institutional ethics committee of Kasturba Medical College, Mangaluru, India (Reg. No. ECR/541/Inst/KA/2014/RR-17). This was approved from 26th September, 2018. We state that this research adheres to the Declaration of Helsinki. The body donors of the cadavers, which are utilized in this study have consented to utilize their body for the medical research along with the medical teaching. They have put their signatures in their body donation form along with the witnesses.", "appendix": "Data availability\n\nFigshare: Medline database search strategy for ‘Morphology of obturator nerve’. https://doi.org/10.6084/m9.figshare.24955383. 16\n\nThe project contains the following underlying data: file name – Obturator Nerve.xlsx\n\nThe statistical analysis was performed by using the recent version of SPSS software. 17\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nFigshare: The strobe checklist. Anatomical study of obturator nerve. https://doi.org/10.6084/m9.figshare.25526056. 18\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nYount M, Peruri A, Morgan A, et al.: Morphology and morphometry of the human obturator nerve in males and females. Anat. Histol. Embryol. 2023; 52(3): 490–499. PubMed Abstract \| Publisher Full Text\n\nJo SY, Chang JC, Bae HG, et al.: A morphometric study of the obturator nerve around the obturator foramen. J. Korean Neurosurg. Soc. 2016; 59(3): 282–286. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKitagawa R, Kim D, Reid N, et al.: Surgical management of obturator nerve lesions. Neurosurgery. 2009; 65(4 Suppl): A24–A28. PubMed Abstract \| Publisher Full Text\n\nAhmadian A, Abel N, Uribe JS: Functional recovery of severe obturator and femoral nerve injuries after lateral retroperitoneal transpsoas surgery. J. Neurosurg. Spine. 2013; 18: 409–414. PubMed Abstract \| Publisher Full Text\n\nMcConaghie FA, Payne AP, Kinninmonth AW: The role of retraction in direct nerve injury in total hip replacement: an anatomical study. Bone Joint Res. 2014; 3: 212–216. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZwolak P, Eysel P, William-Patrick Michael J: Femoral and obturator nerves palsy caused by pelvic cement extrusion after hip arthroplasty. Orthop. Rev (Pavia). 2011; 3: e6. Publisher Full Text\n\nJoniau SG, Van Baelen AA, Hsu CY, et al.: Complications and functional results of surgery for locally advanced prostate cancer. Adv. Urol. 2012; 2012: 1–8. Publisher Full Text\n\nKim SH, Seok H, Lee SY, et al.: Acetabular paralabral cyst as a rare cause of obturator neuropathy: a case report. Ann. Rehabil. Med. 2014; 38: 427–432. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHanna AS: Obturator Nerve. Anatomy and exposures of spinal nerves. Cham: Springer; 2015.\n\nAnagnostopoulou S, Kostopanagiotou G, Paraskeuopoulos T, et al.: Anatomic variations of the obturator nerve in the inguinal region: implications in conventional and ultrasound regional anesthesia techniques. Reg Anesth Pain Med. 2009; 34(1): 33–39. PubMed Abstract \| Publisher Full Text\n\nTshabalala ZN, Human-Baron R, van der Walt S , et al.: The anatomy of the obturator nerve and its branches in a South African cadaver sample. Transl. Res. Anat. 2022; 27: 100201. Publisher Full Text\n\nBerhanu K, Taye M, Abraha M, et al.: Anatomical variations and distributions of obturator nerve on Ethiopian cadavers. Anat. J. Africa. 2020; 9(1): 1671–1677. Publisher Full Text\n\nCampbell AA, Eckhauser FE, Belzberg A, Campbell JN: Obturator nerve transfer as an option for femoral nerve repair: case report. Neurosurgery. 2010; 66(6 Suppl Operative): onsE375. discussion 375. Publisher Full Text\n\nSnela S, Rydzak B: The value of the adductor tenotomy with obturator neurectomy in the treatment of the hips at cerebral palsy children. Early clinical and radiological examination results. Orthop. Traumatol. Rehabil. 2002; 4(1): 11–14.\n\nKendir S, Akkaya T, Comert A, et al.: The location of the obturator nerve: a three-dimensional description of the obturator canal. Surg. Radiol. Anat. 2008; 30(6): 495–501. PubMed Abstract \| Publisher Full Text\n\nPrabhu LV, Vadgaonkar R, Murlimanju BV, et al.: Morphology of obturator nerve. [Dataset]. Figshare. 2024 [cited 2024 Apr 4]. Publisher Full Text\n\nIBM Corp: IBM SPSS Statistics for Windows (Version 27.0) [Computer software]. IBM Corp; 2020.\n\nMurlimanju BV, Vadgaonkar R: Anatomical study of obturator nerve. figshare. Preprint.2024. Publisher Full Text" }	[ { "id": "273599", "date": "10 May 2024", "name": "Rajasekhar SSSN", "expertise": [ "Reviewer Expertise Areas of expertise include gross anatomy", "clinical anatomy", "embalming", "histological techniques", "and histology." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study describes the measurement of obturator morphometric parameters and collation of data without gender differentiation. discussion section: the hypothesis given for the difference between the results of the current study and that of the another study done in Greece is not a valid one \" Ancestral variations\"\nComments:\n\nSchematic diagram representing the measurements can be provided.\nRationale for the study including the rationale for selecting the types of measurements should be given.\n\nThere is a specimen number discrepancy between the abstract and the methods section.\n\nMethods section mentions about the copyright licence for Vernier callipers, please clarify this.\n\nThe term \"gender\" should be used instead of \"sex\". Justify the rationale for the measurement of width of obturator nerve.\n\nTopographical measurement parameters were inconsistent between the methods and the results: obturator nerve division versus obturator nerve.\n\nSpecify which point is taken as distal point for the measurement of length of both anterior and posterior divisaion of the nerve.\n\nGender differentiation is not done, but the measurements such as length and width may be significantly different/smaller in females compared to males, owing to the shorter stature of females compared to males.\nTherefore the combined data that includes males and females cannot be considered as a valid data to apply or generalise the data for the wider population. Consequently, the results of the study may not be valid. The authors need to review the methods used in the study and rework the manuscript with results worked out separately for males and females to obtain meaningful information from the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "279366", "date": "29 May 2024", "name": "Najma Mobin", "expertise": [ "Reviewer Expertise Plastination", "museum techniques", "histological and gross anatomy studies." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe introduction is well written. The methodology and results are explained well. The pictures are self- explanatory. The implications in discussion are well written and explained. Limitations of the study are mentioned. Conclusion requires minor changes, like in what way this study is going to help in nerve repair and transplant.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-329
https://f1000research.com/articles/13-328/v1	23 Apr 24	{ "type": "Research Article", "title": "Automatic Identification of Hate Speech – A Case-Study of alt-Right YouTube Videos", "authors": [ "Johan Eddebo", "Mika Hietanen", "Mathias Johansson", "Johan Eddebo", "Mathias Johansson" ], "abstract": "Background Identifying hate speech (HS) is a central concern within online contexts. Current methods are insufficient for efficient preemptive HS identification. In this study, we present the results of an analysis of automatic HS identification applied to popular alt-right YouTube videos.\n\nMethods This essay describes methodological challenges of automatic HS detection. The case study concerns data on a formative segment of contemporary radical right discourse. Our purpose is twofold. (1) To outline an interdisciplinary mixed-methods approach for using automated identification of HS. This bridges the gap between technical research on the one hand (such as machine learning, deep learning, and natural language processing, NLP) and traditional empirical research on the other. Regarding alt-right discourse and HS, we ask: (2) What are the challenges in identifying HS in popular alt-right YouTube videos?\n\nResults The results indicate that effective and consistent identification of HS communication necessitates qualitative interventions to avoid arbitrary or misleading applications. Binary approaches of hate/non-hate speech tend to force the rationale for designating content as HS. A context-sensitive qualitative approach can remedy this by bringing into focus the indirect character of these communications. The results should interest researchers within social sciences and the humanities adopting automatic sentiment analysis and for those analysing HS and radical right discourse.\n\nConclusions Automatic identification or moderation of HS cannot account for an evolving context of indirect signification. This study exemplifies a process whereby automatic hate speech identification could be utilised effectively. Several methodological steps are needed for a useful outcome, with both technical quantitative processing and qualitative analysis being vital to achieve meaningful results. With regard to the alt-right YouTube material, the main challenge is indirect framing. Identification demands orientation in the broader discursive context and the adaptation towards indirect expressions renders moderation and suppression ethically and legally precarious.", "keywords": [ "Automatic hate speech identification", "Hate speech", "alt-right", "YouTube", "interdisciplinary research" ], "content": "Methods\n\nThere is no cut-and-ready method for our purposes. By necessity our approach is experimental in design and should be seen as exploratory when it comes to how a verbal and contextual phenomenon such as hate speech can be identified automatically. Our twofold purpose has led us to implement two complementary methodological approaches. In the following, we first describe an approach to automatic identification in four steps: gathering an annotated corpus (for this we have used three corpora); text pre-processing; training of the classifier and applying it to the YouTube transcripts. Finally, we engage with the material through a qualitative close reading of select parts to better understand the previous step, and the character of the material in general.\n\nThe challenge of automatically classifying the sentiment of a text has a long history (Biagioni, 2016), and the sub-problem of identifying what is offensive in texts has also been given attention (Schmidt & Wiegand, 2019). A methodologically simple method is the lexical approach: to rely on an annotated lexicon of terms related to the sentiment (positively and negatively) and to count the frequencies of terms in a text. If there are more positive (or negative) terms or phrases in the text it can be classified as positive (or negative). This has some obvious drawbacks: terms are used variously and can relate to a context in contradictory ways. An example of this is sarcasm. A statement or phrasing that uses a term in its non-literal sense is a challenge for language-modelling. This is especially true when such statements are also used in their literal meaning in the same corpus. Hate speech is a specific variation of sentiment analysis; instead of classifying statements on a scale between two opposites (positive and negative) it classifies statements as hate speech or not hate speech. Gitari et al. (2015) perform a series of tests using this lexical approach to the issue of hate speech, with limited success.\n\nWith the advancement of machine learning (ML) and deep learning (DL) methods, the sophistication and range of available methods have increased. These methods tend to share one typical drawback: they are data hungry, that is, they need a lot of data to be trained to perform their task (Ploeg et al., 2014; Adadi, 2021). Typically, the more data and varied data a model is trained on, the better it will generalise what it learns to new data. When data is not readily available, collecting this type of large-scale data is time-consuming, especially if it needs to be annotated. When just having a lot of data is not enough or the required classification is not available it is standard practice to rely on manual annotation. It has become common to crowdsource this task, using volunteers or commissioned individuals using platforms such as Zooniverse and Figure 8 (Wang et al., 2013).\n\nFor this study we combined three openly available hate speech annotated corpora of tweets written in English: Hate-speech-and-offensive-language, HSOL (Davidson et al., 2017), HatEval – as subset of the HatEval corpus (Basile et al., 2019), which in turn is based on a corpus for misogyny identification by Fersini et al., (2019), and Offensive Language Identification Dataset, OLID (Zampieri et al., 2019). These corpora were created with different purposes in mind and their definitions of hate speech are similar but not identical. This is not a problem because together they provide a holistic view of what people consider hate speech.\n\nThe annotation of each corpus was achieved through crowdsourcing – enlisting crowds of people to manually annotate tweets – using a rule of majority to determine each tweet’s de facto category. While this is an effective way to get each tweet annotated by multiple people for large corpora and reducing the bias of the individual annotator, it also adds some opacity to the process. The annotators are anonymous and only one of the three corpora has published the instructions provided to the annotators (Basile, n.d.). While human annotation is considered the golden standard, it is not perfect. Davidson et al. (2017) noted that annotators had more disagreement of what should be regarded as hate speech and what is merely offensive than what is neutral; an observation that reflected in the performance of their model. As our purpose is to make a binary classification between hate speech and not, we discarded tweets belonging to the other categories from each corpus and kept a total of 42,430 tweets from the three corpora that were annotated as hate speech and neutral.\n\nUsing this corpus of 42,430 tweets we proceeded to train a classifier, the first part of which is a simple preprocessing pipeline that transforms the raw text into numeric input for the actual model as follows: (1) cleaning, (2) tokenizing, (3) stemming, (4) removing stop words, and (5) vectorizing. Out of these five steps only the cleaning needs to be customised, which is why it will be explained in more detail in the next subsection.\n\nThe first step, explained in more detail below, homogenises from the raw text format to a lowercase string of characters. These strings are then split into their constituent terms, tokens. These tokens are then stemmed, i.e., reduced to their core meaning or word by removing endings. This step may reduce different meaning tokens to a similar token, such as the verb ‘booking’ and the noun ‘books,’ which both become ‘book.’ This step reduces the number of tokens dramatically and reduces the chance that the model learns too much from a rarely used variant of a word.\n\nFrom these tokens we remove words that are too common to add specific meanings to the texts, words like ‘a,’ ‘of,’ ‘and.’ The tokens that remain after this step make the basis for the model’s vocabulary, the ‘words’ or tokens the model will recognize.\n\nSpecial attention was paid to cleaning the tweets, since their format is different compared to our empirical material of transcriptions from YouTube. There are some conventions of Twitter and other social media that do not translate well to other written media and not at all to spoken work. For example, the use of @USER to direct one’s statement to a particular user, the inclusion of URLs, the use of emojis, and of hashtags. The latter sometimes consist of single words, a phrase, or an acronym, which sometimes can easily be separated automatically into its parts. None of these conventions exist in transcriptions and were therefore removed. The output of this step is a lowercase string of characters without @ or # tags, and without URLs.\n\nFor the training and selection of models we used the SciKitLearn and Tensorflow (Keras) libraries, as these provide a lot of stable and efficient algorithms for ML models and selection. Before vectorizing and standardising the corpus, we split the data 80:20 randomly stratified by the outcome variable, depending on if the tweet was annotated as hate speech or not, to ensure that we have a similar distribution of hate speech and non-hate speech in both segments. The 20% was withheld from the model during training and was at the end used to evaluate the model. This reduces overfitting, that the model learns too much from the specific dataset it was trained on and therefore cannot generalise to new data. Similarly, some ML and DL algorithms withhold parts of the training data during the training for similar effect.\n\nAfter experimenting with simpler models in SciKitLearn, random forests (Breiman, 2001), logistic regression (Menard, 2010), and Naïve Bayes, (Manning et al., 2008), which did not yield satisfactory results, we moved on to working with TensorFlow to train Artificial Neural Network (ANN) models. Specifically, we used Convolutional Neural Networks, CNN (LeCun et al., 1990) and Recurrent Neural Networks, RNN (Hochreiter & Schmidhuber, 1997; both explained in Kotu & Deshpande, 2018, ch. 10) which are more complex in nature and have the potential to solve more complex problems. We used TensorFlow’s ‘hyperband tuning’ feature to select the final RNN architecture with a testing performance of f-1 score of .854.\n\nThe end-product of this process is a trained classifier that takes texts as an input and returns a value within the range of [0,1] which can be interpreted as an intensity or probability of hate speech within that text. Table 1 contains the confusion matrix of the model’s predictions based on the testing data, the 20% of the corpus withheld during training. We can see that the model manages to correctly classify 89% of the hate speech tweets as hate speech but only identifies 74% of the non-hate speech tweets as non-hate speech. We can therefore expect it to reliably predict when a text does not contain hate speech, but we should be more sceptical when a text is predicted as hate speech.\n\nThe limit imposed on tweets is on character level, namely 280 characters (since 2017; earlier 140 characters; Rosen & Ihara, 2017). Roughly speaking, this restricts tweets to at most three sentences. Simultaneously, there is no technical restriction for how long a sentence can be and our transcripts lack punctuation.\n\nWorking from the concept of sentences we segmented the transcripts into synthetic sentences by dividing the texts into atoms of seven words and joining every three consecutive atoms into sentences. In this way we have 21-word sentences and atoms are included in three sentences, see Table 2.\n\nWe overlapped the sentences to reduce the chances that we split a spoken sentence in ways that remove words from their context. The three-atom schema is the smallest combination that ensures that each atom is at the centre of the selected context. We experimented with different atom-lengths on a few different pieces of the material and inspected the results manually before deciding on the 7-word atom. With shorter atoms, many phrases that manually were marked as hate speech, were not identified as such by the algorithm and longer atoms did not improve results.\n\nWhen looking at the transcripts on paragraph level we used a similar approach to aggregate the synthetic sentences into synthetic paragraphs using seven atoms around a paragraph’s central atom using the earlier output from the classifier for full synthetic sentences. As illustrated by Table 3, the first and last atom from each video transcript is only used in one synthetic paragraph. Even so, the central atoms of each paragraph are used up to three times due to how we overlapped the paragraphs.\n\nFor the overall score of each paragraph, we used the mean, median and maximum scores of all full synthetic sentences of the paragraph as independent probabilities of the paragraphs containing hate speech and calculated their complement as a measurement for the likelihood that the paragraph contains hate speech.\n\nThe outcome of the automated identification is evaluated (below) through a close reading approach, discerning the explicit and implicit argumentative structure and significations (Brummett, 2010). The material flagged as likely to be hate speech, as well as the low-probability material, are furthermore scrutinised in relation to a holistic definition of hate speech as well as the textual context as such.\n\nWe base our understanding of hate speech on the discussion in Hietanen & Eddebo (2023) which refers to speech acts or acts of communication which express intended harm, disparagement, or vilification, or inherently imply the same, and target a group or set of groups defined in relation to protected characteristics, such as race, gender, or religion (for lists of protected characteristics, see Table 2 in Hietanen & Eddebo, 2023).\n\n\nMaterial: Alt-Right on YouTube\n\nOur selection of channels and videos for analysis is based on Data & Society’s report Alternative Influence (Lewis, 2018) which maps networks of influencers on YouTube characterised by ‘reactionary’ positions, ‘a general opposition to feminism, social justice, or left-wing politics’ (p. 8). The report presents an overview of channels with right-wing politics as well as a positive approach in relation to the radical right or alt-right movement. The YouTube transcripts, automated or uploaded by the channel, were downloaded as text-files. A manual check indicated that the quality of the transcripts was high and reliably conveyed the oral narrative.\n\nWe further selected a number of channels formally connected to the radical right, specifically, and therefore more likely associated with the sort of politically controversial communications subject to hate speech suppression. For this, we employed Rydgren’s (2018, pp. 23–24) basic definition of the radical right which emphasises ethnonationalism anchored in narratives about the past, directed towards strengthening the nation, returning to traditional values, and establishing a localised, organic, and ethnically homogenous polity. For clarification, ‘radical right’ is an ideological classifier or political preference for which we employ Rydgren’s definition. The alt-right is a contemporary, US-based white nationalist ideological movement characterised by radical right ideology. ‘Far right’ is a broader ideological classifier than ‘radical right,’ yet which overlaps with the latter to a great extent. ‘White supremacist’ is a particular ideological position which is generally a component part of these frameworks.\n\nFrom this basis, we made a sub-selection of the nine most popular channels (based on the number of subscribers) from Data & Society’s report, all of which are in English. The 15 most popular video clips (in number of views) were selected from each channel. Except for the control, this selection excluded the rare material that had no political content nor any connections to radical right narratives whatsoever. The selection was made during spring and summer of 2019, apart from the control channel, where the final selection was made in June 2021.\n\nWe selected a control channel, also in English, assumed to contain very little hate speech, namely ‘History Time’ (Kelly, n.d.). This channel exhibits a certain thematic and conceptual overlap with the other material due to its focus on ethnicities in conflict and narratives about the past.\n\nFor contrast we included sentences from the English-speaking white supremacist forum Stormfront (Stormfront, n.d.; dataset Garciá-Pablos & Perez, n.d.). Stormfront is a far-right discussion forum which can be assumed to contain a high degree of explicit hate speech (Costello & Hawdon, 2019).\n\n\nResults\n\nTable 4 presents descriptive statistics of the model’s predictions for the sentences across all three corpora. On average the model identifies over 50% more hate speech in the alt-right transcripts (.111) than in the history-channel (.069), and even more in the Stormfront material (.159). Though the difference is less pronounced across the quartiles, the level of identified hate speech in the alt-right corpus is consistently nested between the other two corpora.\n\na The respective quartile of scores given by the model.\n\nb Share of units that are predicted to be hate speech with a score >.5.\n\nc The relative change from ‘History’ to ‘Alt-right.’\n\nThe second part of Table 4 contains the descriptive statistics of the predicted hate on the paragraph level (described above) for the alt-right and history channel; the Stormfront data consists largely of short posts across different threads which prevents aggregation into paragraphs. With this approach the overall level of hate is pronounced; a much higher level of hate speech is identified across both corpora and the relative difference between the two is decreased. Still, the overall level of identified hate speech remains notably higher in the alt-right corpus (M = .463, SD = .296; 43% were predicted to contain hate speech).\n\nOn average, the model noted 4,8 percentage points more hate speech in the Stormfront data than in the alt-right YouTube data (.159–.111); 4,2 percentage points more hate speech in the alt-right YouTube data than in the History Time data; and, finally, 9 percentage points more hate speech in the Stormfront data than in the History Time data. This is consistent with the expectation that the control, History Time, contains the least amount of hate speech, and that the Stormfront data contains the most amount of hate speech.\n\nSince the Stormfront corpus was annotated for hate speech, we can confirm that our model missed 80% of those instances that were annotated for hate speech. At the same time, the model correctly identified 90% of the instances of non-hate speech.\n\nWe evaluated the outcome of the automated identification through a close reading approach. The material flagged as likely to be hate speech, as well as the low-probability material, were furthermore scrutinised in relation to our view on hate speech as well as the textual context.\n\nA subsidiary category of proximate hate speech was used to identify videos, synthetic sentences, or paragraphs, which were not themselves possible to categorise as hate speech, but which nonetheless were clearly parts of broader acts of hate speech or narratives identifiable as such in connection to the discursive context. The synthetic sentences can for instance be considered proximate hate speech in relation to the meso level of paragraphs, and the paragraphs (or sentences) in relation to the macro level of the video clip as such (a distinction elaborated below).\n\nAn example of proximate hate speech defined in relation to overarching levels would be a statement about the lower IQ scores of sub-Saharan native tribes within the context of a video that, considered as a whole, purveys scientific racism. The statement as such, while precarious, could be neutral in another context, but is here auxiliary to a claim of racial inferiority on a higher level, and should therefore be categorised as hate speech.\n\nIt is not our intention to support any particular definition of hate speech, nor its implementation in a context of moderation or censorship, but rather to explore the various outcomes of such an implementation of a normative understanding of hate speech.\n\nIn our qualitative assessment, we examined three categories of material in detail. We ran synthetic sentences derived from the transcripts through the classifier, the outcome of which served to flag and identify synthetic paragraphs constituted by said sentences, as well as entire videos.\n\nThree levels of contextual proximity were brought to bear both on the methodological framing of the material analysed, as well as in the qualitative analysis as such: sentences, paragraphs, and videos.\n\nThe sentences represent the micro context, and it is on this level that the classifier operates directly. As an example, in the micro context of a synthetic sentence certain concepts can amount to propositions expressing speech acts that match the definition of hate speech. The sentences can also express complex ideas that likewise match the definition, or be sufficiently close thereto, to be flagged as hate speech. The micro context in our analysis consists of the synthetic sentence and the immediate text fragments before and after the synthetic sentence.\n\nThe synthetic paragraphs on the level above function as the meso context. Here, sets of related statements are interpreted in a manner similar to how we approach the sentences.\n\nFinally, the videos are the macro context. It should be noted that several additional levels above the videos implicitly will follow from this sort of classification, such as the channels themselves or the entire U.S. alt-right discourse of the late 2010s. In the qualitative evaluation, we did not consider these additional levels of a macro or meta context other than in the sense of identifying overarching well-known ideological anchor points such as the great replacement theory or scientific racism, when interpreting statements at the lower levels.\n\nWe analysed the top 1,000 and the bottom 10,000 synthetic sentences through close reading. This tenfold difference between the groups stems from the model predicting that hate speech sentences are greatly outnumbered and this group therefore needs to be scrutinised closer. Table 5 summarises the results.\n\nThe outcomes here are strongly divergent. In the top category, we consider 27.2% of the sentences to be hate speech, either explicitly or indirectly. Of this set we considered only about a third as proximate hate speech through the qualitative analysis.\n\nThe bottom category is almost devoid of material categorised as hate speech. The result of the close reading is that only 13 sentences out of 10,000 carry that designation, and 50 (5%) in total are either explicitly or indirectly considered hate speech. Here, on the other hand, 37 (0.4%) of the designated set was considered proximate hate speech.\n\nThe evaluation of paragraphs also gave us a marked division between top and bottom (Table 5, above). We scrutinised 124 paragraphs, each at the respective ends of the hate speech probability hierarchy. In the top, 17 were considered incorporating hate speech, or were as such designated hate speech. Nineteen paragraphs contained material proximate to hate speech or could as such be considered proximate hate speech, whereas the remaining 88 paragraphs were found to be neutral.\n\nIn contrast, the bottom set contained almost nothing that could be considered even proximate to hate speech. Two were placed in this category, while the remaining 122 paragraphs were designated neutral. In addition, the two paragraphs in the proximate category were not very strong examples of this intermediate category, with one (Supplementary Material, channel 7_RIT_66560, line 70) containing a quite tacit allusion to an antisemitic sentiment, and the other (channel 6_BP_26276, line 115) a veiled reference to race realism with regard to the video as broader context.\n\nThe 14 videos whose transcripts contained the highest ratio of synthetic sentences likely to contain hate speech were qualitatively assessed in detail. Four of these were considered explicitly to incorporate hate speech. In these, hate speech was not connected to individual synthetic sentences, but to larger sections of information across the video. Four additional videos were categorised as considered proximate hate speech. By analysing content and presentation, we designated the remaining six videos as neutral. Nine of these have since been removed from the platform, after an update of YouTube’s guidelines in the Summer of 2019 (YouTube, 2019; Hern, 2020).\n\nThe 14 videos whose transcripts contained the lowest ratio of synthetic sentences classified as probably containing hate speech were likewise qualitatively assessed in detail. Of these, none could be considered incorporating hate speech per se. Five could be classified as containing material proximate to hate speech or as such considered proximate hate speech in accordance with the above. The remaining nine were designated as neutral. Eight of these videos have since been removed.\n\n\nDiscussion\n\nA key implication of this study is the fact that hate speech narratives in our material seem to be tacitly constructed at more complex levels of discourse. Explicit acts of immediate hate speech are almost non-existent, something that partly is due to the nature of the material, which is intended to disseminate a point of view before a neutral or amicable audience. But the lack of explicit hate speech is likely also due to the creators’ awareness of moderation and suppression of hate speech.\n\nInitial observations to this effect compelled us to approach the material through three levels of analysis, the micro, meso, and macro levels, which confirmed the tendency towards positions and narratives being indirectly structured at more complex levels of discourse. This is focused through the non-binary distinction between hate speech and proximate hate speech.\n\nSimilar studies generally use a binary approach (e.g., hate/non-hate) when annotating, which inevitably obscures a more nuanced characterization (Vrysis et al., 2021) and entails certain issues of definition.\n\nWhen we move from sentences towards paragraphs, we can see how the proximate hate speech category grows. Something designated as proximate hate speech essentially ‘points upwards’ towards more complex levels of discourse involving a broader sphere of meaning. Paragraphs with the highest number of proximate-flagged synthetic sentences are thus being indicated in this way, and the same holds for entire videos. The false positive rate (i.e., sentences, paragraphs, and videos flagged by the model as hate speech) is similar for sentences (72.8%) and paragraphs (70.1%), but lower for videos (42,8%; 6 out of 14).\n\nThe false negative rate does not reflect the same pattern. While false negatives fall when we move from sentences to paragraphs, of the set of videos with the lowest ratio of flagged synthetic sentences, all of 5 out of 14 (35.7%) were considered proximate hate speech. This is likely an artefact of the general character of the material as such which overwhelmingly tacitly affirms or reproduces narratives that can be categorised as hate speech.\n\nThis upwards indication also implies that any actual reception of hate speech narratives is mainly indirect. In other words, we are here dealing with something much more akin to Ellul’s notion of integration propaganda (or sociological propaganda) than agitprop (Ellul, 1973, ch. 1.3, sect. ‘Propaganda of Agitation and Propaganda of Integration’). This would imply that our corpus exemplifies long-term consensus building approaches rather than explicit calls to action or concrete efforts of organisation.\n\nWe illustrate the qualitative designation of proximate hate speech by giving two examples from the top and bottom categories of sentences, respectively, in relation to their associated meso and macro levels.\n\nSynthetic sentence 301 in the bottom 5% category reads: ‘group’s average IQ and sub-Saharan Africans would also have some of the most conservative and racist societies based on their group’s’ (Supplementary material, tab ‘bottom 5%’). This sentence immediately signifies an attribution of a causal relationship between IQ scores and political tendencies. In the context of the radical right discourse on race, this sort of causal inference is common and immediately invokes the discursive attribution of essential racial characteristics we for instance find in the framework of scientific racism (Farber, 2011, ch. 2). The sentence does not explicitly signify hate speech by any stretch of the imagination, but it immediately appeals to an essential association between race and intelligence and a factor of comparison between distinct racial groups.\n\nWhen we look for more information on the meso level, i.e., the synthetic paragraph in which the sentence in question is embedded, we find an explicit juxtaposition between the IQ scores of Aborigines and sub-Saharan Africans and that of East Asians and Japanese, with an added emphasis on the association between a lack of understanding of ‘the intricacies of the world’ and the lower IQ scores. We also see more of the implied connection between IQ scores and political affiliation which evidently is a polemic against a posited correlation between racism and lower intelligence such as in this transcribed synthetic paragraph:\n\na person to not understand the intricacies of the world and this in turns makes him a racist well then there’s a lot of explaining to do that would then make Australian Aborigines on average the most politically conservative as well as racist leaning groups of people on earth according to the same survey and their groups average IQ and sub-Saharan Africans would also have some of the most conservative and racist societies based on their group’s average IQ so by nations East Asians and the Japanese in particular would be the most welcoming to foreigners as their median IQ places them as among the (Supplementary Material, tab ‘Paragraphs,’ line 2257).\n\nIn other words, in maintaining that Aborigines on average would be the most politically conservative as well as racist leaning group, the author is actually saying that Aborigines are the least intelligent people in the world, with the worst capacity to ‘understand the intricacies of the world.’ Thus, the synthetic sentence, at the micro level, is categorised as proximate hate speech since it immediately implies the propositional content at the meso level. This notwithstanding, neither the sentence nor the paragraph was flagged by the filter as likely to contain hate speech.\n\nWhen we look at an example from the top-level sentences categorised as proximate hate speech, the situation is similar. Sentence 209 reads: ‘thousands of people from the Middle East pouring into Europe at least let people talk about their fears right he’ll talk.’ The immediate signification here has little to do with hate speech. It connects high levels of immigration to ‘fears,’ and vaguely implies that there are efforts to suppress discussion of these fears.\n\nLooking to the meso level, i.e., the transcribed synthetic paragraphs, the latter point is emphasised, explicitly mentioning forceful discursive repression of such discussion, yet there is still nothing akin to hate speech here:\n\nthe problem is that I really am always suspicious when there are significant social problems that nobody can talk about when when facts become a problem to the discussion the discussion itself has turned cancerous quote unquote and speech yami no we look I mean if you want to [assuage] people’s fears about hundreds of thousands of people from the Middle East pouring into Europe at least let people talk about their fears right he’ll talk about the facts that give them concern but everybody gets screamed down and that is not a good sign here’s another example so forty years ago the Swedish (Supplementary Material, tab ‘Paragraph,’ line 376; word within brackets added due to an error in the automatic transcription).\n\nHowever, on the macro level, i.e., in the context of the entire video, a fuller picture emerges. The ‘fears’ of the lower levels are here connected to claims of mass rapes specifically targeting European women, the intentional displacement of white populations through the mass immigration of high-fertility non-white population groups, all of which are also associated to issues of racial characteristics as well as Marxist and feminist collusions to ‘destroy the West.’\n\nAs additional comparison we give two examples from the macro level, one video each from the top and bottom categories. We begin with the video ‘Milo obliterates student’ from September 2016, randomised from our bottom 10% of videos, i.e., the 10% with the lowest number of sentences assessed as likely to be hate speech. Incidentally, the video has since been removed. The video presents a rather short monologue by Milo Yiannopoulos who laments what he perceives as a suppression of humour in the media. He connects this process to authoritarian policies and adds that he embraces politically incorrect humour since he simply finds such things as ‘AIDS,’ ‘Islam,’ and ‘trannies’ funny. The speaker is then interrupted by a person from the audience and responds with a few sentences which include the clause ‘fuck your feelings.’ We designated this video clip as not containing hate speech, either immediately or proximately, in relation to our definitions above. Criticising content moderation policies is obviously not hate speech, nor is incivility, and the admittedly demeaning approach to the groups in question does not fulfil the requisites of hate speech, notwithstanding any protected characteristics.\n\nThe video ‘What the Founders Really Thought about Race’ is randomised from the top 10% of videos. The video clip in question is from May 2017 and features a documentary-style presentation of the ‘actual’ views on race held by the U.S. founding fathers. This video is also removed. The presenter begins by disputing the idea that racial equality was not affirmed by the founding fathers and adds that black slaves were held by around 40% of the land-owning colonists and that a segregationist perspective was dominant. It is further argued that the founding fathers and influential early politicians, including Lincoln, desired to expel blacks from the United States, not least due to the widespread disgust over ‘miscegenation.’ The presentation sums up by arguing that different races build different types of societies and implies that the evident contemporary social ills can be connected to a divergence from these ostensibly traditional views of the founding fathers. During the close reading, we designated this video clip as containing explicit hate speech in accordance with the above definitions, in part due to the express usage of ‘miscegenation’ and the implicit racial supremacist message at the end.\n\nIn the following, we give examples of sentences automatically classified as hate speech and non-hate speech. We compare twelve synthetic sentences from the top and bottom categories, respectively. Three from each category designated as hate speech or proximate hate speech (including immediate context fragments before and after), and three from each found to not contain hate speech. The selection is made in order of appearance in the set, i.e., the six sentences from the top category are the first hate speech and non-hate speech sentences encountered when the set is sorted by highest to lowest likelihood of containing hate speech. The opposite holds for the bottom category.\n\nHate Speech, Top 5% (Supplemental Material, tab ‘Sentence top 5%’)\n\n1. for [the patriarchy] is what took us to space you just want build roads build roads it is what build the (line 2)\n\n2. because Trump said pussy and they were fine with that grab [them] by the pussy but never mind about what rap (line 3)\n\n3. conditions in black ghettos but what caused the ghettos here’s their answer white society is deeply implicated in the ghetto white (line 4)\n\nNot Hate Speech, Top 5% (Supplemental Material, tab ‘Sentence top 5%’)\n\n4. is a mosque don’t have any idea you want to guess an animal your basic bitch who is the vice president (line 8 (semi-duplicate on line 15))\n\n5. ginger here come up here come up here come on stand here come on stand here anymore Ginger’s no wages limit (line 22)\n\n6. 1978 a country that starts with a you utopia you went full retard man never go full retard what do you (line 35)\n\nHate Speech, Bottom 5% (Supplemental Material, tab ‘Sentence bottom 5%’)\n\n7. there are deliberate policies to make us a minority anywhere we live policies intended to destroy us as a whole as (line 92)\n\n8. can replace them (Jewish journalist) wrote America is tearing itself apart as an embittered quite conservative minority clings to power terrified at (line 95)\n\n9. rights) activists who support everything that weakens the nation-state. This Western mindset and this activist network is perhaps best represented by [George Soros] (line 98)\n\nNot Hate Speech, Bottom 5% (Supplemental Material, tab ‘Sentence bottom 5%’)\n\n10. a trump presidency might signal a sea change with Brexit happening all the anti-globalist anti-globalization movements the sort of populist conservative (line 2)\n\n11. conservatives going progressives and progressive go and conservative talk shows I think it’d be really interesting I was a bit annoyed (line 3)\n\n12. Qatari government is so morally upright and ethical now you can bring on all sorts of conservative writers conservative people in (line 4)\n\nInteresting to note here is that all the hate speech designated sentences or context fragments from the bottom set invoke the great replacement, with the latter two connecting with explicit antisemitism in their broader context. The great replacement hypothesis refers to the idea that native Western populations are being intentionally replaced by racial others, chiefly Muslims, a process often assumed to be the effort of a Jewish conspiracy (Betz, 2018).\n\nWhereas the great replacement hypothesis of the alt-right discourse is clearly framed as support for purported victims of an ongoing genocide and only designated as hate speech precisely in relation to its generally accepted and quite implicit connections to antisemitic organization, it is perhaps not surprising that allusions to replacement will generally not be flagged as forms of hate speech.\n\nSentence three invites a clear example of the contextual analysis behind the ‘proximate’ designation. This fragment connects to American Renaissance’s themes of white supremacy in its framework (the actual implication is that it’s absurd that ‘white society’ has anything to do with the emergence of ‘ghettos’ and that these are a fruit of inherent racial inferiority).\n\nOf the top-scoring videos, only two out of 14 (14.2%) were removed from YouTube after the material was collected. Both (100%) were designated as proximate hate speech. Of the remaining videos, four (33.3%) were designated as hate speech, two (16.6%) as proximately hate speech, and four (33.3%) as not containing hate speech.\n\nOf the lowest-scoring videos, eight out of 14 (57.1%) were removed. Three of these (37.5%) were found to be proximate hate speech. Of the remaining six, only one (16.6%) was designated as proximate hate speech, and five (83.3%) was found not to contain hate speech.\n\nBy a quick assessment, if most of the videos removed after our data gathering were targeted due to perceived problematic content, it seems that our model is validated by the moderation policies of the platform. However, the significant gap between the number of videos removed in the respective categories is counter intuitive. Due to the small numbers involved, and the wide variety of potential factors behind channel or video removal, little can be concluded from this gap.\n\nThe number of views of the videos in question surprisingly stands in a clearly negative rather than positive relation to a video being removed. Almost all the removed videos in the top category had a significantly lower view count at the time of our data collection than the videos not removed, whereas one immediate assumption would be that higher view counts would increase negative attention and thus the likelihood of removal.\n\nThematically speaking there seems to be little difference between the two categories. Both the removed and remaining videos of the 10% top category engage with issues of mass immigration to Europe, feminism, gender issues, Islam, and race – all in approximately equal measure. Furthermore, several titles of the unaffected videos (‘The rape of Europe,’ ‘The Islamic state of Sweden’) are more obviously inflammatory than many of the removed clips (e.g., ‘Did Trump just save Western civilization?’ and ‘Response to Contrapoints on Degeneracy’).\n\n\nConclusions\n\nOur purposes with this paper were to 1) transparently account for the steps needed when utilizing automatic hate speech identification, including key challenges in the process, while in relation to alt-right hate speech specifically, and (2) to identify the challenges in identifying hate speech in popular alt-right YouTube videos.\n\nOur study addresses the issue of the automatic identification of contentious speech acts with a particular focus on the high-context character of the meanings conveyed. In this approach, which combines a quantitative and a qualitative analysis, our study is novel since previous research has combined qualitative analyses with distant reading. The results obtained from this approach, not least the high false negative rates which became obvious through close reading, clearly indicate that effective and consistent identification of hate speech communication necessitates qualitative interventions by human reviewers to avoid arbitrary or misleading applications. Indeed, the comparatively low accuracy of the filters determined through our qualitative review of the automatic flagging implies possible limitations of studies which claim a consistently high accuracy of automatic identification, e.g., data chiefly characterised by explicit discourses, or the omission of high-context communications in favour of a binary reading based on keywords.\n\nThis commonplace binary approach tends to force the rationale for designating content as hate speech to be self-contained within the literal meaning conveyed. Otherwise, it will entail an arbitrary and misleading designation of high-context content as explicit hate speech in and of itself. Even studies which explicitly engage with this issue risk falling into this trap. Paasch-Colberg et al. (2021) make a point of going beyond the ‘hate/no-hate’ dichotomy and provide a useful analysis of various possible characteristics and rhetorical strategies of hate speech communications. Nevertheless, they employ a binary classification which requires the problematic signification to be self-contained within a narrowly delimited act of communication for the requisite of hate speech to be fulfilled.\n\nA simple context-sensitive qualitative approach like ours can remedy this by bringing into focus the indirect character of many of these communications which also will tend to characterise a discursive landscape where moderation and censorship is intensifying. This, incidentally, also precludes much of the value of purely automatic approaches.\n\nThere are structural impediments which render effective unsupported automatic identification of high-context communications difficult in principle. Automatic identification or moderation cannot account for an evolving, complex context of often indirect signification, which is hardly feasible in practice even with much more advanced algorithmic systems.\n\nIn general, this study in detail exemplifies a process whereby automatic hate speech identification could be utilised effectively. We see that several methodological steps are needed to operate in concert for the outcome to be useful, with both highly technical quantitative processing and traditional qualitative analysis being vital to achieve meaningful results.\n\nWith particular regard to the alt-right YouTube material, the main challenge in terms of detection and precise identification of hate speech relates to the often tacit and indirect framing. Identification demands orientation in the broader discursive context and the adaptation towards indirect expressions renders moderation and suppression both ethically and legally precarious. In concert with this finding, we saw significantly more material being automatically classified as hate speech in the comparatively private and unmoderated far-right Stormfront forum in comparison with the YouTube material, yet here also, the false negative rate was high (see Stormfront, n.d.).\n\nA challenge for the study was that the YouTube material consists of proficient speakers’ text where the avoidance of hate speech is a priority. In voiding suppression or banning from the medium, they use indirect and contextually dependent forms of hate speech, which is considerably more difficult to detect than the more overt forms of hate speech found on some discussion fora with less stringent rules of expression. Consequently, it is unsurprising that the accuracy of the model was not very high. At the same time, it is precisely these types of narratives which use concealment techniques, rhetoric, and indirect hate speech that we need to be able to better identify in contemporary online communication.\n\nNatural Language Processing is a field that is developing quickly, and new methods and datasets continue to appear. In this study we have limited ourselves to a relatively small corpus and simple methods in part to demonstrate what can be done without a complicated or state of the art setup. In the future we hope to see more studies that combine the quantitative methodologies from Data Science with traditional hermeneutic analyses.\n\nFinally, the relationship of our findings to Overton window issues is important. A comparison of our dated material (mainly 2015–2018) to both earlier and later sets, with an eye to the political background discourse, would provide data towards ascertaining the correlations between efforts toward discursive subtlety and both the creators’ assumptions of popular reception and the character of acceptable discourses, and the level and character of actual suppression.", "appendix": "Data availability statement\n\nTop and bottom sentences and paragraphs with unique identifiers calculated from YouTube transcriptions. Supplemental data for this article can be requested from mailto:mika.hietanen@kom.lu.se.\n\n\nReferences\n\nAdadi A: A survey on data-efficient algorithms in big data era. J. Big Data. 2021; 8(24): 1–54. Publisher Full Text\n\nAlonso P, Saini R, Kovacs G: TheNorth at SemEval-2020 Task 12: Hate speech detection using RoBERTa. Proceedings of the Fourteenth Workshop on Semantic Evaluation. 2020, December; pp. 2197–2202. Publisher Full Text\n\nBadjatiya P, Gupta S, Gupta M, et al.: Deep Learning for Hate Speech Detection in Tweets. Proceedings of the 26th international conference on World Wide Web companion. 2017, April; pp. 759–760. Publisher Full Text\n\nBasile V: Hateval Annotation Guidelines.Github.; n.d.Reference Source\n\nBasile V, Bosco C, Fersini E, et al.: SemEval-2019 Task 5. Multilingual Detection of Hate Speech Against Immigrants and Women in Twitter. Proceedings of the 13th International Workshop on Semantic Evaluation, June 6–7, 2019, Minneapolis, MN, USA. Association for Computational Linguistics. 2019; pp. 54–63. Reference Source\n\nBetz H-G: The Radical Right and Populism.Rydgren J, editor. The Oxford Handbook of the Radical Right. Oxford University Press; 2018; Vol. 1. : pp. 86–104. Publisher Full Text\n\nBiagioni R: Sentiment Analysis. The SenticNet Sentiment Lexicon. Exploring Semantic Richness in Multi-Word Concepts. SpringerBriefs in Cognitive Computation. Springer; 2016; 4. : pp. 7–16. Publisher Full Text\n\nBreiman L: Random forests. Mach. Learn. 2001; 45(1): 5–32. Publisher Full Text\n\nBrummett BS: Techniques of Close Reading. SAGE; 2010.\n\nCobbe J: Algorithmic censorship by social platforms Power and resistance. Philos. Technol. 2021; 34(4): 739–766. Publisher Full Text\n\nCostello M, Hawdon J: Hate Speech in Online Spaces. The Palgrave Handbook of International Cybercrime and Cyberdeviance. Cham: Palgrave Macmillan; 2019. Publisher Full Text\n\nDavidson T, Warmsley D, Macy M, et al.: Automated hate speech detection and the problem of offensive language. Proceedings of the International AAAI Conference on Web and Social Media. 2017; 11(1): 512–515. Publisher Full Text\n\nDowlagar S, Mamidi R: Hasocone@ fire-hasoc2020. Using BERT and multilingual BERT models for hate speech detection. arXiv:2101.09007.2021. Publisher Full Text\n\nd’Sa AG, Illina I, Fohr D: BERT and fastText Embeddings for Automatic Detection of Toxic Speech. SIIE 2020. Information Systems and Economic Intelligence. International Multi-Conference on: ‘Organization of Knowledge and Advanced Technologies’ (OCTA), February, 2020, Tunis, Tunisia. hal-02448197v2. 2020, February. Reference Source\n\nEllul J: Propaganda: The Formation of Men’s Attitudes. Vintage Books; 1973.\n\nEuropean Commission: Council of the European Union 12522/19. Information note. Assessment of the Code of Conduct on Hate Speech online.2019. https://commission.europa.eu/strategy-and-policy/policies/justice-and-fundamental-rights/combatting-discrimination/racism-and-xenophobia/eu-code-conduct-countering-illegal-hate-speech-online_en\n\nFarber PL: Mixing Races. From Scientific Racism to Modern Evolutionary Ideas. Johns Hopkins University Press; 2011. Publisher Full Text\n\nFarrell T, Fernandez M, Novotny J, et al.: Exploring misogyny across the manosphere in reddit. WebSci’19. Proceedings of the 10th ACM Conference on Web Science. Boston, MA, USA, June 30–July 3, 2019. Association for Computing Machinery. 2019, June; pp. 87–96. Publisher Full Text\n\nFersini E, Nozza E, Rosso P: Overview of the Evalita 2018 Task on Automatic Misogyny Identification (AMI). EVALITA Evaluation of NLP and Speech Tools for Italian. Proceedings of the Final Workshop 12–13 December 2018, Naples. Accademia University Press. 2019; pp. 59–66. Publisher Full Text\n\nGarcía-Pablos A, Perez N: Hate Speech Dataset from a White Supremacy Forum. GitHub; n.d.Reference Source\n\nGitari ND, Zuping Z, Damien H, et al.: A lexicon-based approach for hate speech detection. Int. J. Multimedia Ubiquitous Eng. 2015; 10(4): 215–230. Publisher Full Text\n\nHern A: Facebook, YouTube, Twitter and Microsoft sign EU hate speech code. The Guardian News. 2016, May 31. https://www.theguardian.com/technology/2016/may/31/facebook-youtube-twitter-microsoft-eu-hate-speech-code\n\nHern M: YouTube bans David Duke and other US far-right users. News, The Guardian. 2020, June 30. Reference Source\n\nHietanen M, Eddebo J: Towards a Definition of Hate Speech. With a Focus on Online Contexts. J. Commun. Inq. 2023; 47(4): 440–458. Publisher Full Text\n\nHochreiter S, Schmidhuber J: Long short-term memory. Neural Comput. 1997; 9(8): 1735–1780. Publisher Full Text\n\nKelly P: History Time. [Channel]. YouTube. n.d.Reference Source\n\nKotu V, Deshpande B: Data science. Concepts and Practice. 2nd ed.Morgan Kaufmann; 2018.\n\nLeCun Y, Boser B, Denker J, et al.: Handwritten Digit Recognition with a Back-Propagation Network., Advances in neural information processing systems.1990; 2: 396–404.\n\nLewis R: Alternative Influence: Broadcasting the Reactionary Right on YouTube. Data Soc. 2018. Reference Source\n\nManning CD, Raghavan P, Schütze H: Introduction to information retrieval. Cambridge University Press; 2008; pp. 234–265. Ch. 13. Publisher Full Text\n\nMaslej-Krešňáková V, Sarnovský M, Butka P, et al.: Comparison of Deep Learning Models and Various Text Pre-Processing Techniques for the Toxic Comments Classification. Appl. Sci. 2020; 10(23): 8631. Publisher Full Text\n\nMenard SW: Logistic regression. From introductory to advanced concepts and applications. SAGE; 2010. Publisher Full Text\n\nNockleby JT: Hate speech.Levy LW, Karst KL, editors. Encyclopedia of the American Constitution. 2nd ed. vol. 3. . Macmillan Reference USA; 2000; pp. 1277–1279.\n\nOttoni R, Cunha E, Magno G, et al.: Analyzing Right-wing YouTube Channels: Hate, Violence and Discrimination. Proceedings of the 10th ACM Conference on Web Science. [cs.SI]. 2018.arXiv:1804.04096v1\n\nPaasch-Colberg S, Strippel C, Trebbe J, et al.: From Insult to Hate Speech. Mapping Offensive Language in German User Comments on Immigration. Media Commun. 2021; 9(1): 171–180. Publisher Full Text\n\nRosen A, Ihara I: Giving you more characters to express yourself. Blog. 2017, September 26. Reference Source\n\nRydgren J: The Radical Right: An Introduction.Rydgren J, editor. The Oxford Handbook of the Radical Right. Oxford University Press; 2018; pp. 1–14. Publisher Full Text\n\nSchmidt A, Wiegand M: A survey on hate speech detection using natural language processing. Proceedings of the Fifth International Workshop on Natural Language Processing for Social Media, April 3, 2017, Valencia, Spain, Association for Computational Linguistics. 2019; pp. 1–10. Publisher Full Text\n\nStormfront: [Online Forum]. White Nationalist Community.n.d.Reference Source\n\nVrysis L, Vryzas N, Kotsakis R, et al.: A Web Interface for Analyzing Hate Speech. Future Internet. 2021; 13(3): 80. (18 pp.). Publisher Full Text\n\nZampieri M, Malmasi S, Nakov P, et al.: Predicting the type and target of offensive posts in social media. arXiv:1902.09666.2019. Publisher Full Text\n\nvan der Ploeg T , Austin PC, Steyerberg EW: Modern modelling techniques are data hungry: a simulation study for predicting dichotomous endpoints. BMC Med. Res. Methodol. 2014; 14(137): 1–13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang A, Hoang CDV, Kan MY: Perspectives on crowdsourcing annotations for natural language processing. Lang. Resour. Eval. 2013; 47: 9–31. Publisher Full Text\n\nWulczyn E, Thain N, Dixon L: Ex machina: Personal attacks seen at scale. Iben Proceedings of the 26th international conference on world wide web. arXiv:1610.08914. 2017, April; pp. 1391–1399. Publisher Full Text\n\nYouTube: Our ongoing work to tackle hate. YouTube Official Blog; 2019, June 5. Reference Source" }	[ { "id": "294951", "date": "09 Jul 2024", "name": "Richard Sear", "expertise": [ "Reviewer Expertise My research focuses on online hate and extremist speech. I study automated detection methods using NLP as well as the mechanisms of how it spreads between online communities at scale. My team has run into some of the same issues and concerns the authors address in this study." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary This study presents 1) an automated hate speech detection method and 2) challenges in identifying hate speech used in popular moderation-dodging alt-right YouTube channels. The methodology of developing an automated classifier builds on the well-established field and uses pre-existing annotated corpora of tweets as training/test data for a standard NLP classification task pipeline. The final model selected is high-performing and uses an RNN architecture.\nTo study the YouTube transcripts, the authors construct synthetic sentences and paragraphs out of \"atoms\" (7-word chunks) using a sliding window technique. A length of 7 was decided based on manual experimentation and inspection. Sentence scores were then aggregated into video-level scores.\nYouTube audio transcripts are taken from the 15 most popular clips (by view count) from the nine most popular channels (by subscriber count) in a set of channels filtered from Data & Society's Alternative Influence 2018 report using various established hate definitions. As controls, text from a history YouTube channel and a white supremacist forum were also analyzed.\nDuring qualitative close reading, researchers identified \"proximate hate speech\" as well as direct hate speech. Researchers examined text at the sentence level, paragraph level, and full video level. The upshot is that this analysis found relatively little explicit hate speech (likely due to awareness of moderators) and increasing proportions of proximate hate speech with more complex analysis levels (sentence to paragraph to video). The authors conclude that it is important to go beyond a hate/no-hate dichotomy or classifying content for hate speech without its context. Future directions for this work could include improved datasets (i.e. more up to date) and more sophisticated models.\nConcerns The authors identify three openly available datasets (HSOL, HatEval, OLID) they used. They then selected a subset of these, but identified the criteria used to do so, which allows me to recreate their training dataset. However, neither the Tensorflow code used to train the model nor the model itself are linked, with the only specification for the final model being that it used an \"RNN architecture\". This is too generic for me to be able to accurately replicate the authors' model but could easily be solved by publishing the training code/final hyperparameters.\nOn a broader level, I was a little concerned to see Twitter data being used to train a classifier that was ultimately used for YouTube transcripts (a very different writing style), but the authors appear to be aware of this mismatch and make several notes about ways their methodology accounts for it. As the authors note in their \"Future Work\" section, new data regularly becomes available which could solve this issue.\nStrengths The study is thorough and identifies many widespread issues with the current state of hate speech detection, as well as showcases useful insights that come from the authors' detailed analysis of the data. I particularly liked the incorporation of multiple levels of close reading to both validate the automated results and gain a human understanding of how real hate speech appears on YouTube. Though this level of detailed analysis is perhaps not feasible for the sheer volume of potentially hateful online content that exists today, it shows the valuable insights that, when teams are able to do so, come from applying multiple methods in concert. I also thought the identification of \"proximate\" hate speech was both spot-on and extremely important for future work. As the authors note, a simple binary classification of hate speech will often fall short and lose non-literal or contextual information that is essential to analyzing how hate speech spreads online.\nAdditionally, authors were communicative and forthcoming when I requested access to their dataset on Zenodo.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "309594", "date": "10 Aug 2024", "name": "Tommi Buder-Gröndahl", "expertise": [ "Reviewer Expertise My current research concerns the interpretation of LLMs (and", "more generally", "any language-processing cognitive systems) in terms of linguistic and semantic theory. I have also worked on HS detection as well as the application of NLP in security-sensitive settings more generally." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper analyses hate speech (HS) in alt-right Youtube videos, by combining automatic and manual methodologies. The authors train an RNN classifier on prior manually labeled HS data from tweets, apply it to video transcripts from Youtube (synthetically divided into pseudo-sentences and pseudo-paragraphs), and inspect the results both quantitatively and qualitatively. Their main take-home message is that alt-right videos utilize indirect means of expressing HS on a higher contextual level than sentences. This constitutes a serious challenge for automatic classification schemes that are built for finding explicit HS in narrow contexts.\nTwo main concerns arise based on the study's methodology and quantitative results. First, the authors chose an RNN classifier, after experimenting with simple machine learning techniques (random forests, logistic regression, and naïve Bayes) and CNNs. However, for many years already, the Transformer architecture has been the leading deep learning architecture in NLP – specifically, large pre-trained Transformer-based large language models (LLMs) such as BERT or GPT. It is therefore unclear (1) why the authors did not experiment on Transformers, and (2) why transfer learning on an LLM was not considered. The RNN does not seem to represent the contemporary state-of-the-art in text classification.\nSecond, the numerical results (Table 4) are somewhat hard to interpret: it is unclear what they actually tell us about HS on alt-right videos, Stormfront, or the control History channel. Since we lack an established ground-truth on which parts of the alt-right videos or the History channel are genuine HS, it is hard to say if the results tell us more about the frequency of HS or about deficiencies in the RNN classifier.\nI do not believe that either concern is ultimately detrimental to the paper, since its main value lies in the close qualitative reading of HS. That being said, there is a predictable response to the authors' conclusions about the limits of automatic HS detection: high-level contextual information might indeed be unavailable for simple machine learning systems or even RNNs trained from scratch; but pre-trained LLMs might access it significantly better. Even though I do not believe that this reply is sufficient to remove the authors' worries, it deserves more consideration in future work.\nIn terms of strengths, the most notable contribution of the paper is the close reading of video transcript results. As the authors note, prior work on automatic HS detection has tended to limit qualitative methods to distant reading. While close reading cannot achieve the same level of coverage, it is indispensable for properly understanding HS. The division of the analysis into three levels (micro, macro, meso) is also an important addition, especially given the contrasting results between levels. The hypothesis that alt-right influencers lean less on explicit HS and more on indirect expressions is intuitively valid, but the further empirical support provided for it in the paper is clearly valuable.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "298551", "date": "12 Aug 2024", "name": "Somaiyeh Dehghan", "expertise": [ "Reviewer Expertise I am an NLP specialist currently working on a hate speech detection project. My research focuses on developing automated methods to identify and analyze online hate speech and target detection. My team and I have encountered similar issues and concerns to those addressed in this study. Our work aims to enhance the understanding and detection of hate speech to contribute to a safer and more inclusive digital environment." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: This paper addresses the critical task of automatically detecting hate speech, focusing on popular alt-right YouTube channels that utilize moderation-dodging techniques. The study is highly relevant given the increasing prevalence of hate speech online and the sophisticated methods used by certain groups to evade detection. The authors aim to contribute to the field by exploring binary classification (hate speech vs. non-hate speech) using a substantial dataset of 42,430 tweets derived from three publicly available, annotated hate speech corpora. The study employs both traditional and neural network-based classification methods, implemented through SciKitLearn and TensorFlow, respectively. The authors report their best results with an RNN (Recurrent Neural Network) classifier model, which is a notable finding given the complexity and context-dependency of hate speech.\nRelevance: The relevance of this study lies in its potential to improve the accuracy and robustness of hate speech detection systems, particularly in contexts where language and content are manipulated to avoid moderation. The work has significant implications for social media platforms, content moderators, and policymakers concerned with curbing the spread of hate speech while respecting free speech.\nMajor Points:\nLack of Clarity in Data Selection Criteria: The authors mention that their training data was selected from three publicly available datasets but fail to provide any criteria or justification for this selection. It is crucial to understand why these particular datasets were chosen over others and how representative they are of the broader spectrum of hate speech. Without this information, the study's findings may lack generalizability. Unclear Test Data Description: The paper does not adequately describe the test data used to evaluate the models. A clear understanding of the test data is essential for assessing the validity and reliability of the results. The authors should specify whether the test data comes from the same datasets as the training data or if it was sourced independently. Additionally, details on how the test data was selected, including any preprocessing steps, should be provided. Insufficient Explanation of Methods: While the authors list the classification methods used (e.g., random forests, CNNs, RNNs), they do not provide sufficient details about the implementation of these methods. This is particularly important for the neural network models, where the architecture, hyperparameters, loss functions, and optimization strategies are critical to understanding the model's performance. Including this information would allow other researchers to replicate the study and assess its robustness. Lack of Comparative Analysis: The results of different classification methods (e.g., random forest, CNN, RNN) are not compared in detail. A comparative analysis is essential to determine which method performs best under specific conditions and why. This analysis could provide insights into the strengths and weaknesses of each approach and guide future research in this area.\n\nMinor Points:\nModeration-Dodging Techniques: The paper briefly mentions that the alt-right YouTube channels employ moderation-dodging techniques, but it does not explore this aspect in depth. A more detailed discussion on how these techniques impact the detection of hate speech could enhance the paper's contribution. Presentation of Results: The results section could benefit from a clearer presentation of the performance metrics for each model. Tables or graphs that compare the accuracy, precision, recall, and F1-scores of the different models would make the findings more accessible and easier to interpret. Constructive Feedback: The study addresses an important problem and makes a valuable contribution to the field. However, to enhance its impact, the authors should provide more detailed explanations of their data selection process, test data, and the specifics of their classification models. Additionally, a thorough comparative analysis of the results would strengthen the study's conclusions and offer more actionable insights for future research. By addressing these points, the paper could serve as a more comprehensive and reliable resource for those working on hate speech detection and related NLP tasks.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "309593", "date": "20 Aug 2024", "name": "Surabhi Adhikari", "expertise": [ "Reviewer Expertise Natural Language Processing" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article describes a study that aimed to automatically identify hate speech in YouTube videos associated with the alt-right movement. The researchers developed a machine learning model to classify text as hate speech or not, using a combination of three existing annotated corpora of tweets. They then applied this model to transcripts from selected YouTube channels, comparing results from alt-right channels to a control history channel and a white supremacist forum (Stormfront). The methodology involved several steps:\nGathering and combining annotated corpora Text preprocessing Training a Recurrent Neural Network (RNN) classifier Applying the classifier to YouTube transcripts Qualitative close reading of select parts\nThe researchers segmented the YouTube transcripts into synthetic sentences and paragraphs to apply the classifier. They found that the model identified more hate speech in the alt-right content compared to the control, but less than in the Stormfront forum. They also conducted a qualitative analysis to evaluate the model's performance and examine the context of identified hate speech.\nStudy Design and Technical Soundness: The study design appears appropriate for an exploratory investigation into automatically identifying hate speech. The researchers acknowledge the experimental nature of their approach and its limitations. They use a combination of quantitative and qualitative methods, which strengthens the overall design.\nThe technical aspects of the machine learning approach seem sound. The researchers experimented with multiple models before settling on an RNN, used proper train-test splits to prevent overfitting, and employed hyperparameter tuning. Their approach to segmenting the YouTube transcripts into synthetic sentences and paragraphs is creative and well-reasoned.\nThe study design is appropriate and the work is technically sound. The researchers employed a well-structured approach combining machine learning techniques with qualitative analysis. Their use of multiple datasets, including a control group and a high-hate speech forum for comparison, strengthens the design. The technical aspects, including the development and application of the RNN classifier, are implemented with care and attention to best practices in machine learning.\nThe paper provides sufficient details of methods and analysis to allow replication by others. The researchers offer clear explanations of their data sources, preprocessing steps, model training process, and application to YouTube transcripts. They also describe their approach to segmenting transcripts into synthetic sentences and paragraphs. While some additional details could enhance replicability, the core methodological components are well-documented.\nThe statistical analysis and its interpretation are appropriate for this study. The researchers present relevant descriptive statistics of the model's predictions across different corpora. Their interpretation of these results is measured and takes into account the exploratory nature of the study. The analysis aligns well with the study's objectives and provides a solid foundation for understanding the performance of their hate speech detection model across different contexts.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-328
https://f1000research.com/articles/13-326/v1	23 Apr 24	{ "type": "Case Report", "title": "Case Report: Copper sulphate related hemophagocytosis with lymphohistiocytosis", "authors": [ "Koushik Ramachandra", "Amruth Reddy Narayana", "Samyuktha Srinivas", "Sridevi H B", "Amruth Reddy Narayana", "Samyuktha Srinivas", "Sridevi H B" ], "abstract": "Abstract* The accidental, suicidal, and homicidal toxicities of copper sulfate have been extensively documented. The later stages of the disease demonstrate signs of systemic toxicity, characterized by intravascular hemolysis, oliguric renal failure, convulsions, and circulatory collapse. Despite the extensive description of life-threatening intravascular hemolysis, Hemophagocytic Lymphohistiocytosis (HLH) related to copper sulfate poisoning has not been described. A 45-year-old male presented with accidental consumption of copper sulfate. Laboratory evaluation revealed leukocytosis, intravascular hemolysis, acute liver injury, acute kidney injury, severe metabolic acidosis, and hyperkalemia. The patient was shifted to the Intensive Care Unit and hemodialysis was initiated. On the 9th day, he developed high-grade fever with chills. With the suspicion of a central line-associated bloodstream infection, empirical antibiotic therapy was initiated, and the lines were revised. On the 19th day, the high-grade fever recurred. Investigations revealed trilineage cytopenias. With a high degree of suspicion for HLH, further investigations revealed increased ferritin levels. Bone marrow aspiration cytology showed evidence of reactive marrow with haemophagocytic lymphohistiocytosis. The patient was initiated on corticosteroid therapy, after which symptomatic and laboratory recovery was noted. Although copper sulfate poisoning is potentially fatal in large quantities, few studies have examined the possible immune-mediated abnormalities in individuals. Owing to the direct membranolytic effect of copper sulfate, it is not unreasonable to have immune-mediated organ damage. To the best of our knowledge, this is the first report of Hemophagocytic Lymphohistiocytosis attributed to copper sulfate intoxication. The present case demonstrates that the diagnosis of HLH must be considered when treating a case of copper sulfate poisoning; however, the exclusion of the most common complications must be first established.", "keywords": [ "Hemophagocytic Lymphohistiocytosis (HLH)", "Copper Sulphate", "Immune-mediated", "Intravascular hemolysis", "Acute Kidney Injury" ], "content": "Introduction\n\nAcute copper intoxication is often the result of accidental consumption, suicide, or homicidal attempts. Bordeaux mixture, a copper-based fungicide used in agricultural practice, is widely available in the Indian sub-continent.1,2 Ingestion of more than 1 g of copper sulfate results in manifestations of symptoms while–20 g may be lethal.3,4 The clinical manifestations of toxicity predominantly involve erosive gastropathy, hepatitis, acute kidney injury, rhabdomyolysis, convulsions, circulatory collapse, and haematological complications.5\n\nThe major haematological manifestations include intravascular Haemolysis and Methemoglobulinemia.5 Intravascular hemolysis often starts as early as 12-24 hours after ingestion of the substance owing to the direct membranotoxic and oxidative stress caused to the erythrocyte membrane, whereas methemoglobinemia occurs because Cu2+ ions oxidize Fe2+ in hemoglobin to Fe3+.6 Although these two manifestations have been described extensively in the literature, the occurrence of Hemophagocytic Lymphohistiocytosis (HLH) due to copper sulfate ingestion has not been described.\n\nHLH is a disease of multi-organ dysfunction that can have extremely nonspecific presentations.7 These include prolonged fever, cytopenia, hepatosplenomegaly, liver dysfunction, and neurological dysfunction.8 The broad range of presentations and lack of specificity make the diagnosis of HLH quite challenging, requiring the ruling out of alternative diagnoses.7\n\nHerein, we describe a case of Hemophagocytic Lymphohistiocytosis attributed to accidental copper sulfate poisoning.\n\n\nCase report\n\nA male in his 40s with an unremarkable medical history was referred to our center with an accidental, alleged consumption of copper sulfate while under the influence of alcohol. He was treated at a nearby regional hospital with gastric lavage and intravenous fluids before referral. On reporting, the patient was conscious, well-oriented, and hemodynamically stable. Tachypnea, pallor, and icterus were also noted. Initial laboratory evaluation revealed anemia with a hemoglobin level of 12.6% and leukocytosis with a white blood cell count of 23500 cells/μL, evidence of hemolysis, acute liver injury, acute kidney injury, and severe metabolic acidosis with hyperkalemia. The patient was admitted to the Intensive Care Unit for further care.\n\nThe following day, his hemoglobin dropped to 6.9 gm%, the leukocyte count increased to 41400 cells/μL, and platelet count dropped to 1.01 lakh cells/μL. His serum creatinine elevated by 2.96 units and serum urea by 70 units above the baseline, suggesting worsening renal function owing to the extensive damage caused to the kidney by copper sulfate. Hyperkalemia persisted. The patient remained oliguric with increasing acidosis and was initiated on supportive hemodialysis. He underwent six cycles of hemodialysis during his hospital stay. Supportive blood transfusions were also started.\n\nOn the 9th day of hospitalization, the patient developed high-grade fever with chills. With suspicion of Central Line Associated Blood Stream Infection (CLABSI), he was started on empirical antibiotics following collection of appropriate cultures, and the lines were revised. No growth was observed in the culture medium. The patient continued to be dialysis dependent due to ongoing oliguric renal failure.\n\nOn the 19th day of hospitalization, a similar episode of high-grade fever with normal leukocyte counts recurred, along with anemia. A peripheral Smear was unremarkable. Blood cultures were resent, and the lines were revised. However, the fever persisted. As a result of persistent fever, investigations revealed trilineage cytopenia, and HLH was suspected. Targeted investigations have revealed increased serum ferritin and D-dimer levels. The bone marrow aspirate showed evidence of reactive marrow with Hemophagocytic Lymphohistiocytosis, as depicted in Figure 1. Repeated blood cultures were considered sterile. The patient was initiated on corticosteroids for HLH, following which his fever subsided, with improvement in cytopenia. Supportive care was then continued. Renal function tests showed gradual recovery with improved urine output. The dialysis sessions were gradually spaced, stopped, and then discharged. He was followed up as an outpatient until his kidney function normalized.\n\nSerial investigations are tabulated in Table 1.\n\n\nDiscussion\n\nCopper sulfate, a herbicide commonly used in agricultural practice in the Indian subcontinent, is commonly abused in suicidal or homicidal attempts.9 Following the initial symptoms of metallic taste, salivation, thirst, nausea, abdominal pain, recurrent vomiting, and painful diarrhea, signs of systemic toxicity appear, which are characterized by intravascular hemolysis, oliguric renal failure, convulsions, and circulatory collapse.\n\nHLH, often described as a diagnostic conundrum, is a life-threatening manifestation of uninhibited activation of immune cells to secrete excessive amounts of cytokines, leading to tissue destruction and multi-organ failure.10 HLH can be of two types: familial and sporadic. The latter tends to occur with autoimmunity, malignancies, infection.8 Common clinical manifestations include prolonged fever, erosive gastropathy, hematemesis, melena, acute liver failure due to direct copper toxicity, hepatosplenomegaly, anuria following acute kidney injury, and neurologic dysfunction, such as seizures, ataxia, and paraplegia.5 Elevated serum ferritin, pancytopenia, deranged liver function tests, kidney function tests, elevated D-dimer, hypertriglyceridemia, and hypofibrinogenemia are laboratory abnormalities that should be considered when diagnosing HLH.11–13\n\nHere, we describe the case of a male in his 40s with an alleged accidental consumption of an unquantified amount of copper sulfate who developed features of HLH during his hospital stay. Although the presence of intravascular hemolysis-related complications, which occur as early as the first 12-24 hours have been extensively documented in copper sulfate poisoning, the occurrence of HLH has not been reported. Few studies have described possible immune-mediated abnormalities in individuals with copper sulfate poisoning.\n\nOn arrival, the patient experienced intravascular hemolysis, leukocytosis, acute kidney injury, acute liver injury, and severe metabolic acidosis with hyperkalemia. He underwent supportive transfusions and six cycles of hemodialysis. There are multiple factors contributing to the development of AKI in copper sulfate toxicity, including direct oxidative damage to the proximal tubules, hemoglobinuria, rhabdomyolysis, and pre-renal failure.14 Recurrent episodes of fever after repeated line revisions and culture negativity raised the suspicion of HLH. Bone marrow aspiration cytology and elevated D-dimer and ferritin levels confirmed the suspicion of HLH and specific treatment was initiated. The patient recovered with the normalization of renal function.\n\nTo the best of our knowledge, this is the first report of Hemophagocytic Lymphohistiocytosis attributed to copper sulphate toxicity. The present case demonstrates that HLH could be one of the differential diagnoses for fever in such patients, although it should be considered after the exclusion of common etiologies.\n\n\nEthical approval\n\nEthical approval not required.\n\n\nConsent\n\nWritten informed consent was given by the patient.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAgrios GN: Plant pathology. Amsterdam: Elsevier Academic; 2004.\n\nBagchi D, Bagchi M: Metal toxicology handbook. Boca Raton: CRC Press, Taylor & Francis; 2021.\n\nSinkovic A, Strdin A, Svensek F: Severe acute copper sulphate poisoning: a case report. Arh. Hig. Rada Toksikol. 2008 Mar; 59(1): 31–35. PubMed Abstract \| Publisher Full Text\n\nEllenhorn MJ, Barceloux DG: Ellenhorn’s medical toxicology: Diagnosis and treatment of human poisoning. Baltimore: Williams & Wilkins; 1997.\n\nSaravu K, Jose J, Bhat MN, et al.: Acute ingestion of copper sulphate: A review on its clinical manifestations and management. Indian J. Crit. Care Med. 2007; 11(2): 74–80. Publisher Full Text\n\nTrottestam H, Horne A, Aricò M, et al.: Histiocyte Society. Chemoimmunotherapy for hemophagocytic lymphohistiocytosis: long-term results of the HLH-94 treatment protocol. Blood. 2011 Oct 27; 118(17): 4577–84. Epub 2011 Sep 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaçar AG, Celkan TT: Hemophagocytic Lymphohistiocytosis. Balkan Med. J. 2022 Sep 9; 39(5): 309–317. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGamakaranage CS, Rodrigo C, Weerasinghe S, et al.: Complications and management of acute copper sulphate poisoning; a case discussion. J. Occup. Med. Toxicol. 2011 Dec 19; 6(1): 34. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrzybowski B, Vishwanath VA: Hemophagocytic Lymphohistiocytosis: A Diagnostic Conundrum. J. Pediatr. Neurosci. 2017 Jan-Mar; 12(1): 55–60. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNiece JA, Rogers ZR, Ahmad N, et al.: Hemophagocytic lymphohistiocytosis in Texas: observations on ethnicity and race. Pediatr. Blood Cancer. 2010 Mar; 54(3): 424–428. PubMed Abstract \| Publisher Full Text\n\nOkamoto M, Yamaguchi H, Isobe Y, et al.: Analysis of triglyceride value in the diagnosis and treatment response of secondary hemophagocytic syndrome. Intern. Med. 2009; 48(10): 775–781. Epub 2009 May 15. PubMed Abstract \| Publisher Full Text\n\nFukaya S, Yasuda S, Hashimoto T, et al.: Clinical features of haemophagocytic syndrome in patients with systemic autoimmune diseases: analysis of 30 cases. Rheumatology (Oxford). 2008 Nov; 47(11): 1686–1691. PubMed Abstract \| Publisher Full Text\n\nDash SC: Copper sulphate poisoning and acute renal failure. Int. J. Artif. Organs. 1989 Oct; 12(10): 610. PubMed Abstract \| Publisher Full Text\n\nMalik M, Mansur A: Copper sulphate poisoning and exchange transfusion. Saudi J. Kidney Dis. Transpl. 2011 Nov; 22(6): 1240–1242. PubMed Abstract" }	[ { "id": "288685", "date": "20 Jun 2024", "name": "Nur Soyer", "expertise": [ "Reviewer Expertise hematological disorders and HLH" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe history and progression of the case is described in sufficient detail. Sufficient detail is given about the physical examination and diagnostic tests, the treatment administered and its results. There is sufficient discussion of the significance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment. The case is presented in sufficient detail to be useful for other practitioners.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "11832", "date": "21 Jun 2024", "name": "Koushik Ramachandra", "role": "Author Response", "response": "Thank you for reviewing our case report Dr. Nur Soyer." } ] }, { "id": "328792", "date": "17 Oct 2024", "name": "Ajith Kumar", "expertise": [ "Reviewer Expertise Sepsis/ Shock/ ARDS/ Extra corporeal therapies" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is an interesting case report showing a temporal association of copper sulfate ingestion with the development of secondary HLH. The adapted 2004 HLH guidelines, & H- Score are important tools for helping clinicians arrive at secondary HLH diagnosis. The latter was found to have excellent sensitivity & good specificity in diagnosing secondary HLH.\n\nWe are not sure if any chemical interaction might have happened between Ethanol and copper sulfate with the resultant compound further causing the observed feature of secondary HLH. I would like to know the H-Score calculations, &details about individual components of HScore in this case. Moreover, one needs to be aware that severe sepsis also can cause HLH changes in the bone marrow.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "12662", "date": "18 Oct 2024", "name": "Koushik Ramachandra", "role": "Author Response", "response": "We thank you for reviewing our report Sir. As you have pointed out interactions between ethanol and copper sulphate could have set off an immune response. Though chemically, ethanol is known to precipitate copper sulphate into a salt, we are uncertain as to how their interactions behave invivo and how they affect human tissues. H Score calculations: Prior to Bone Marrow studies- 200 points HScore; 80-88% Probability of hemophagocytic syndrome INPUTS: Known underlying immunosuppression —> 0 = No, Temperature, °F (°C) —> 49 = >102.9 (>39.4), Organomegaly —> 38 = Hepatomegaly and splenomegaly, Number of cytopenias —> 34 = 3 lineages, Ferritin, ng/mL (or μg/L) —> 35 = 2,000–6,000 [3343], Triglycerides, mg/dL (mmol/L) —> 44 = 132.7-354 [250], Fibrinogen, mg/dL (g/L) —> 0 = >250 [300], AST, U/L —> 0 = <30 [13], Hemophagocytosis features on bone marrow aspirate —> 0 = No After Bone Marrow studies- 235 points HScore; 98-99% Probability of hemophagocytic syndrome INPUTS: Known underlying immunosuppression —> 0 = No, Temperature, °F (°C) —> 49 = >102.9 (>39.4), Organomegaly —> 38 = Hepatomegaly and splenomegaly, Number of cytopenias —> 34 = 3 lineages, Ferritin, ng/mL (or μg/L) —> 35 = 2,000–6,000 [3343], Triglycerides, mg/dL (mmol/L) —> 44 = 132.7-354 [250], Fibrinogen, mg/dL (g/L) —> 0 = >250 [300], AST, U/L —> 0 = <30 [13], Hemophagocytosis features on bone marrow aspirate —> 35 = Yes As mentioned in your comment, there was good agreement between the score and diagnosis of secondary HLH." } ] } ]	1	https://f1000research.com/articles/13-326
https://f1000research.com/articles/13-320/v1	23 Apr 24	{ "type": "Opinion Article", "title": "Monitoring Open Science as transformative change: Towards a systemic framework", "authors": [ "Ismael Rafols", "Ingeborg Meijer", "Jordi Molas-Gallart", "Ingeborg Meijer", "Jordi Molas-Gallart" ], "abstract": "Background Following a flurry of policies for Open Science (OS), there is now a wave of initiatives to monitor its adoption. However, the great diversity of understandings and activities related to Open Science makes monitoring very challenging. There is a danger that by focusing on what can be readily observed (e.g. publications) many other OS activities are overlooked (e.g. participation), with a potential narrowing of OS scope, streetlight effects, and deviation from the values of OS. Since Open Science can be understood as a systemic transformation of the research system, we have borrowed concepts from Transformative Innovation Policies frameworks which aim at evaluating socio-technical transitions. In accordance with this view of OS as a systemic transformation, we propose that the new monitoring efforts should shift towards: (i) systemic perspectives which considers the various actions related to OS, including policies and outputs (e.g. datasets) but also processes (e.g. participatory events), outcomes (e.g. citizen interest in science) and expected impacts (e.g. better scientific contributions to addressing societal problems); (ii) implementation of monitoring as reflexive learning (rather than accountability or benchmarking); (iii) mapping the directionality of the activities and the values associated with the choices in directions. In summary, a monitoring framework for OS requires a profound change in conventional monitoring practices. The scope should broaden from current focus on outputs (such as publications) towards the processes of connection that make science ‘open’ (usage, co-creation and dialogue), as well as towards outcomes (changes in practices) and the longer-term impacts that reflect the values and normative commitments of OS.", "keywords": [ "Open Science", "Monitoring", "Evaluation", "Open Access", "Open Data" ], "content": "1. Introduction\n\nIn the wake of a flurry of policies and investments in Open Science (OS), there is now a wave of efforts to monitor its promotion and adoption. Institutions such as the European Commission1, the French2 and Finish3 governments, and the European Open Science Cloud (EOSC)4 are gathering statistics on OS outputs, policies and practices and making them available in dedicated websites. The European Commission has funded a string of projects aimed at capturing and understanding uptake and effects of Open Science, for example through the development of indicators for research assessment (Opus and GraspOS projects) and on the impacts of OS (PathOS project). The UNESCO has a Working Group to monitor the implementation of its 2021 Recommendations on OS (UNESCO, 2021, p. 33) for the 193 countries that signed it5 and has published its first outlook of OS activities in December 2023 (UNESCO, 2023).\n\nMonitoring Open Science poses major challenges. Different stakeholders hold disparate understandings of OS, often associated with different conceptual models and interests about what science is and aims to accomplish. Most national and institutional policies on OS are recent and thus changes are incipient, with a degree of engagement that varies largely across geographies, disciplines and topics. Some developments are hotly contested, since they run against some of the principles of equity and inclusion espoused by OS, such as open access of publication via Article Processing Charges (APCs) (Ross-Hellauer et al., 2022). While the dimensions of open access (OS) publications and open data (OD) sets are covered, many other relevant activities, such as engagement with societal actors, are seldom covered and others, like open educational resources, are just beginning to be scanned in a few pioneering countries. There is the danger that this lack of monitoring attention has a ‘street-light effect’ against the adoption of these activities (UNESCO, 2023).\n\nYet in our view, the main challenge is that ‘monitoring OS’ also requires a transformation of what ‘monitoring science’ means, since the shift towards OS implies a deep transformation of science itself. In this paper, we propose that this change in the understanding of monitoring cannot be a replacement of old output indicators with new output indicators, as it is often assumed. Instead, new conceptual frameworks and practices for monitoring are required that align with the conceptual shifts associated with OS. We suggest that conceptual frameworks from recent work on evaluation of Transformative Innovation Policies can be useful for thinking how to monitor OS (Haddad & Bergek, 2023; Molas-Gallart et al., 2021). These frameworks propose to shift efforts towards understanding monitoring as learning, as awareness of values and directionality, with more focus on processes and outcomes.\n\nThis study is prompted by our engagement with the UNESCO Working Group on Monitoring OS (UNESCO, 2023). Therefore, it aims to gain insights on the overall progress of OS across the world, which results from a large variety of national and institutional policies and social developments, rather than assessing specific initiatives. Given that UNESCO’s OS framework is broader and more explicitly normative than many previous OS policies, we bring to the fore the need to monitor OS of transformative change at a global scale.\n\nA number of OS monitors are already in place. The most relevant feature is that they tend to focus on the outputs of research (publications, data, software, etc.) that are accessible from digital platforms. While this is important, we propose that monitors should embrace an understanding of OS as a transformation of the research systems, and therefore encompass a broader range of dimensions, which include:\n\n• policies for OS.\n\n• OS outputs such as publications and datasets,\n\n• OS processes such as increasing collaborative practices (including public engagement) and evaluation approaches in line with OS,\n\n• OS outcomes such as increased attention by researchers to societal problems, or evaluations that don’t discriminate by gender or social group,\n\n• impacts such as the values highlighted in the list of values of UNESCO OS Recommendation: integrity, inclusion, epistemic diversity, or identifiable contributions for addressing of societal problems.\n\nWe first discuss the diversity of activities and the plural (and sometimes conflicting) understandings of OS. Second, we make the case that OS is a systemic transformation of research. Third, we review how models of science are associated with particular monitoring frameworks. Fourth, we describe concepts that can be useful for monitoring OS as a transformation. In particular, we propose:\n\n• to broaden out the monitoring OS from a focus on scientific outputs (e.g. datasets), to processes (e.g. participatory events), outcomes (e.g. better public engagement) and impacts (e.g. contributions to the achievement of SDGs);\n\n• to adopt a learning approach to monitoring, aimed at informing future-oriented strategies, i.e. helping navigate and make choices among options within OS;\n\n• to consider directionality, i.e. to open up the monitoring so as to map the different trajectories within each OS dimension (e.g. different colours of the routes to OS), as well as their potential effects and associated values.\n\nIn the conclusions we discuss the implications for this perspective for current OS policies.\n\n\n2. What is Open Science? A plurality of views on a diversity of activities\n\nA first difficulty in monitoring Open Science is the vast diversity of activities that it encompasses, from Open Access (OA) publishing to transparency and citizen engagement6. It is often said that OS is an umbrella term or better, a mushroom (as illustrated in Figure 1), in the sense that it consists of many visible practical activities (often digital) and that it also concerns, below its surface, many underlying institutional issues such as integrity, infrastructure and evaluation.\n\nLegend: This figure was drawn by Judit Eva’s Fazekas-Paragh based on Eva Méndez (2021, p. 5). Source: https://www.openaire.eu/blogs/hungary-on-the-move-1.\n\nThe programmatic definition of the European Commission (2016, p. 33), highlighted two aspects: first, the mainstream focus on (digital) access and collaborative activities and, second, the expectation that it would transform relations between science and society: ‘Open Science represents a new approach to the scientific process based on cooperative work and new ways of diffusing knowledge by using digital technologies and new collaborative tools. (…) allowing end users to be producers of ideas, relations and services and in doing so enabling new working models, new social relationships and leading to a new modus operandi for science.’ (see (Leonelli, 2023, p. 18). A definition of OS with these two sides is often found: on the one hand sharing or collaborative (digital) practices; on the other hand an explicit reference to the societal benefits in terms of participation and inclusion (Arza & Fressoli, 2017).\n\nNormative commitments to equity and inclusion have been common in the OS movement as launched in 2001 in the Budapest Open Science Initiative (Ross-Hellauer et al., 2022, p. 3). Nevertheless, definitions and policies have been diverse and ambiguous, depending on the underlying political programmes. For example, whereas many organisations in Latin America highlighted the role of OS for advancing science as a public good (Babini, 2019), policy adoption in the European context initially viewed the benefits of OS in terms of improvement in quality, efficiency, optimization, integration and potential of science (Shelley-Egan et al., 2020, p. 11), in a way that emphasized ‘market principles of competition foregrounding its economic role in training the workforce and fostering new products and services’ (Ross-Hellauer et al., 2022, p. 18). To put some light in this diversity, Fecher and Friesike (2014) proposed five main ‘schools of thought’ (narratives) depending on the focus and goals of OS: infrastructure (platforms), pragmatic (efficiency), public (access), measurement (evaluation) and democratic (free knowledge) schools, as shown in Figure 2.7\n\nThere is a strong contrast between the initial aspirations towards global equity of the OS discourse, and the narrower policies on access. Ironically, these policies have actually resulted in greater inequalities in some dimensions, in particular in terms of OA and APCs. This dissonance has led some OS advocates to state that, for all the claimed benefits, the current OS model has not made science more inclusive. Instead, it is still keeping many scientists underrepresented; new technologies exclude those with limited digital rights; and citizens seldom can shape research agendas (see review by Ross-Hellauer et al., 2022). The Manifesto of the Open and Collaborative Network (OCSDNet) (Albornoz et al., 2020) is an example of this perspective.\n\nIn recent years, one can observe policy trends towards a broadening of the OS agenda from more technical aspects of accessibility (e.g. OA and OD) towards more process-oriented aspects (e.g. citizen science and evaluation) and values (diversity and inclusion, the distribution of research benefits). The International Science Council (ISC) has now defined OS as ‘best characterised as the necessary transformation of scientific practice to adapt to the changes, challenges and opportunities of the 21st century digital era to advance knowledge and to improve our world. (…) One of the purposes of Open Science viewed as a call for transformation, is to ensure that ‘no-one is left behind” (ISC, 2020, p. 2). Also the European Commission states in its Open Science Portal that ‘when partners from across academia, industry, public authorities and citizen groups are invited to participate in the research and innovation process, creativity and trust in science increases.’ 8\n\nSome critical voices stress this shift from an understanding of OS as the ‘possibility of access’ towards an understanding of OS as the ‘process of connection’ in accordance with values related to integrity and epistemic justice. Chan proposes that ‘the ability to participate, to connect, and to co-produce knowledge with others who share common concerns is far more important than simply access to content or resources’ (Chan et al., 2020, p. 2). Leonelli argues that ‘… from being solely a question of sharing resources, openness is thereby conceptualized as the opportunity to make and maintain connections among relevant stakeholders (…) in ways that help to develop ever more relevant forms of interaction with the world’ (Leonelli, 2023, p. 66). Ross-Hellauer has stressed that enabling access is not enough to foster equity in science in the face of huge disparities in resources (Ross-Hellauer et al., 2022).\n\nThe UNESCO recommendation on OS is the first internationally agreed definition of OS (UNESCO, 2021). As a consensus document it exemplifies the breadth, ambiguity and transformative nature of OS discourses. This document made explicit two further steps. First, as illustrated in Figure 3, it highlighted the diversity of activities related to OS, particularly by giving more prominence to issues such as open engagement and dialogue with non-academic and marginalised actors (process-oriented practices), as already highlighted by the OECD (Dai et al., 2018). Second, as shown in Figure 4, it made explicit the values and principles associated with OS. Some of these values and principles are related to rigor in scientific practices (quality, integrity, transparency, reproducibility, etc.). Others are more related to notions of justice within science (equity and fairness), and some more associated with the properties of the social contributions (diversity, inclusiveness, responsibility, participation) and their impacts (collective benefits). Many of these values are shared by other high level STI policy formulations, even by organisation’s which had traditionally focused on economic impacts, as illustrated in the OECD’s recent report (OECD, 2023, pp. 87–121).\n\nOS is seen as having four pillars: 1) Scientific Knowledge (publications, data, educational resources, software, hardware); 2) Infrastructure (virtual and physical); 3) Engagement of societal actors (citizen and participatory science, volunteering, crowdsourcing, crowdfunding); and 4) Dialogue with other knowledge systems (indigenous peoples, marginalised scholars and local communities). Source: UNESCO (2021).\n\nSource: UNESCO (2021).\n\nBoth OECD and UNESCO’s comprehensive perspectives allow different stakeholders to highlight those activities and values which are most precious to them. However, this colourful palette also reveals that stakeholders hold a plurality of views on OS, with a battery of disparate activities. In consequence, its monitoring framework has to embrace this diversity of activities in a pluralistic way for its application in different contexts.\n\n\n3. Open Science as a transformation of the research system\n\nWhile stakeholders may not agree on the full range of activities or values of OS, a recurrent theme in OS discourse is that Open Science is about a transition or transformation of the research system (Shelley-Egan et al., 2020). The transformation is seen as a more collaborative way of doing research, partly driven by the application in science of digitalisation and associated information and communication technologies (Nielsen, 2011). However, it is also related to the perception of a major change in the contract between science and society, as discussed by various science policy discourses, including Mode-2 and transdisciplinary research (Gibbons, 1999; Nowotny et al., 2003), Responsible Research and Innovation (RRI) (Owen et al., 2012; Shelley-Egan et al., 2020), mission-oriented research (Mazzucato, 2018), Transformative Innovation Policies (Loorbach & Wittmayer, 2024; Schot & Steinmueller, 2018) and science for SDGs (Ciarli, 2022). In all these discourses, there is a call for transformative changes that are related to the changing relationship between science and society (Shelley-Egan et al., 2020, p. 11).\n\nLet us then take OS as transformation of the research system in all its dimensions: social, epistemic, institutional, organisational – even geographical9. Then, OS would entail the evolution of the current research system towards a future research system in which free information flows and collaborative activities would play a more prominent role than they play nowadays. However, if we think of science as an evolutionary system with many-fold potential futures there is not one, but many potential OS futures, depending on the direction of change. This plurality of potential futures reflects the ambiguity of the concept and implies that the transformation it entails is open-ended, with different potential but uncertain futures (Stirling, 2011).\n\nThus, the direction of this transformation will be given by the relative importance or the balance of efforts put into the different OS activities. A concentration of efforts around certain activities reflects a particular school of thought, and a particular model of what OS should be. From this evolutionary perspective, the key question is not if there is more or less OS, but which type of OS progresses, i.e. towards which type of (OS) practices the research system is being pushed and it evolves.\n\nIf one accepts that OS is a transformation of the science system, then the monitoring should aim at capturing the directions of transformative change. In the next section, we examine how changes in the models of science have been historically associated with reformulation of monitoring systems.\n\n\n4. New models of science require new monitoring frameworks\n\nMonitoring has the aim to check, show and justify that policy interventions, activities or organisations deliver the desired outcomes and impacts. Explicitly or not, monitoring and evaluation systems, as well as associated indicators, are derived from conceptual models on how some policies and activities lead to change towards the expected outcomes and impacts. These models guide the search of the properties that should be monitored and where possible measured (Smith, 2004). If the models and systems under observation seriously evolve, the tools and methods of description also need to undergo a transformation. Yet monitoring tools and indicators are applied through existing (and thus old) institutional channels. As a result, efforts to capture new systemic changes are always difficult to adopt as they pose conceptual, technical, organisational and institutional challenges: institutions have a strong inertia to monitor according to past frameworks.\n\nHowever, at some point monitoring and classification systems evolve in accordance with social transformations. For example, the logics of wine classification in bottle labels shifted from specific territory (terroir) (as traditionally done in France) to wine grape varieties (cépage) as a strategy by Californian companies in a context of globalisation in which the drinkers know little about local wine regions. Or dictionaries of commerce radically changed their classification of trade activities from the 18th to the 19th century, when the industrial revolution reconfigured the understandings of manufacture (Douglas, 1986, pp. 91–109).\n\nLet’s apply this idea of changes in monitoring to changing models of science. Schot and Steinmueller (2018) have proposed that there have been three main conceptual models about policies for science, technology and innovation (STI): the linear model (frame 1), the innovation systems model (frame 2), and more recently a model of transformative research and innovation policies (cf. Haddad & Bergek, 2023).\n\nThe linear (‘science-push’) model assumes an unproblematic flow from R&D investments to scientific knowledge, to technological inventions, and to market innovations that will eventually result in economic growth and increased well-being. Therefore, monitoring in policy frame 1 is conducted focusing on R&D inputs (investments) and S&T outputs. The OECD’s statistical manual for R&D data collection, known as the Frascati Manual (OECD, 2015) is the main instrument to collect R&D investments. Scholarly publications are conventionally used as proxies for scientific output (the supply side), and patents as proxies for technological output10. The linear model became increasingly questioned when it was realised that some countries (such as Japan in the 1980s) and organisations were very successful at innovation without being leaders in formal R&D. Publications and patents allow fine-grained analyses of the S&T contents, but they are poor in terms of tracing how and where this knowledge is used.\n\nThe perspective of the innovation systems model (frame 2) shifts the analysis towards the interactions between actors and the process of innovation in the firm (Kline & Rosenberg, 1986; Smith, 2004). Here, the assumption is that innovation is best achieved when knowledge flows across academic organisations and industry. Since these processes of knowledge exchange were not captured in formal R&D measured by frame 1 statistics, the so-called Community Innovation Surveys (CIS) were developed to gather information directly from companies on how they create and introduce innovations. This effort consolidated in 1992 in the OECD’s Oslo Manual for innovation data in a long process that involved testing, trials-and-errors and learning through the engagement of policymakers and researchers (Arundel & Smith, 2013; OECD & Eurostat, 2018). The European Innovation Scoreboard of the European Commission is another example of a monitoring framework based on the innovation system perspective. In this case, the approach takes a broad battery of about 25-30 indicators that describe different aspects of an innovation system, including education of human resources, attractiveness of research systems, R&D investments, innovation data (from CIS), firm and academic collaborations, and employment and sales impacts, among others.\n\nWe can take several lessons from these previous monitoring frameworks. First, their development takes time and is achieved through the creation of communities of practice at the interface of policy and research (Godin, 2004). Second, monitoring frameworks are adjusted to adapt to evolving conceptualisations11. Third, the focus of monitoring changes in accordance with the logics at the heart of each model: from inputs and outputs of formal research activities (frame 1) to the network of knowledge activities and introduction of market innovations (frame 2). In consequence of this drift in location, the new frameworks do not substitute but rather complement previous ones.\n\nIn recent decades, the idea that more innovation would always lead to more societal benefits has become increasingly questioned. It is now widely accepted that innovation in itself can lead to both desirable and undesirable societal impacts for example in terms of either lack of attention or negative impacts on health or the environment (OECD, 2023, p. 87). As a response, a third model of innovation policy has been gradually emerging, with some STI policies explicitly directed at supporting transformative change towards desired goals in specific sectors such as food, health or mobility systems. This frame 3, known as Transformative Innovation Policies, shifts the focus towards innovation for transformative change in socio-technical systems such as those of energy, mobility or health, etc. particularly to address societal challenges such as climate change, urban sustainability, aging society (Schot & Steinmueller, 2018; Weber & Rohracher, 2012). In frame 3, co-creation and transdisciplinary approaches are crucial to align research with societal needs.\n\nLet us now take science as a socio-technical system in itself, the one concerned with the production of knowledge. If we then think of OS as a transformative agenda of this socio-technical system, as argued in the previous section, then OS policies can be understood as transformative policies for science. We can then apply the theoretical developments on Transformative Innovation Policies to OS. It might be argued that the research system differs from health, mobility or food systems in that it is not a tangible societal need. Still, the research system produces ‘knowledge’ for which there is a social demand, and then OS initiatives can be seen as innovations in the (socio-technical) system of knowledge production (Loorbach & Wittmayer, 2024).\n\nLet us then examine the recent insights on STI evaluation and monitoring from a frame 3 perspective, following the recent publication of a string of contributions (Haddad & Bergek, 2023; Janssen et al., 2022; Kofler & Wieser, 2023; Molas-Gallart et al., 2021; Rohracher et al., 2023). In summary, we find that these studies (actually more focused on evaluation than on monitoring) suggest a shift in focus towards:\n\n1. A systemic perspective of the various activities related to OS, including policies and outputs (e.g. software) but also processes (e.g. new evaluation methods in line with OS), outcomes (more inclusive recruitment of researchers) and expected impacts (e.g. scientific contributions to societal problems so far non-addressed);\n\n2. Learning with regards to strategic choices and reflexive evaluation, with participatory processes and mixed methods if possible;\n\n3. Directionality of the activities and the values associated with the choices in directions.\n\nSince the purpose of monitoring in this frame 3 is not accountability or benchmarking, but learning (i.e. informing future strategy for specific different contexts), the methods and tools for conducting the monitoring do not need to be unidimensional indicators. Instead, new methodological tools can be created, for example showing collaborative networks, science maps or other visualisations that ‘open up’ reflexive thinking on the OS trajectories to be pursued (Barre, 2010; Ràfols, 2019)12.\n\nIn the next three sections we explore how these concepts could be applied in the context of a general OS monitoring, this is, a monitoring which aims to promote OS by capturing overall trends affected by a variety of (OS) policies, rather than assessing specific transformative programmes or policies.\n\n\n5. Towards a systemic monitoring: broadening the palette towards processes and outcomes\n\nMost initial initiatives towards monitoring OS have focused on describing whether research outputs such as publications, datasets or software are publicly accessible. Here we argue that a broader palette is needed for OS monitoring, for two reasons. First, because OS is defined as a broader set of activities than just outputs (which are the first pillar in Figure 3). Second, because public access to outputs in itself does not mean that the information or knowledge can be mobilised. As Michel Callon argued, science is not a conventional ‘public good’ because to make fruitful use of it, the potential beneficiaries need to invest or have invested previously in developing capabilities (Callon, 1994). This is why firms invest in ‘absorptive capacity’, to ‘be able to recognize the value of new, external information, assimilate it and apply it’ (Cohen & Levinthal, 1990, p. 128).\n\nBy focusing on accessibility without considering the capabilities needed to use information, there is the danger that outputs will not be utilized. Thus, policies have been developed to foster knowledge exchange, both within science (interdisciplinarity), and with specialised stakeholders (translational efforts, transdisciplinary projects and transfer offices) (Molas-Gallart et al., 2016).\n\nSince open outputs will mainly benefit those organisations or territories with absorptive capacities, generic open outputs from science may sometimes reinforce inequalities (see discussion on OD in the Global South (Bezuidenhout & Chakauya, 2018; Bezuidenhout et al., 2017)). Development and innovation studies have documented that in many middle and low- income regions, science has not generated local benefits due to lack of local learning capabilities or absorptive capacity (Arocena & Sutz, 2010; Bell & Pavitt, 1995). Yet, as Leonelli argues, genuine research openness is not about accessibility but about developing relevant interactions with the world (Leonelli, 2023, p. 66).\n\nAn open publication (or dataset or software) may be formally accessible but created and communicated in such a way that it does not reach its potential beneficiaries. Either within or beyond academia, explicit efforts have to be made to search for users, to learn about their needs (participatory agenda setting), to engage them (co-creation), and to communicate to them the knowledge in meaningful ways (outreach). Therefore, a systemic perspective of OS also needs to track in what ways knowledge is created and used: whether it is generated and used through plural collaborations (processes) involving learning to and from stakeholder engagement (outcomes) and leading eventually to some social contributions (impacts).\n\nTherefore, we propose that a systemic perspective would include a description of OS policies (enabling conditions) and OS outputs (e.g. publications), but crucially it should also include a monitoring of OS processes (e.g. public engagement, dialogue), outcomes (e.g. policy uptake) and, where possible, broader impacts (e.g. contributions to societal goals). This broadening of the monitoring to the full palette of scientific activities should allow to see changes towards more inclusive research processes, and whether the accessible scientific outputs are actually accessed and put to social use. Such a breadth is consistent with the ‘opening of monitoring’ and the ‘people-centred’ (process) framework suggested by the UNESCO OS Outlook (UNESCO, 2023, pp. 27, 30). And this is important to avoid a streetlight effect (Davies et al., 2021; Molas-Gallart & Rafols, 2018).\n\nFigure 5 and Table 1 aim to summarise our proposal for a monitoring framework that is comprehensive and systemic, including the various aspects of OS: policies, outputs, processes, outcomes, and impacts. It should be noted that the distinction between processes, outcomes and impacts depends on the underlying evaluation theory, i.e. the specific theory of change on how the policy intervention achieves its goals. Since we are discussing OS policies in general, there is a degree of ambiguity regarding which actions can be considered processes, outcomes and/or impacts.\n\n* https://datacite.org/ see UNESCO Outlook (UNESCO, 2023, p. 40).\n\nFor example, stakeholder engagement can be interpreted as a research practice (a process in itself), a change in a practice (and thus an outcome of the OS policy), and it may translate as goal in itself (an impact towards inclusion). We don’t think this ambiguity is problematic, as far as each dimension is transparently defined in a specific monitoring context. Thus, from a more nuanced perspective, the specific instances of monitoring can contextualise the aspect of stakeholder engagement captured, making the distinction between counting a given participatory event (a process), reporting of stakeholder learning during participation (an outcome), or reporting of inclusion of marginalised communities (an impact).\n\nThe monitoring of enabling conditions refers to the description of dimensions that will facilitate or hinder the progress of OS. This comprises policies and institutional initiatives aimed at fostering OS, including specific OS action plans (e.g. infrastructure investment, training for FAIRisation of data) as well as transversal policies with major effects in OS (e.g. evaluation reform). The EOSC Observatory provides an example of policy monitoring at the EU level. The Finish OS monitor has designed a survey to institutions about their practices to support OS. The first step in UNESCO OS monitoring has been the development of a survey for the Member States to report their policies for promoting OS.13 These surveys provide a solid ground for exploring institutional policies and commitments to OS.\n\nThe tracking of OS outputs in the form of OA publications or Open datasets is the most established monitoring practice. Bibliometric databases allow to conduct fine-grained analyses of the growth in the accessibility of the scientific literature. A problem is the uneven coverage of most commercial databases of across countries, disciplines and language, which marginalises knowledge relevant some world regions and communities (Mongeon & Paul-Hus, 2016). Initiatives are under way across continents to address this issue (Maricato et al., 2023). The French OS Monitor offers an example of the feasibility of rigorous analysis with highly comprehensive coverage using open scholarly infrastructure. Initiatives that make this tracking possible deserve to be valued and supported: for example, National CRIS systems like the Norwegian (CRISTIN), regional bibliometric databases like SciELO (Latin America) and J-Stage (Japan), or portal for local OA scholarly journals (such as Catalonia’s raco.cat).\n\nThe tracking of open research data, open educational resources, open software, and open hardware is patchy but illustrative of growing efforts (UNESCO, 2023, pp. 40–42), although the estimates of numbers of datasets, scripts or courses as general indicators is problematic given the large difference in size and efforts invested per unit.\n\nBroadening out the palette of OS activities\n\nWhile counting outputs is a key monitoring tool, we should bear in mind that open outputs do not always lead to more OS. First, because, as argued above, since openness is situated and the capabilities of beneficiaries are unequal, potential access does not necessarily translate into the possibility of reaching, understanding and mobilising the knowledge (Callon, 1994; Chan et al., 2020).\n\nAlso, because there can be instances in which the conventional ‘open’ routes of the outputs may not be associated with an increased flow of knowledge. For example, for a political scientist in Sweden publishing an opinion piece in Sweden in a newspaper behind paywall or in the local grey literature may achieve more readers and influence (in this sense more academic ‘openness’) than publishing an article in an OA academic journal in the US (Salö et al., 2023). Or for an agricultural engineer in Colombia, publishing in Spanish in non-OA professional newsletter may be more important to reach her stakeholders (farmers) than publishing in English in a European OA academic journal (Chavarro et al., 2017). For the particular case of policy influence of OS practices, Cole et al. (2023, p.1) study found that:\n\n‘…there is little evidence that Open Research products, namely Open Access and open data (…) are useful in integrating science into policy-making. Instead, we found that the cognitive accessibility of research outputs is more important than their physical accessibility, and that inclusive and collaborative Open Research processes, like upstream engagement, co-creation and Citizen Science, are most effective at doing so.’\n\nProcesses of interactions such as collaborations and engagement are seen as separate dimensions to accessibility, and leading to different types of benefits (Arza et al., 2017). This is why, in the UNESCO framing, as depicted in Figure 3, OS involves not only outputs (in green (1) pilar), but also research processes: in terms of collaboration in infrastructures (pink (2) pilar), stakeholder and citizen participation (orange (3) pilar), and dialogue with other knowledge systems (blue (4) pilar). These processes should also be monitored to assess progress in OS. Unfortunately, according to the recent UNESCO OS Outlook, they are poorly captured by OS reports at the moment: new methods need to be developed (UNESCO, 2023).\n\nHaving made the argument that OS is a transformation of the research system, it is also important to monitor the changes in practices and behaviours induced by OS, i.e. the outcomes. Indeed, proposals for monitoring Transformative Innovation Policies agree that monitoring should focus on outcomes; that is, on assessing the ‘changes in the behaviour, relationships, activities, or actions of the people, groups, and organizations (…)’ (Molas-Gallart et al., 2021, p. 435). Monitoring outcomes concerns questions such as how Open Data is re-used and by whom, and how public engagement influences research agendas.\n\nOne first approach to monitoring processes and outcomes is to approximate them through some relevant characteristics of the scientific outputs; for example, estimating frequency and type of exchanges with policy, industrial and civic organisations through formal co-authorship in publications (Tijssen, 2006), or through the mention of scientific publications in social media or policy documents (Díaz-Faes et al., 2019). But whereas many studies have looked at whether OA leads to more citations, let us emphasise here that for the benefits do not just lie on the amount of interaction and usage, but on the distributions across epistemic and geographical spaces. For example a recent study has reported that OA publications (even more if green OA) are cited in more diverse ways: they garner citations from more territories (countries and regions) and more disciplines (Huang et al., 2024). This is a good example of an outcome (a change induced by OA: broader reach) aligned with the value of making science more diverse.\n\nThe need to gather new data sources and surveys\n\nWhile analyses of usage of outputs are worth conducting and provide some information, qualitative studies have concluded that interactions between social actors and academics are extremely diverse (Molas-Gallart et al., 2002). As a result, traces of interaction through some channels tend to be specific (biased) to certain socio-economic sectors and issues. For example, with some scientific issues (e.g. food consumption) are often mentioned in social media, while other (e.g. food production) receive more mentions in policy documents, and still others (e.g. agricultural methods) are only shared across professional information channels (Noyons & Rafols, 2018). Moreover, many exchanges between academic knowledge and professions are not conducted through scientific publications, but through direct interactions and grey literature reports, often in the local languages (Salö et al., 2023; Thune et al., 2023).\n\nIn conclusion, it is generally not possible to capture knowledge exchange trends reliably by using only traces left by conventional scientific outputs in digital platforms. In order to know how researchers share and use materials and data, how they interact with non-academics, etc., it is necessary to collect new data. Surveys are an obvious source of information. Some of the OS pilot monitors have started to conduct surveys. For example, the Finish monitor has proposed to conduct biannually a survey especially on ‘the development of services, policy documents, research assessment and culture of open scholarship’.\n\nThere is a long research experience of conducting surveys in order to understand the knowledge exchange practices in relation to a variety of collaborative practices (Díaz-Faes et al., 2023), modes of knowledge exchange with industry (D’Este & Patel, 2007), exchange with policy (Thune et al., 2023), innovation practices in industry through the Oslo Manual (Bloch, 2007; Gault, 2020; OECD & Eurostat, 2018), innovation in the public sector (Arundel et al., 2019), and practices of Responsible Research and Innovation (RRI) (Holtrop et al., 2022). Some studies aimed at monitoring OS processes also relied on surveys: for example on sharing of research materials (Shibayama et al., 2012), open peer review (Ross-Hellauer et al., 2017), policy use (Cole et al., 2023), engagement with non-academics (Lawson et al., 2019), integrity (Schneider et al., 2023), or broader perceptions and habits of OS (Ollé et al., 2023). To our knowledge, Arza et al. (2017) conducted the only survey looking into the multiple dimensions of OS, showing differences by field and region.\n\nFinally, there is the monitoring of the benefits of IS. It is common in evaluation theory to distinguish between ‘outcomes’ (changes in behaviours, practices, organisations directly induced by a policy intervention, e.g. more stakeholder participation), and ‘impact’ (referring to the ultimate changes that the intervention pursues such as societal benefits derived from scientific activity or gender balance) (Molas-Gallart et al., 2021). Notice that in the UNESCO framing, the impacts refer the values expressed in Figure 4, which can be considered goals in themselves: more collective benefits, more equal, diverse and inclusive science.14\n\nWe argue that the ways in which outputs, processes, outcomes and final impacts are related to each other should be mapped. In this way, monitoring may capture whether the evolution of the research system leads towards desired directions. This is important, because in a complex system one cannot assume that achieving the desired outputs (e.g. more open datasets) will lead to the desired outcomes (e.g. broader societal participation in specific research area) and desired impacts (the achievement of the collective benefits). Moreover, since the impacts are multifactorial, even if OS is pushing in a desired direction, other larger factors may counter the positive effects – and complementary policies may need to be considered. For example, evaluation reform may be needed to stimulate data sharing, because good open data repositories on their own may not be enough to trigger such behavioural change.\n\nAs potential dimensions of impact of OS, we propose those dimensions in the values of the UNESCO OS Recommendation, such as contributions to SDGs (collective benefits), distribution of research across countries (geographical diversity), distribution of research across languages (linguistic and cultural diversity), and balance in gender and ethnic group representation in scientific institutions (social inclusion).\n\n\n6. Learning: reflexive monitoring for supporting strategic decision-making\n\nVarious studies have proposed that the learning function of evaluation should be emphasised in Transformative Innovation Policies (Janssen et al., 2022; Molas-Gallart et al., 2021; Rohracher et al., 2023).\n\n‘Reflexive monitoring and evaluation’ has emerged as a specific approach that distinguishes itself from more common ‘result-oriented’ evaluations by considering learning how to contribute to system innovation the central goal of evaluation. ‘Result-oriented approaches’ focus on accountability and steering, and on a set of predefined objectives, while ‘reflexive monitoring and evaluation’ put ‘the prevailing values and institutional settings up for discussion’ (Van Mierlo et al., 2010, p. 36).\n\nKofler and Wieser (2023) have suggested the metaphor of ‘reflexive navigation system’ to convey the idea of monitoring for learning through engagement with stakeholders. The monitoring thus designed ‘organises information and knowledge flows, offering stakeholders an overview of achievements and challenges’, and this is used in expert panels in ‘regular exchanges and inclusive conversations with decision-makers’.\n\nThe idea is that the main use of monitoring should shift from accountability towards fostering thinking over strategic choices. In sociotechnical transformations there is great uncertainty regarding which of the many potential futures will be reached. This means, for example, that there is not one single trajectory or pathway to monitor, but a gamut of possible trajectories of which only one will be realised (Stirling, 2011). Thus, in a transition towards a low-carbon energy technologies, a range of disparate energy portfolios is possible in a given territory or community (some dominated by wind-turbines, others by photovoltaics), with different environmental, security and economic consequences. Lessons learned from monitoring can facilitate debates towards re-balancing the portfolio in strategic ways, as exemplified in the RIPEET project.\n\nSimilarly, OS monitoring can facilitate this type of reflexive learning. For example, a given organisation has the potential to invest relatively more or less efforts across the activities showed in Figure 3, e.g. on how much resource goes to open data vs. engagement or collaborative infrastructure. OS monitoring of institutions can show that they have strengths and weakness over a portfolio of OS activities – and thus help reflection on developing strategies towards addressing these. The question is not whether the organisation has more or less OS (an accountability logic), but what types of OS it has and with what consequences in relation to its goals (a learning logic).\n\nWhen monitoring aims to have a learning component, it should be comprehensive and contextual about the activities carried out (or not) (as discussed in the previous sections) and allow to reflect on the various available options. This type of information then empowers stakeholders to express preferences and make relevant normative choices. As put by the in the UNESCO OS Outlook, ‘[c] onsidering science as a global public good, it is important not to reduce open science to a few standardized metrics monitored in a top-down approach. Masking variations, particularly those between and within countries, may undermine the transition to a genuinely open science, accessible to all and with benefits for all’ (UNESCO, 2023a, p. 18).\n\nGiven the current policy inclination for narrow monitoring focused on accountability or efficiency, re-purposing monitoring to support learning will require new monitoring designs and training of users. This means in particular, applying monitoring methods in such a way that they facilitate the use of indicators as ‘debatable devices, enabling collective learning’ through contextualisation and stakeholder engagement (Barre, 2010; Ràfols, 2019). To do this, monitoring can be enriched by ‘broadening out’ the range of issues considered in a given dimension (vertical axis in Figure 6) and by allowing users to ‘open up’ the indicators to scrutiny under various conditional perspectives (vertical axis in Figure 6) (Leach et al., 2010; Stirling, 2008). Ideally, these ‘indicators frameworks’ would need to change according to different monitoring purposes and contexts (Wouters et al., 2019).\n\nLegend: Framework of ‘broadening out’ (vertical axis: including more information in the analysis) and ‘opening up’ (horizontal: presenting an analysis allowing choices), based on Leach et al. (2010). Source of graph with trends: UNESCO (2023, p. 32).\n\nFor example, for Open Access monitoring an initial analysis might just focus into the growth of the number of OA publications (top left of Figure 6) and conclude that the trends are positive. By ‘broadening out’ the type of issues to type of OA, the analysis opens up a new perspective by visualising the types of OA which are growing fastest (gold and hybrid) – thus raising critical questions. A further step would be to consider the geographical distribution of publications. In contrast to rigid ranking lists which fostered narrow interpretations, the development in recent years of monitoring systems based on interactive visualisation platforms with filtering possibilities, has greatly facilitated ‘unpacking’ of indicators, mappings or collaborative networks (Rafols & Stirling, 2021).\n\n\n7. Directionality: visualising normative choices over trajectories of science\n\nDirectionality refers to the notion that science, technology and innovation (STI) systems follow certain trajectories (or pathways) rather than others. Evolutionary understandings have shown that STI systems develop along sociotechnical trajectories with path dependency (Stirling, 2011). Different organisations or countries may follow alternative pathways. For example, Denmark committed to wind energy whilst France to nuclear energy as a result of divergent social and political commitments. Therefore, STI trajectories do not evolve over one dimension, but across a multidimensional space with a plurality of potential directions. There is a diversity of optional STI futures and different actors may favour different choices depending on their values and interests. A key insight from frame 3 of innovation policy (Section 3) is that a specific STI system (e.g. mobility or energy) are locked-in in problematic pathways (e.g. due to pollution and CO2 emissions) and changes need to be supported towards alternative sustainable trajectories (e.g. wind-turbines, or nuclear).\n\n‘Directionality means that innovation policy will not just stimulate specific technological options, but will look into the social and environmental drivers and consequences of each option, then aim for a deliberation on desirable pol-icy directions and eventually foster some desired directions for innovation, while blocking undesirable ones.’ (Molas-Gallart et al. 2021)\n\nTo sum up, in any given transformation, the socio-technical trajectory is also associated with social commitments related to certain values. Monitoring should help in visualising alternative trajectories (wind vs. nuclear; green, diamond vs. gold OA). Where possible, the monitoring framework would inform of the broader social implications of each trajectory in terms of values, e.g. in alignment with SDGs, inclusion, distribution of benefits across stakeholders, etc.\n\nIn the case of OS, the notion of directionality means that OS will follow different trajectories, depending on the choices made regarding the adoption (or not) of particular commitments (e.g. FAIR, CARE datasets). A frame 3 perspective helps understand why monitoring the directions is so important: these choices define the OS future against alternative (not adopted) trajectories, often with broad, and sometimes unexpected, societal consequences.\n\nLet us look for example, on how values are associated with different trajectories of Open Access in Figure 6. One of the key rationales for supporting an OA trajectory was to foster inclusion of researchers from Global South in transnational research communities through access to all journals. However, in the case of the gold and hybrid OA trajectories, access to reading is being (partly) achieved through the use of Article Processing Charges (APCs). Since these APCs are not affordable to many researchers in the Global South, these trajectories become a major barrier for researchers without resources to publish in highly visible journals or to publish in OA in hybrid journals, thus enhancing inequity.\n\nIn terms of outputs, these trajectories seem successful (they have higher % of Open Access articles), but the overall outcome goes against the value of inclusion. Olejniczak & Wilson (2020) show that men, older faculty, private and elite universities are more likely to publish in gold OA. This is a Lampedusian transition15 in the sense that publishing practices change, but the incumbent actors (the large publishing corporations) preserve their interests and dominant position by using existing path dependency to shape the OS transformation towards those trajectories that favour them (Larivière et al., 2015; Stirling, 2019). A monitoring strategy that is sensitive to value commitments, should not just look at the percentage of OA, but at the distribution of OA modes (green, gold, diamond, etc.) and its consequences in terms of equity, as illustrated in Figure 6.\n\nSimilarly, the apparently technical choices made on the implementation of Open Data (OD) can be analysed as representing different data sharing trajectories, with different ethical and social implications. On the one hand, data sharing is discussed according to the relative value of OD under different curation and infrastructure situations. This led to the proposal of the FAIR principles (Findable, Accessible, Interoperable and Reusable), with attributes that have implications in terms of the value of efficiency rather than fairness, in spite of its name (Wilkinson et al., 2016). However, other framings like the CARE Principles for Indigenous Data Governance (Collective Benefit, Authority to Control, Responsibility, and Ethics) (Carroll et al., 2020) put the values of equity and collective benefits at the centre, highlighting that there are major challenges on the usability of data by social actors (Dosemagen & Williams, 2022), on data control and equity, and on the distribution of the benefits across Northern vs. Southern researchers (Bezuidenhout et al., 2017) and stakeholders (e.g. communities endowed with genetic or natural resources). Given the implications of the different data sharing modes on OS values (as suggested by UNESCO), it seems relevant to include compliance or not with FAIR and CARE principles in a monitoring exercise. This means that, in terms of monitoring OD, the information should be provided with the particular OD trajectory (FAIR, CARE, both or other).\n\nA third example is the choice regarding the governance data infrastructures in terms of centralised vs decentralised/federated architectures, which have implications on the geographical balance of power across countries and organisations, data control or accessibility (Bezuidenhout & Havemann, 2020).\n\nIn summary, for each dimension of OS, there are alternative trajectories with different social implications.\n\n\n8. Conclusions: ‘Opening up’ the monitoring of Open Science\n\nAs we are writing this paper in early 2024, many governments and scientific institutions have adopted OS policies and are developing methods to monitor progress toward the goals of OS. We observe that there is a tendency to focus the analysis on growth along those dimensions of OS that can be more easily measured, generally via the analysis of publications. However, these early measurements show already that ‘progress’ (adoption of OA) is not necessarily aligned with some of the OS policy goals (increased equity and inclusion in science) (UNESCO, 2023).\n\nSuch choices have practical implications. Monitoring tools created by national governments and supranational organisations such as the UNESCO may appear to be far away from most OS research practices. However, one should not underestimate the influence of monitoring systems in shaping practices. Norms on how to develop and govern science are strongly influenced by (inter-)governmental institutions (Finnemore, 1993) and practices on quantitative monitoring and evaluation constitute a key technology for governance (Rottenburg & Merry, 2015). Traditional monitoring approaches have often suppressed diversity in research and its interactions with society in ways that run against the values of OS (Rafols et al., 2012; Sugimoto & Larivière, 2023).\n\nIn this article, we propose an approach to monitoring that aims to engage with the complexity and ambiguity of OS (Fecher & Friesike, 2014), and is aware of the potential suppression diversity associated with streetlight effects. Our point of departure is the assumption that OS is a transformation of the research system. Therefore its monitoring will require to map dimensions of research that have not been considered relevant in previous science models. Building on insights from the evaluation literature of transformative innovation policies, we have proposed strategies for monitoring OS (systemic view, learning and directionality), as summarised in Table 2 (compare with Leonelli (2023, p. 64, Table 3)).\n\nFirst, we propose to ‘broaden out’ the dimensions to be monitored, adopting a systemic perspective which considers the various actions related to OS, including processes (e.g. participatory events), outcomes (e.g. use of knowledge in policy) and expected impacts (e.g. increased contribution to societal problems). This means going beyond the current focus on the science supply, on monitoring policies and outputs (e.g. datasets). Such a pluralistic perspective is warranted by an ongoing shift in the conceptualisation of OS from ‘accessibility to research outputs’ towards ‘judicious interactions’ (Leonelli, 2023) both in the scientific practices and the societal usages of research. The type of information needed cannot be garnered only from research output data in digital platforms. Therefore existing data sources on outputs (objects) will have to be complemented with new data sources on researchers’ OS activities, especially interactive processes. Given that many collaborative practices and science-society exchanges are invisible in outputs or digital platforms, we believe that direct inquiries are needed, via surveys or qualitative approaches, to understand OS dynamics.\n\nSecond, given the uncertainty associated with sociotechnical transformations, and the unexpected outcomes of transformative policies (as illustrated by increased publishing inequity generated by OA), monitoring should be oriented towards supporting reflective learning – rather than a focus on accountability and benchmarking. Monitoring should be understood as a navigation instrument that helps to set sails towards the desired goals in the face of hidden currents and shifting winds.\n\nThird, monitoring should be ‘opened up’ by making directionality visible. Since there a many potential futures in a transformation and contending visions, monitoring OS should not be only about tracking more or less OS, but about what trajectories of OS are developed and with what consequences. Different trajectories (e.g. green vs. gold OA; FAIR vs. CARE OD) are associated with different interests and values – and therefore lead to different OS futures. In order to map choices, it is necessary to adopt multidimensional monitoring tools and visualisations.\n\nA final consideration is the diversity of contexts of science and society. This means that flexibility (an OS principle in the UNESCO Recommendation) will be required to apply monitoring in different locations or organisations (Wouters et al., 2019). The strength of a monitoring framework is its capacity to summarise a diverse world. But this can become a liability without a good dose of humility and reflexivity (Stirling, 2023, p. 5). As Leslie Chan reminds us:\n\n‘… there is no single or universal concept of Open Science that is sufficient to encompass the diversity of knowledge traditions and practices from around the world. Hence the term Open Science and the notion of “openness” is highly situated, constantly subjected to negotiation according to local contexts and historical contingencies. Our collective observations therefore challenge the tendency to define Open Science as a set of technical infrastructure, workflow, protocols, and licensing conditions that can be universally applied regardless of context, history, and human agency.’ (Chan et al., 2020, p. 17)\n\nJust like the wealth of ecosystems in the Earth cannot be described by simply counting the number of individuals of each species, the transformation towards OS cannot be described by counting open outputs. Instead, the evolution of ecosystems is understood through the changes in the network of interactions among species in each ecosystem. Similarly, the evolution of OS needs to be monitored through the trajectories in the exchanges of scientists and citizens – learning and adapting dynamically in situated knowledge ecosystems.", "appendix": "Data and software availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nEarlier versions of this work were presented in the 2023 Eu-SPRI conference, the 2023 STI Indicators Conference, and as an LSE Blog post. We are grateful for fruitful exchanges with colleagues in these events, in particular in discussions in the UNESCO Working Group on Monitoring OS, with special thanks to UNESCO OS team (Ana Peršić, Fereshteh Rafieian and Tiffany Straza). We also thank Valeria Arza, Anestis Amanatidis, André Brasil, Louise Bezuidenhout, Diana Hicks, Thed van Leeuwen, Matías Milia, Alex Rushforth, Jonas Torrens, Vincent Traag, Harald Wieser, Iris Wanzenböck and Ludo Waltman for fruitful discussions.\n\n\nReferences\n\nAlbornoz D, Hillyer B, Posada A, et al.: Principles for an Inclusive Open Science: The OCSDNet Manifesto.Chan IL, Okune A, Hillyer B, et al., editors. Contextualizing Openness: Situating Open Science. University of Ottawa Press; 2020; pp. 23–50.\n\nArocena R, Sutz J: Weak knowledge demand in the South: Learning divides and innovation policies. Sci. Public Policy. 2010; 37(8): 571–582. Publisher Full Text\n\nArundel A, Bloch C, Ferguson B: Advancing innovation in the public sector: Aligning innovation measurement with policy goals. Res. Policy. 2019; 48(3): 789–798. Publisher Full Text\n\nArundel A, Smith K: History of the community innovation survey.Gault F, editor. Handbook of innovation indicators and measurement. Edward Elgar Publishing; 2013; pp. 60–87.\n\nArza V, Fressoli M: Benefits of Open Science: An Analytical Framework Illustrated with Case Study Evidence from Argentina. Expanding Perspectives on Open Science: Communities, Cultures and Diversity in Concepts and Practices. Proceedings of the 21st International Conference on Electronic Publishing. IOS Press; 2017.\n\nArza V, Fressoli M, Lopez E: Ciencia abierta en Argentina: Un mapeo de experiencias actuales. Ciencia, Docencia y Tecnología. 2017; 55: 78–114.\n\nBabini D: La comunicación científica en América Latina es abierta, colaborativa y no comercial. Desafíos para las revistas. Palabra Clave (La Plata). 2019; 8(2): e065. Publisher Full Text\n\nBarre R: Towards socially robust ST indicators: Indicators as debatable devices, enabling collective learning. Res. Eval. 2010; 19(3): 227–231. Publisher Full Text\n\nBell M, Pavitt K: The development of technological capabilities. Trade, Technology and International Competitiveness. 1995; 22(4831): 69–101.\n\nBezuidenhout L, Chakauya E: Hidden concerns of sharing research data by low/middle-income country scientists. Glob. Bioeth. 2018; 29(1): 39–54. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBezuidenhout L, Havemann J: The varying openness of digital open science tools. F1000Res. 2020; 9: 1292. Publisher Full Text\n\nBezuidenhout LM, Leonelli S, Kelly AH, et al.: Beyond the digital divide: Towards a situated approach to open data. Sci. Public Policy. 2017; 44(4): 464–475. Publisher Full Text\n\nBloch C: Assessing recent developments in innovation measurement: The third edition of the Oslo Manual. Sci. Public Policy. 2007; 34(1): 23–34. Publisher Full Text\n\nCallon M: Is Science a Public Good? Fifth Mullins Lecture, Virginia Polytechnic Institute, 23 March 1993. Sci. Technol. Hum. Values. 1994; 19(4): 395–424. Publisher Full Text\n\nCarroll SR, Garba I, Figueroa-Rodríguez OL, et al.: The CARE Principles for Indigenous Data Governance. Data Sci. J. 2020; 19: 43. Publisher Full Text\n\nChan L, Okune A, Hillyer B, et al.: Contextualizing Openness: Situating Open Science. University of Ottawa Press; 2020.\n\nChavarro D, Tang P, Ràfols I: Why researchers publish in non-mainstream journals: Training, knowledge bridging, and gap filling. Res. Policy. 2017; 46(9): 1666–1680. Publisher Full Text\n\nCiarli T: Changing Directions: Steering science, technology and innovation towards the Sustainable Development Goals. University of Sussex; 2022. Publisher Full Text\n\nCohen WM, Levinthal DA: Absorptive Capacity: A New Perspective on Learning and Innovation. Adm. Sci. Q. 1990; 35(1): 128–152. Publisher Full Text\n\nCole NL, Reichmann S, Ross-Hellauer T: The potential of inclusive and collaborative Open Research processes at the science-policy interface [Preprint]. SocArXiv.2023. Publisher Full Text\n\nDai Q, Shin E, Smith C: Open and inclusive collaboration in science: A framework (OECD Science, Technology and Industry Working Papers 2018/07; OECD Science, Technology and Industry Working Papers.2018; Vol. 2018/07. Publisher Full Text\n\nDavies SW, Putnam HM, Ainsworth T, et al.: Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science. PLoS Biol. 2021; 19(6): e3001282. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nD’Este P, Patel P: University–industry linkages in the UK: What are the factors underlying the variety of interactions with industry? Res. Policy. 2007; 36(9): 1295–1313. Publisher Full Text\n\nDíaz-Faes AA, Bowman TD, Costas R: Towards a second generation of ‘social media metrics’: Characterizing Twitter communities of attention around science. PLoS One. 2019; 14(5): e0216408. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDíaz-Faes AA, Llopis O, D’Este P, et al.: Assessing the variety of collaborative practices in translational research: An analysis of scientists’ ego-networks. Res. Eval. 2023; 32(2): 426–440. Publisher Full Text\n\nDosemagen S, Williams E: Data Usability: The Forgotten Segment of Environmental Data Workflows. Front. Clim. 2022; 4: 785269. Publisher Full Text\n\nDouglas M: How institutions think. Syracuse University Press; 1986.\n\nEuropean Commission: Open Innovation, Open Science, Open to the World: A Vision for Europe. European Commission; 2016. Reference Source\n\nFecher B, Friesike S: Open Science: One term, five schools of thought.Bartling S, Friesike S, editors. Opening Science. Springer International Publishing; 2014. Publisher Full Text\n\nFinnemore M: International organizations as teachers of norms: The United Nations Educational, Scientific, and Cutural Organization and science policy. Int. Organ. 1993; 47(4): 565–597. Publisher Full Text\n\nGault F: Measuring Innovation Everywhere. Edward Elgar Publishing; 2020. Publisher Full Text\n\nGibbons M: Science’s new social contract with society. Nature. 1999; 402: c81–c84. Publisher Full Text\n\nGodin B: Measurement and Statistics on Science and Technology. Routledge; 0th ed2004. Publisher Full Text\n\nGault F: The Oslo Manual.Gault F, editor. Handbook of innovation indicators and measurement. Edward Elgar Publishing; 2013; pp. 41–59.\n\nHaddad CR, Bergek A: Towards an integrated framework for evaluating transformative innovation policy. Res. Policy. 2023; 52(2): 104676. Publisher Full Text\n\nHoltrop T, Meijer I, Otero-Hermida P, et al.: Translating between diverse stakeholders in regional RRI projects. Fteval Journal. 2022; 53: 77–84. Publisher Full Text\n\nHuang C-K, Neylon C, Montgomery L, et al.: Open access research outputs receive more diverse citations. Scientometrics. 2024; 129: 825–845. Publisher Full Text\n\nISC: Open Science for a Global Transformation. Committe on Data (CODATA), International Science Council; 2020.\n\nJanssen MJ, Bergek A, Wesseling JH: Evaluating systemic innovation and transition programmes: Towards a culture of learning. PLOS Sustainability and Transformation. 2022; 1(3): e0000008. Publisher Full Text\n\nKline SJ, Rosenberg N: An overview of innovation.Edquist C, McKelvey M, editors. Systems of innovation: Growth, competitiveness and employment. Edward Elgar; 1986; pp. 3–33.\n\nKofler J, Wieser H: Navigating transitions: A ‘reflexive navigation system’ for monitoring and learning in mission-oriented innovation policies. Eu-SPRI Conference. Brighton, UK: 2023.\n\nKozlowski D, Larivière V, Sugimoto CR, et al.: Intersectional inequalities in science. Proc. Natl. Acad. Sci. 2022; 119(2): e2113067119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLarivière V, Haustein S, Mongeon P: The Oligopoly of Academic Publishers in the Digital Era. PLoS One. 2015; 10(6): e0127502. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLawson C, Salter A, Hughes A, et al.: Citizens of somewhere: Examining the geography of foreign and native-born academics’ engagement with external actors. Res. Policy. 2019; 48(3): 759–774. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeach M, Scoones I, Stirling A: Dynamic sustainabilities: Technology, environment, social justice. Earthscan; 2010.\n\nLeonelli S: Philosophy of Open Science. 1st ed.Cambridge University Press; 2023. Publisher Full Text\n\nLoorbach DA, Wittmayer J: Transforming universities: Mobilizing research and education for sustainability transitions at Erasmus University Rotterdam, The Netherlands. Sustain. Sci. 2024; 19(1): 19–33. Publisher Full Text\n\nMaricato J d M, Mazoni A, Mugnaini R, et al.: SciELO as an open scientometric research infrastructure: General discussion of coverage in OpenAlex, WoS, Scopus and Dimensions. S&T Indicators Conference.\n\nMazzucato M: Mission-oriented innovation policies: Challenges and opportunities. Ind. Corp. Chang. 2018; 27(5): 803–815. Publisher Full Text\n\nMéndez E: Open Science por defecto. La nueva normalidad para la investigación. Arbor. 2021; 197(799): a587. Publisher Full Text\n\nMolas-Gallart J, Boni A, Giachi S, et al.: A formative approach to the evaluation of Transformative Innovation Policies. Res. Eval. 2021; rvab016. Publisher Full Text\n\nMolas-Gallart J, D’Este P, Llopis O, et al.: Towards an alternative framework for the evaluation of translational research initiatives. Res. Eval. 2016; 25(3): 235–243. Publisher Full Text\n\nMolas-Gallart J, Rafols I: Why bibliometric indicators break down: Unstable parameters, incorrect models and irrelevant prope. BiD: Textos Universitaris de Biblioteconomia i Documentació. 2018; 2018: 40. Publisher Full Text\n\nMolas-Gallart J, Salter A, Patel P, et al.: Measuring third stream activities. Final Report to the Russell Group of Universities. Brighton: SPRU, University of Sussex; 2002.\n\nMongeon P, Paul-Hus A: The journal coverage of Web of Science and Scopus: A comparative analysis. Scientometrics. 2016; 106(1): 213–228. Publisher Full Text\n\nNielsen M: Reinventing Discovery: The New Era of Networked Science. Princeton University Press; 2011.\n\nNowotny H, Scott P, Gibbons M: Introduction. ‘Mode 2’ Revisited: The New Production of Knowledge. Minerva. 2003; 41(3): 179–194. Publisher Full Text\n\nNoyons E, Rafols I: Can bibliometrics help in assessing societal contributions of agricultural research? Exploring societal interactions across research areas. Proceedings of the 23rd International Conference on Science and Technology Indicators. 2018; pp. 1049–1057.\n\nOECD: Frascati Manual 2015: Guidelines for Collecting and Reporting Data on Research and Experimental Development. OECD; 2015. Publisher Full Text\n\nOECD: OECD Science, Technology and Innovation Outlook 2023: Enabling Transitions in Times of Disruption. OECD; 2023. Publisher Full Text\n\nOECD & Eurostat: Oslo Manual 2018: Guidelines for Collecting, Reporting and Using Data on Innovation. 4th Edition.OECD; 2018. Publisher Full Text\n\nOlejniczak AJ, Wilson MJ: Who’s writing open access (OA) articles? Characteristics of OA authors at Ph.D.-granting institutions in the United States. Quant. Sci. Stud. 2020; 1(4): 1429–1450. Publisher Full Text\n\nOllé C, López-Borrull A, Melero R, et al.: Habits and perceptions regarding open science by researchers from Spanish institutions. PLoS One. 2023; 18(7): e0288313. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOwen R, Macnaghten P, Stilgoe J: Responsible research and innovation: From science in society to science for society, with society. Sci. Public Policy. 2012; 39(6): 751–760. Publisher Full Text\n\nPurnell PJ: A comparison of different methods of identifying publications related to the United Nations Sustainable Development Goals: Case study of SDG 13—Climate Action. Quant. Sci. Stud. 2022; 3(4): 976–1002. Publisher Full Text\n\nRàfols I: S&T indicators in the wild: Contextualization and participation for responsible metrics. Res. Eval. 2019; 28(1): 7–22. Publisher Full Text\n\nRafols I, Leydesdorff L, O’Hare A, et al.: How journal rankings can suppress interdisciplinary research: A comparison between Innovation Studies and Business & Management. Res. Policy. 2012; 41(7): 1262–1282. Publisher Full Text\n\nRafols I, Stirling A: Designing indicators for opening up evaluation: Insights from research assessment.Dahler-Larsen P, editors. A research agenda for evaluation. Edward Elgar; 2021. Publisher Full Text Reference Source\n\nRohracher H, Coenen L, Kordas O: Mission incomplete: Layered practices of monitoring and evaluation in Swedish transformative innovation policy. Sci. Public Policy. 2023; 50: 336–349. Publisher Full Text\n\nRoss-Hellauer T, Deppe A, Schmidt B: Survey on open peer review: Attitudes and experience amongst editors, authors and reviewers. PLoS One. 2017; 12(12): e0189311. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoss-Hellauer T, Reichmann S, Cole NL, et al.: Dynamics of cumulative advantage and threats to equity in open science: A scoping review. R. Soc. Open Sci. 2022; 9: 211032. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRottenburg R, Merry SE: A World of Indicators. The Making of Governmental Knowledge through Indicators. The world of indicators: The making of governmental knowledge through quantification. Cambridge University Press; 2015; pp. 1–33.\n\nSalö L, Hammarfelt B, Nelhans G: Sources of policy: Knowledge brokering in governmental reports.Mattsson IP, Perez Vico E, Salö L, editors. Making universities matter: Collaboration, engagement, impact. Springer Nature; 2023; pp. 185–210. Publisher Full Text\n\nSchneider JW, Allum N, Andersen JP, et al.: Is something rotten in the state of Denmark? Cross-national evidence for widespread involvement but not systematic use of questionable research practices across all fields of research. [Preprint]. MetaArXiv. 2023. Publisher Full Text\n\nSchot J, Steinmueller WE: Three frames for innovation policy: R&D, systems of innovation and transformative change. Res. Policy. 2018; 47(9): 1554–1567. Publisher Full Text\n\nShelley-Egan C, Gjefsen MD, Nydal R: Consolidating RRI and Open Science: Understanding the potential for transformative change. Life Sci. Soc. Policy. 2020; 16(1): 7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShibayama S, Walsh JP, Baba Y: Academic Entrepreneurship and Exchange of Scientific Resources: Material Transfer in Life and Materials Sciences in Japanese Universities. Am. Sociol. Rev. 2012; 77(5): 804–830. Publisher Full Text\n\nSingh VK, Singh P, Karmakar M, et al.: The journal coverage of Web of Science, Scopus and Dimensions: A comparative analysis. Scientometrics. 2021; 126(6): 5113–5142. Publisher Full Text\n\nSmith K: Measuring innovation.Fagerberg J, Mowery DC, Nelson RR, editors. The Oxford handbook of innovation. Oxford University Press; 2004; pp. 148–177.\n\nStirling A: ‘Opening Up’ and ‘Closing Down’: Power, Participation, and Pluralism in the Social Appraisal of Technology. Sci. Technol. Hum. Values. 2008; 33(2): 262–294. Publisher Full Text\n\nStirling A: Pluralising progress: From integrative transitions to transformative diversity. Environ. Innov. Soc. Trans. 2011; 1(1): 82–88. Publisher Full Text\n\nStirling A: How deep is incumbency? A ‘configuring fields’ approach to redistributing and reorienting power in socio-material change. Energy Res. Soc. Sci. 2019; 58: 101239. Publisher Full Text\n\nStirling A: Against misleading technocratic precision in research evaluation and wider policy – A response to Franzoni and Stephan (2023), ‘uncertainty and risk-taking in science’. Res. Policy. 2023; 52(3): 104709. Publisher Full Text\n\nSugimoto CR, Larivière V: Equity for Women in Science: Dismantling Systemic Barriers to Advancement. Harvard University Press; 2023.\n\nThune T, Reymert I, Gulbrandsen M, et al.: Populating the science-policy co-production space: Academic and policymaker perspectives on knowledge exchange. Stud. High. Educ. 2023; 48(5): 733–746. Publisher Full Text\n\nTijssen RJW: Universities and industrially relevant science: Towards measurement models and indicators of entrepreneurial orientation. Res. Policy. 2006; 35(10): 1569–1585. Publisher Full Text\n\nUNESCO: UNESCO Recommendation on Open Science. UNESCO; 2021. Publisher Full Text\n\nUNESCO: Open science outlook 1: Status and trends around the world. UNESCO; 2023. Publisher Full Text\n\nVan Mierlo B, Arkesteijn M, Leeuwis C: Enhancing the Reflexivity of System Innovation Projects With System Analyses. Am. J. Eval. 2010; 31(2): 143–161. Publisher Full Text\n\nWeber KM, Rohracher H: Legitimizing research, technology and innovation policies for transformative change. Res. Policy. 2012; 41(6): 1037–1047. Publisher Full Text\n\nWilkinson MD, Dumontier M, Aalbersberg IJ, et al.: The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016; 3(1): 160018. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWouters P, Rafols I, Oancea A, et al.: Indicator frameworks for fostering open knowledge practices in science and scholarship.European Commission Directorate General for Research and Innovation. Publications Office; 2019. Publisher Full Text\n\n\nFootnotes\n\n1 https://research-and-innovation.ec.europa.eu/strategy/strategy-2020-2024/our-digital-future/open-science/open-science-monitor_en\n\n2 https://frenchopensciencemonitor.esr.gouv.fr/software/general\n\n3 https://avointiede.fi/en/policies-materials/monitoring\n\n4 https://eoscobservatory.eosc-portal.eu/home\n\n5 https://unesdoc.unesco.org/ark:/48223/pf0000383805\n\n6 It should be noted that the breadth of the concept of science is ambiguous. In accordance with most science policy, here we take a broad definition: we use it for all scholarly disciplines including social science and humanities, as well as research activities outside of academia. We would prefer using the terms research and open research, but we keep the term science in order to align with current policy discourse on OS.\n\n7 While their framing in terms the five schools is possibly outdated, it illustrates that very disparate understandings on OS have long existed.\n\n8 The recent addition of ‘trust in science’ shows again the political nature of the definition of OS, now a major issue following the battle for public confidence in COVID-19 responses.\n\n9 A more inclusive science should be more less concentrated in rich nations and rich cities (Ciarli, 2022; UNESCO, 2023, p. 36).\n\n10 See for example, the description of ‘U.S. and Global Science and Technology Capabilities’ in the Science and Engineering 2022 report.\n\n11 The Oslo manual (as the Frascati) has undergone various revisions. For example the definition of innovation has broadened from only technological product and process innovation in the first edition (1992), to include also non-technological products and processes, new marketing methods, or a new organization method in business practices, workplace organization or external relations, in the third edition in 2005. Also, an annex was added to the Oslo Manual in 2005 for its use in developing countries, after the experience provided by the Ibero-American Network of Indicators of S&T (RICYT) in Bogotá Manual (Gault, 2013, p. 51). In recent years, proposal have been made to include public sector innovations (which are not counted currently since they are not market-oriented), social and household innovations and innovations in the informal sector (Gault, 2020). Similarly, the battery of indicators of the Innovation Scoreboard has evolved over time – for example, with the introduction of indicators of environmental sustainability in recent years (which is a hint of a shift towards frame 3).\n\n12 We thank Anestis Amanatidis for suggesting this point.\n\n13 https://unesdoc.unesco.org/ark:/48223/pf0000386862\n\n14 Here it should be noted that, if inclusiveness or integrity are considered to be instrumental properties (rather than a value in itself ), then they will be considered a change in practice (an outcome) that is expected to contribute to higher order values (for instance by contributing to the achievement of social goals).\n\n15 After Tommaso Di Lampedusa, the author of the novel The Leopard which describes how the old Sicilian aristocracy preserved their power through the unification of Italy and the ascent of capitalism: ‘Everything must change for everything to remain the same’.\n\n16 https://datacite.org/ see UNESCO Outlook (UNESCO, 2023a, p. 40)." }	[ { "id": "282406", "date": "05 Jun 2024", "name": "Hans De Jonge", "expertise": [ "Reviewer Expertise Open Science", "monitoring" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this opinion article the authors argue that the way open science is being monitored is in need of a fundamental revision. Traditional open science monitors have very much focused on outputs using quantitative approaches: analyzing the number of open access publications over time. More recently, these reports have been complemented with attempts to monitor open availability of research data and code / software. The authors – in my view, rightly – argue that these narrow approaches can lead to streetlight effects (counting what can be counted) and misrepresentation of the much broader open science agenda as systematic transformation of the research system. Informed by the literature about Transformative Innovation Policies the authors call for a shift along three lines:\n\nThe dimension of monitoring should be broadened as to include not only (more) outputs but also processes, outcomes and impacts. Open Science monitoring exercises should be more directed towards learning instead of only accountability and benchmarking. Monitoring should open up by making visible the ‘directionality’, especially the problematic sometimes unintended consequences of certain choices.\n\nGiven the enormous proliferation OS monitoring worldwide I think the authors view is very valuable and topical. The article is well structured and overall, well written (see editorial notes below) and is very well supported by the most recent literature on the topic.\nI have only a few comments and leave it to the authors to take them into consideration or discard them.\n\nDirectionality.\n\nI struggled with the concept of directionality. It is only very briefly introduced in the abstract and the introduction (p. 4) and again on p. 10. but for me not to an extend that I understood what was meant by it. I didn’t find the examples (“e.g. different colour of the routes to OS”) very helpful. Only on p. 16 the authors explain that directionality means that in the adoption of certain OS practices different choices (trajectories) can be made, that some of these trajectories can have unintended consequences or even outcomes that are outright in conflict with the values of open science (three examples are given that conflict with the equity value). I completely concur with the authors that being open to negative, unintended or conflicting consequences need to part of a more comprehensive open science monitoring but I think some readers might need some help in understanding this point throughout the article.\n\nSchools of thought\nI am very happy to see that the authors take the effort of making clear that Open Science is a very broad concept which encompasses a multitude of activities, practices and agendas. In that context reference is being made to the seminal work of Fecher and Friesike who have argued that under the broader umbrella term of Open Science five schools of thought can be distinguished. Each school has its own focus, depending on what each school thinks is the most pressing problem in the current science system. While I applaud the authors for emphasizing the plurality of the Open Science movement, I cannot completely escape the impression that they themselves feel more closely associated with one particular school (the public school) and less with others, leading to – in my view - a somewhat narrow definition of what Open Science is aiming for. Two examples to make this clear.\n\nFirst, when arguing that monitoring should not only focus on policies and outputs but also on processes and outcomes, this is consistently illustrated by the authors with examples from the intended ‘societal’ benefits of OS: OS leading to more citizen engagement, researchers more focusing on societal problems, more participatory events, open engagement and dialogue with non-academic actors. (Also in figure 5 and table 1 outcomes and impacts of OS are only defined in terms of societal benefits). While I agree that these are very important objectives of OS, I do not think they are the only ones. Much of what is being done in Open Science is – I would argue – to improve to research process itself. To make science more transparent, more reproducible, more efficient, more interoperable, the dissemination more quick and efficient. All to ensure the quality of science increases and trust in science (by scientists and society) increases. This notion that one of the intended and hoped for outcomes of Open Science is increased quality and integrity is markedly missing from the narrative of the authors, although quality and integrity is the first of the 4 values mentioned by UNESCO and the authors stress the importance to focus monitoring OS on these UNESCO values. A dimension that is – in my view - also somewhat under represented is that one of the ‘collective benefits’ of Open Science is its potential economic impact. Although I agree, that many of the initial aspirations (for instance the Budapest Declaration) were to do with global equity and fair participation of underrepresented parts of the world in the research system, one cannot deny, that a lot of the policy debates around open science are motivated by considerations around unlocking publicly funded research for innovation, knowledge transfer and economic growth. Indeed, much of the early government support for Open Access in countries like the NLs and the UK were motivated by Open Science as potential driver for economic impact. Apart from the quality/trust motivation, this economic dimension is also absent from the authors narrative.\n\nI would encourage the authors to think of their own position in the ‘five schools of thought’ and consider whether in presenting examples of how to monitor OS outcomes and OS impacts they have struck the right balance. Do these examples cover the broadness of the Open Science agenda and the plurality of activities, practices and motivations that are currently covered by Open Science?\n\nUNESCO survey\nThe work of this opinion article is being done as the result of the authors’ engagement with the UNESCO working group on Open Science monitoring. The authors present a very interesting framework for future Open Science monitoring which is much more comprehensive and systematic in nature than much of the older monitoring exercises. For the moment, however, it seems that UNESCO has not chosen to adopt this model, which – to me at least – feels like a missed opportunity. Instead, UNESCO will put out a survey which – at this stage at least – will focus on supporting actions taken by member states to foster open science. I would be interested to learn the authors view on this decision and since this is an opinion article encourage to take a more critical stance, maybe as part of footnote 13.\nMinor issue:\nSince the writing of this article an important initiative has been launched to support the move towards open bibliometric metadata: the Barcelona Declaration. This is at least partly motivated by the increase in open science monitoring activities and the importance to base these monitors on open instead of proprietary data. The authors might consider referring to this initiave as part of paragraph 5.1 (p.12).\nEditorial:\nChange ‘gathering statistics’ to ‘collecting statistics’ p. 3\nChange ‘this study is prompted’ by ‘this article is prompted’ p. 3\nChange ‘for addressing of societal problems’ to ‘for addressing societal problems’\nChange ‘the one concerned with’ to ‘one concerned with’ p. 9\nChange ‘FAIRisation’ to ‘FAIRification’ p.12\nChange ‘most commercial databased of across countries’ to ‘most commercial databased across countries’\nElaborate this statement: ‘The tracking of open research data, open educational resources, open software, and open hardware is patchy but illustrative of growing efforts (UNESCO, 2023, pp. 40–42), although the estimates of numbers of datasets, scripts or courses as general indicators is problematic given the large difference in size and efforts invested per unit’. I don’t understand the problem.\nTable 1 p. 11 Change ‘Extracted from ORCID’ – I am not sure what is meant. The French OS monitor can be found online.\nTabel 1 p. 11 ‘Integrity practices’ – consider ‘Open methods’ as an umbrella term for all methods like preregistration, open reporting, registered reports, etc.\nChange ‘(in the sense more’ to ‘(in the sense of more’ p. 13\nChange ‘publishing in Spanish in non-OA professional newsletter’ to ‘publishing in Spanish in a non-OA professional newsletter’ p. 13\nReview this sentence: ‘let us emphasize here that for the benefits do not just lie on the amount of interaction and usage, but on the distributions across epistemic and geographical spaces’ p. 13.\n\n> ‘for’ seems to be not right here?\nRewrite ‘even more if green OA’ > too informal?\nChange ‘IS’ to ‘ OS’ p. 14\nChange ‘impacts refer the values’ to ‘impacts refer to the values’ p. 14\nConsider to further support the suggestion: ‘As potential dimensions of impact of OS, we propose those dimensions in the values of the UNESCO OS Recommendation,’ p. 14\nReview quotation ‘to contribute to system innovation the central goal’ p. 14 > word seems missing. Innovation ‘as’?\nChange ‘As put by the in the UNESCO OS Outlook’ to ‘ As put in the UNESCO OS Outlook’ or even ‘As argued by UNESCO OS Outlook’ p.15\nChange ‘By ‘broadening out’ the type of issues to type of OA’ to ‘By ‘broadening out’ to type of OA’ p. 15\nChange ‘pol-icy’ to ‘policy’ p.16\nExplain ‘A frame 3 perspective’ p.16\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [] }, { "id": "282405", "date": "06 Jun 2024", "name": "Francesca Di Donato", "expertise": [ "Reviewer Expertise Political philosophy", "Open science", "Research on research" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article first discusses the plural understandings of Open Science (OS), focusing on the OS definition provided by the UNESCO Recommendation of 2021, endorsed by 193 countries, which provides the most complex yet inclusive definition available. This definition implies a shift from an understanding of OS as the ‘possibility of access’ towards an understanding as the ‘process of connection’ in accordance with values related to integrity and epistemic justice.\n\nBased on this premise, the article makes the case that OS is a systemic transformation of research in all its dimensions (social, epistemic, institutional, organisational and geographical). It then reviews how models of science are associated with particular monitoring frameworks, considering several lessons learnt from the existing ones and how they complement each other, and it specifically focuses on the frame known as Transformative Innovation Policy (TIP), which shifts the focus towards innovation for transformative change in socio-technical systems such as those of energy, mobility or health, particularly to address societal challenges.\n\nFurthermore, the paper describes concepts that can be useful for monitoring OS as a transformation, suggesting a shift in monitoring frameworks for OS towards three directions, aimed at adopting: (i) a systemic perspective, switching from an outputs oriented perspective towards a wider one, focusing on policies and outputs, processes, outcomes and impacts; (ii) a learning approach to monitoring, i.e. helping taking decision considering diverse options within OS; (ii) and a directional perspective, which considers the different trajectories within OS dimensions and the associated values and potential effects.\n\nThe opinion article is based on a very accurate analysis of the current literature, including a documented literature analysis which supports the developed arguments; in particular, all factual statements are adequately supported by citations, and the conclusions are on these basis fully justified.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-320
https://f1000research.com/articles/13-318/v1	23 Apr 24	{ "type": "Genome Note", "title": "Two draft genomes of enigmatic Solenogastres (Mollusca, Aplacophora) Epimenia babai and Neomenia megatrapezata", "authors": [ "Meghan K. Yap-Chiongco", "Stacy Pirro", "Rebecca M. Varney", "Hiroshi Saito", "Kenneth M. Halanych", "Kevin M. Kocot", "Meghan K. Yap-Chiongco", "Stacy Pirro", "Rebecca M. Varney", "Hiroshi Saito", "Kenneth M. Halanych" ], "abstract": "Abstract* Many molluscan genomes have been published to date, however only three are from representatives of the subphylum Aculifera (Polyplacophora, Caudofoveata, and Solenogastres), the sister taxon to all other molluscs. Currently, genomic resources are completely lacking for Solenogastres. This gap in knowledge hinders comparative and evolutionary studies. Here, we sequenced the genomes of the solenogaster aplacophorans Epimenia babai Salvini-Plawen, 1997 and Neomenia megatrapezata Salvini-Plawen & Paar-Gausch, 2004 using a hybrid approach combining Oxford Nanopore and Illumina reads. For E. babai, we produced a 628 Mbp haploid assembly (N50 = 413 Kbp, L50 = 370) that is rather complete with a BUSCO completeness score of 90.1% (82.0% single, 8.1% duplicated, 6.0% fragmented, and 3.9% missing). For N. megatrapezata, we produced a 412 Mbp haploid assembly (N50 = 132 Kbp, L50 = 881) that is also rather complete with a BUSCO completeness score of 85.1% (81.7% single, 3.4% duplicated, 8.1% fragmented, and 6.8% missing). Our annotation pipeline predicted 25,393 gene models for E. babai with a BUSCO score of 92.4% (80.5% single, 11.9% duplicated, 4.9% fragmented, and 2.7% missing) and 22,463 gene models for N. megatrapezata with a BUSCO score of 90.2% (81.0% single, 9.2% duplicated, 4.7% fragmented, and 5.1% missing). Phylogenomic analysis recovered Solenogastres as the sister taxon to Polyplacophora and Aculifera as the sister taxon to all other sampled molluscs with maximal support. These represent the first whole-genome resources for Solenogastres and will be valuable for future studies investigating this understudied group and molluscan evolution as a whole.", "keywords": [ "Aculifera", "Aplacophora", "Solenogastres", "genome" ], "content": "Introduction\n\nWith their incredible diversity in morphology, life history and ecology, molluscs are of great interest to diverse fields of biology ranging from ecology to evolutionary developmental biology to biomechanics. To date there are high-quality genomes available for six of the eight molluscan classes publicly available, although sampling is heavily biased toward the economically and ecologically important members of the clade Conchifera (e.g. Gastropoda, Bivalvia and Cephalopoda; reviewed by Gomes-dos-Santos et al. 2020 and Sigwart et al. 2021). As the sister taxon to all other molluscs, the clade Aculifera (Polyplacophora + Aplacophora) is important to our understanding of molluscan evolution and innovation. Despite their importance, only three aculiferan genomes have been published to date, two species of chitons (Polyplacophora; Varney et al. 2021; Varney and Yap-Chiongco et al. 2022) and one species of Caudofoveata (Wang et al. 2024). Therefore, we sequenced the genomes of two species of Solenogastres – Neomenia megatrapezata Salvini-Plawen & Paar-Gausch 2004 and Epimenia babai Salvini-Plawen, 1997 – to facilitate further study of this evolutionarily important taxon.\n\nThe two clades of aplacophoran molluscs are united by their distinctive vermiform shape, loss or reduction of the foot, and a chitinous cuticle covered by calcareous integumental spines and scales (sclerites). Solenogastres are distinctive with the presence of a ciliated foot restricted to a ventral groove, an undifferentiated gut, and the lack of true ctenidia, while members of Caudofoveata lack a foot entirely and have the presence of a specialized oral shield used for burrowing in mud (Todt 2013). The current taxonomy of Solenogastres divides the group into 24 families and four orders (Pholidoskepia, Cavibelonia, Sterrofustia, and Neomeniamorpha) although recent phylogenomic analyses have indicated the need for significant taxonomic revision within this group (Kocot et al. 2019; Yap-Chiongco et al. 2024).\n\nWhereas most solenogasters are just a few millimeters in length (Todt 2013) both N. megatrapezata and E. babai are large enough to obtain high-quality genomic and transcriptomic data from a single individual. E. babai is a species of Cavibelonia that is relatively easily collected at SCUBA-accessible depths where it feeds on the soft coral Scleronephthya gracillima (Okusu 2002). Because of its relatively large-body size (up to 20 cm in length) and reliable spawning within the laboratory, E. babai remains one of very few species of Solenogastres in which development has been described (Baba 1938, 1940, 1951; Okusu, 2002; Todt and Wanninger 2010). Sequencing of its genome coupled with characterized development and reliability of spawning make E. babai a desirable species to serve as a developmental model within Solenogastres. N. megatrapezata (up to 18 cm in length) is a species of Neomeniamorpha found in the Southern Ocean off Antarctica (Salvini-Plawen & Paar-Gausch 2004; Kocot et al. 2019). Neomenia is interesting to study trait evolution within Solenogastres as species within this genus have a complex accessory genital apparatus and lack both ventral foregut glands and a radula (García-Álvarez & Salvini-Plawen 2007). Together, the sequencing of these two species expands our ability to explore solenogaster evolution and, more broadly, provides an important resource in identifying large-scale patterns in molluscan evolution.\n\n\nMethods\n\nEpimenia babai was collected by Akiko Okusu as described in Okusu (2002). The specimen of Neomenia megatrapezata (collector number Ap227) used for genome and transcriptome sequencing was collected by Ken Halanych and Kevin Kocot on 3 February 2013 near the Ross Ice Shelf in Antarctica (NBP12-10 Station 22; 76° 59.8965′ S, 175° 05.5920′ W, 541 m depth) via Blake trawl and is deposited in the Alabama Museum of Natural History (ALMNH) under catalog number ALMNH:Inv:25736.\n\nAdditional solenogasters were used for transcriptome sequencing to provide evidence for genome annotation. A second individual of N. megatrapezata (Ap259) was collected by Ken Halanych and Kevin Kocot on 28 November 2013 near Recovitza Island, Antarctica (LMG13-12 Station 2; 64° 24.672′ S, 61° 57.790′ W, 664 m depth) via Blake trawl. A second individual from the same collection event has been deposited in ALMNH under catalog number ALMNH:Inv:25732 as a voucher. A specimen of Neomenia aff. herwigi (Ap20; same individual used to generate a 454 transcriptome by Kocot et al. 2011; NCBI SRA accession number SRR108985) was collected by Ken Halanych on 6 December 2004 off Argentina (63°23′ 03.0″ S, 60° 03′ 24.0″ W, 277 m depth) via Blake trawl. A specimen of Neomenia permagna (Ap26) was collected on 15 May 2006 by Ken Halanych off Argentina (LMG06-05; 53°47′ S, 60°42′ W; 170 m depth) via Blake trawl and is deposited in ALMNH under catalog number ALMNH:Inv:25733. A specimen of an unidentified species of Epimenia (possibly also E. babai) was collected on 29 June 2015 by Hiroshi Saito off Osezaki, Japan (55 m depth) by SCUBA diving and a tissue sample is deposited in ALMNH under catalog number ALMNH:Inv:25734.\n\nTo produce short-read genomic data, DNA was extracted using the CTAB-phenol-chloroform method employed by Varney et al. (2021), which was based on Doyle & Doyle (1991). For E. babai, DNA was extracted from a piece of midbody tissue and sent to Iridium Genomics for Illumina TruSeq sequencing library preparation and 2 X 100 bp paired-end (PE) sequencing on an Illumina HiSeq X. For N. megatrapezata, DNA was extracted from hemolymph and sent to the NY Genome Center for Illumina TruSeq sequencing library preparation and sequencing on an Illumina HiSeq X.\n\nTo produce long-read data via Oxford Nanopore sequencing, a library for N. megatrapezata was produced from DNA extracted from haemolymph using a CTAB-phenol-chloroform method following Varney et al. (2021). For the three libraries for E. babai and the second library for N. megatrapezata, genomic DNA was extracted from cryo-preserved tissue using the EZNA Tissue DNA Kit (Omega Bio-tek) followed by cleaning and size selection for high-molecular-weight fragments with Ampure XP beads. Sequencing libraries were prepared with the LSK-109 ligation-based library preparation kit and sequenced in-house using R9.4.1RevD flow cells on a GridION. Reads were base called with Guppy 4.0 and trimmed with PoreChop (Wick 2018) with the --discard_middle flag.\n\nNew transcriptome data were generated from the same individual used for WGS for each species and from other individuals of the same or closely related species for genome annotation. For E. babai, Epimenia sp., Neomenia aff. herwigi, and Neomenia permagna, RNA was extracted as described by Kocot et al. (2019). RNA concentration was measured using a Qubit 3.0 (Thermo Fisher) fluorometer with the RNA High Sensitivity kit, RNA purity was assessed by measuring the 260/280 nm absorbance ratio using a Nanodrop Lite (Thermo Fisher), and RNA integrity was evaluated using a 1% SB agarose gel. Complementary DNA (cDNA) synthesis was performed using 1 ng of total RNA using the Clontech SMART-Seq HT kit. An Illumina sequencing library was then prepared in house using the Nextera XT DNA Library Preparation Kit with 0.15 ng of cDNA. Final library size and concentration were assessed using an Agilent Fragment Analyzer with the NGS 1-6000 bp kit and sent to Psomagen (Cambridge, MA) for sequencing on an Illumina NovaSeq using a S4 flowcell with 2 X 150 bp PE reads. For N. megatrapezata, RNA was extracted from the individual used for genome sequencing (Ap227) and a second individual (Ap259) as described in Kocot et al. (2019) and sent to the High-Throughput Genomics Shared Resource of the Huntsman Cancer Institute at the University of Utah for Illumina TruSeq Stranded mRNA Sample Prep Kit with oligo (dT) selection. Sequencing was performed on the Illumina HiSeq 2500 system with 2 X 125 bp PE reads.\n\nGenome size and heterozygosity were estimated based on trimmed reads using GenomeScope2 (Ranallo-Benavidez et al. 2020) with a k-mer of 21. Hybrid genome assembly was performed with MaSuRCA 3.3.5 (Zimin et al. 2017). Recommended settings for eukaryotes with >20X Illumina coverage were used. Genome quality was assessed following assembly (and after each step involving filtering or polishing the genome assembly; see below) with QUAST 5.0.2 (Mikheenko et al. 2018) and completeness with BUSCO 5.2.2 (Manni et al. 2021) using the Metazoa odb_10 dataset and the “--long” flag. We then removed redundant haplotigs with Redundans (Pryszcz & Gabaldón 2016) using the flags --noscaffolding --norearangements. Finally, the remaining scaffolds were polished with four rounds of Pilon 1.23 using the Illumina paired-end reads, which were first quality- and adapter-trimmed with trimmomatic 1.8.0 (Bolger et al. 2014) using “ILUMINACLIP:adapters.fasta:2:30:10 LEADING 10 TRAILING 10 SLIDINGWINDOW:4:15 MINLEN:50” for N. megatrapezata and “ILLUMINACLIP:adapters.fasta:3:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MINLEN:50” for E. babai.\n\nFor genome annotation, we followed a bioinformatic pipeline that masked repetitive DNA and leveraged both RNA-seq data from that species and protein sequences from diverse aplacophorans as evidence for gene modeling. Repeats in the final assemblies were annotated and softmasked with RepeatMasker using a custom repeat database generated with RepeatModeler (Smit & Hubley 2015). For RepeatModeler, a maximum genome sample size of 1M and the --LTRStruct option were used. For RepeatMasker, the slow and gccalc options were used. The engine used for both programs was rmblast. Available aplacophoran and select other mollusc proteomes (see data on Figshare for details) were then aligned to the final genome assemblies with ProtHint 2.6 (Brůna et al. 2020) with an e-value cutoff of 1e-25. We ran TrimGalore (Krueger et al. 2021) on the transcriptome reads with the following settings: “-q 30 --illumina --trim-n --length 50.” The trimmed and filtered transcriptome reads were then mapped to the genome using STAR 2.4.0k (Dobin et al. 2013) with “--genomeChrBinNbits 15 --chimSegmentMin 50.” Annotation of protein-coding genes was performed with BRAKER 2.1.6 (Brůna et al. 2021) using the output of ProtHint and STAR with the following settings: “--eptmode --softmasking --crf.”\n\nHomologous protein sequences in our newly sequenced solenogaster genomes and the proteomes of 21 other lophotrochozoans, including 16 other molluscs, two annelids, one brachiopod, one phoronid, and one nemertean were used as input for orthology inference using OrthoFinder 2.4.0 (Emms & Kelly 2019). We then further refined the output of OrthoFinder to construct a matrix of one-to-one orthologs following the pipeline of Varney and Yap-Chiongco et al. (2022) except we retained only genes sampled for 18/23 taxa using PhyloPyPruner (https://gitlab.com/fethalen/phylopypruner). Maximum likelihood phylogenetic analysis was employed on the concatenated supermatrix of amino acid sequences in IQ-Tree 2.1.3 (Minh et al. 2020) using the best-fitting model for each partition (-m MFP) with 1000 rapid bootstraps. The tree was arbitrarily rooted with all non-molluscan taxa. Notably, as the genome of Chaetoderma sp. (Wang et al. 2024) was released following the completion of this analysis, it was not included.\n\n\nResults\n\nFor N. megatrapezata, Illumina genome sequencing yielded 443.02 M reads. Illumina transcriptome sequencing of the same individual of N. megatrapezata used for genome sequencing (Ap227) yielded 29.72 M reads and 32.93 M reads for a second individual of N. megatrapezata (Ap259). Transcriptomes of other Neomenia species resulted in 110.68 M reads for N. aff. herwigi and 24.40 M reads for N. permagna. GenomeScope analysis estimated the genome size of N. megatrapezata to be 294 Mbp and a heterozygosity of 0.142% based on the trimmed PE reads. Following adapter trimming, two flowcells of Oxford Nanopore sequencing yielded 101.31 M reads. Assembly with MaSuRCA resulted in an assembly of 9,870 contigs totaling 347 Mbp (N50 = 119 Kbp, L50 = 1,041) with a BUSCO completeness score of 87.1% (83.9% single, 3.2% duplicated, 8.0% fragmented, and 4.9% missing). After polishing and purging redundant haplotigs, the final N. megatrapezata assembly was reduced to 6,168 contigs totaling 412 Mbp (N50 = 132 Kbp, L50 = 881) with a BUSCO completeness score of 85.1% (81.7% single, 3.4% duplicated, 8.1% fragmented, and 6.8% missing). BRAKER predicted 65,328 gene models with 90.6% of BUSCOs detected (80.5% single, 10.1% duplicated, 4.5% fragmented, and 4.9% missing). Removal of gene models not supported by transcriptome or protein evidence resulted in a final gene set for N. megatrapezata of 22,463 with a BUSCO completeness score of 90.2% (81.0% single, 9.2% duplicated, 4.7% fragmented, and 5.1% missing).\n\nFor E. babai, Illumina PE sequencing yielded 693.24 M reads. Illumina transcriptome sequencing of E. babai and Epimenia sp. yielded 70.06 M and 131.47 M reads, respectively. GenomeScope analysis of PE reads failed to converge for E. babai with k-mer sizes of 17 and 21. Therefore, we used the trimmed nanopore data in the program KMC 3 (Kokot et al. 2017) with the options -k21 -fm -t16 -m500 -ci1 -cs10000 to obtain k-mer statistics followed by kmc-tools with the transform option to create a histogram for input into GenomeScope2. Oxford Nanopore sequencing of three flowcells data yielded 14.79M reads post adapter trimming with PoreChop. The resulting analysis based on Nanopore data estimated a genome size for E. babai of 543 Mbp and heterozygosity of 1.16%. MaSuRCA yielded an assembly of 11,695 contigs totaling 572 Mbp (N50 = 271 Kbp, L50 = 618) with a BUSCO completeness score of 91.3% (77.7% single, 13.6% duplicated, 5.2% fragmented, and 3.5% missing). The final polished and purged Epimenia assembly was reduced to 5,965 contigs totaling 628 Mbp (N50 = 413 Kbp, L50 = 370) with a BUSCO completeness score of 90.1% (82.0% single, 8.1% duplicated, 6.0% fragmented, and 3.9% missing). BRAKER predicted 123,904 gene models with a BUSCO completeness score of 93.3% (80.9% single, 12.4% duplicated, 4.7% fragmented, and 2.0% missing). Removal of genes not supported by transcriptome or protein evidence resulted in a final gene set for E. babai of 25,393 with a BUSCO completeness score of 92.4% (80.5% single, 11.9% duplicated, 4.9% fragmented, and 2.7% missing).\n\nMolluscan genomes sequenced to date range in size from 359 Mbp (Simakov et al. 2013) to over 6 Gbp (Song et al. 2023) and genome size estimates by Adachi et al. (2021) for 141 diverse molluscs (Polyplacophora, Gastropoda, Bivalvia, and Cephalopoda) based on flow cytometry ranged from 469.4 Mbp (measured as a C-value of 0.48) to 5.31 Gbp (C-value of 5.43) with a mean size of 2.61 Gbp (C-value of 2.67) among the sampled molluscan taxa. Kocot et al. (2016) utilized Feulgen image analysis densitometry (FAID) to estimate genome sizes in select species of aplacophorans, including the same individual of Epimenia babai sequenced here. Genome size of E. babai was estimated to be 750 Mbp and that of Neomenia permagna was estimated to be 293 Mbp (Kocot et al. 2016). Genome size for E. babai inferred by GenomeScope based on Oxford Nanopore data is smaller than expected based on FIAD at 543 Mbp. However, we were unable to obtain an estimate based on more accurate PE data as the analysis failed to converge. The estimated genome size for N. megatrapezata of 294 Mbp inferred by GenomeScope is comparable to the FIAD estimate of 293 Mbp for the closely related species N. permagna. With final assembly sizes of 628 Mbp and 412 Mbp for E. babai and N. megatrapezata, respectively, solenogaster genomes are fairly small with respect to other molluscs. Based on computational and FAID genome size estimates, genome size within Aculifera is quite variable ranging from as small as 293 Mbp in N. permagna to 2.84 Gbp in Cryptochiton stelleri (Kocot et al. 2016; Hinegardner, 1974). Comparing the aplacophoran classes, the estimated genome size of Chaetoderma sp. (Caudofoveata) is quite large (2.45 Gbp) in comparison to both E. babai and N. megatrapezata (Table 1). Although in some groups it has been shown that genome size may co-evolve with life-history traits, the observed high level of variation in genome size within Aculifera raises questions about the underlying mechanisms driving this heterogeneity in genome size (Ritchie et al. 2017; Beaudreau et al. 2021). Further comparisons between solenogaster, caudofoveate, and chiton genomes will aid in our understanding of the evolutionary history of Aplacophora and Aculifera and the potential interplay between genome size and, e.g., life history.\n\nComparison of the full set of Epimenia and Neomenia gene models to the gene models from 21 other lophotrochozoans in OrthoFinder resulted in 251,468 groups of homologous sequences. Our pipeline selected 7,561 single-copy genes sampled for at least 18 of the 23 taxa. The final PhyloPyPruner output resulted in a supermatrix of 3,577 genes with a total of 1,169,375 amino acids and 20.3% missing data. Of these, E. babai was sampled for 2,319 and N. megatrapezata was sampled for 2,232.The resulting tree (Figure 1) is strongly supported overall with maximal support for Solenogastres and for Aculifera as the sister taxon to all other sampled molluscs, consistent with recent studies (e.g., Kocot et al. 2020; Song et al. 2023).\n\nBootstrap support values below 100 are displayed at each node. Image of Neomenia megatrapezata was altered from a photo taken by Christoph Held.\n\nIn summary, the genomes of N. megatrapezata and E. babai are relatively complete and comparable to other published aculiferan genomes (Table 1) with BUSCO completeness scores of 85.1% and 90.1%, respectively. These represent the first sequenced genomes for Solenogastres and are a valuable resource for future studies of molluscan evolution.\n\nEthics permits were not required to undertake this research.", "appendix": "Data availability\n\nAssociated raw data is available under NCBI Bioproject PRJNA1071799: https://identifiers.org/bioproject:PRJNA1071799\n\nNCBI Sequence Read Archive (SRA): RNA-Seq of Epimenia babai. Accession number SRX23536357\n\nNCBI SRA: RNA-Seq of Epimenia sp. Accession number SRX23536362\n\nNCBI SRA: RNA-Seq of Neomenia megatrapezata. Accession numbers SRX23536358 and SRX23536359\n\nNCBI SRA: RNA-Seq of Neomenia aff. herwigi. Accession number SRX23536361\n\nNCBI SRA: RNA-Seq of Neomenia permagna. Accession number SRX23536360\n\nNCBI SRA: Illumina Sequencing of Epimenia babai gDNA. Accession numbers SRX5511159 and SRX6730477.\n\nNCBI SRA: Illumina Sequencing of Neomenia megatrapezata gDNA. Accession number SRX23536356\n\nNCBI SRA: GridION Sequencing of Epimenia babai gDNA. Accession number SRX23536354.\n\nNCBI SRA: GridION Sequencing of Neomenia megatrapezata gDNA. Accession number SRX23536355\n\nFigshare: Additional tables with the list of proteomes used for gene annotation and the full BUSCO reports of gene models are available under the file: YapChiongco_2024_SupplementaryTables.doc. Neomenia_Nanopore_GenomeFiles.zip and Epimenia_Nanopore_GenomeFiles.zip each contain the content below for the respective species, https://doi.org/10.6084/m9.figshare.25111997.v1 (Yap-Chiongco, 2024).\n\n- 01_GenomeScope\n\n- 02_MaSuRCA\n\n- 03_Redundans\n\n- 04_Pilon\n\n- 05_GenomeAssembly_BUSCOandQuast\n\n- 06_RepeatModelerandMasker\n\n- 07_BRAKER\n\n- 08_AnnotationBUSCO\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe are extremely grateful to Akiko Okusu for kindly sharing the specimen of Epimenia babai used for genome and transcriptome sequencing. We thank Hiroshi Takashige who assisted in sampling of Epimenia sp. We thank the crew and scientists of the Icy Inverts cruises aboard the RV Lawrence M. Gould and RVIB Nathaniel B. Palmer for help in collecting Antarctic solenogasters. We also thank Scott Santagata for facilitating sequencing of the Neomenia megatrapezata transcriptomes.\n\nThe authors gratefully acknowledge use of the resources of the Alabama Water Institute at The University of Alabama.\n\n\nReferences\n\nAdachi K, Yoshizumi A, Kuramochi T, et al.: Novel insights into the evolution of genome size and AT content in mollusks. Mar. Biol. 2021; 168:1–7. Publisher Full Text\n\nBaba K: The later development of a solenogastre, Epimenia verrucosa. Journal of the Department of Agriculture, Kyusyu Imperial University. 1938; 6: 21–40. Publisher Full Text\n\nBaba K: The early development of a Solenogastre, Epimenia verrucosa (Nierstrasz). Annot. Zool. Jpn. 1940; 19: 107–113.\n\nBaba K: General sketch of the development in a Solenogastre, Epimenia verrucosa (Nierstrasz). Miscellaneous Reports of the Research Institute for Natural Resources. 1951; 19–21: 38–46.\n\nBeaudreau N, Massamba-N’Siala G, Belzile C, et al.: Life-history traits display strong associations to genome size in annelids. Hydrobiologia. 2021; 848: 799–810. Publisher Full Text\n\nBolger AM, Lohse M, Usadel B: Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–2120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrůna T, Hoff KJ, Lomsadze A, et al.: BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom. Bioinform. 2021; 3(1): lqaa108. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrůna T, Lomsadze A, Borodovsky M: GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genom. Bioinform. 2020; 2(2): lqaa026. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDobin A, Davis CA, Schlesinger F, et al.: STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29(1): 15–21. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDoyle J, Doyle JL: CTAB total DNA isolation. Molecular Techniques in Taxonomy. 1991; 283–293. Publisher Full Text\n\nEmms DM, Kelly S: OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20(1): 214–238. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarcía-Álvarez O, Salvini-Plawen LV: Species and diagnosis of the families and genera of Solenogastres (Mollusca). Iberus. 2007; 25(2): 73–143.\n\nGomes-dos-Santos A, Lopes-Lima M, Castro LFC, et al.: Molluscan genomics: the road so far and the way forward. Hydrobiologia. 2020; 847(7): 1705–1726. Publisher Full Text\n\nHinegardner R: Cellular DNA content of the Mollusca. Comp. Biochem. Physiol. A Physiol. 1974; 47(2): 447–460. Publisher Full Text\n\nHui JH, Chan TF, Chan L, et al.: Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873). bioRxiv. 2024; 2024–01. Publisher Full Text\n\nKocot KM, Cannon JT, Todt C, et al.: Phylogenomics reveals deep molluscan relationships. Nature. 2011; 477(7365):452–456. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nKocot KM, Jeffery NW, Mulligan K, et al.: Genome size estimates for Aplacophora, Polyplacophora and Scaphopoda: small solenogasters and sizeable scaphopods. J. Molluscan Stud. 2016; 82(1): 216–219. Publisher Full Text\n\nKocot KM, Todt C, Mikkelsen NT, et al.: Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster without a foot. Proc. R. Soc. B. 2019; 286(1902): 20190115. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKocot KM, Poustka AJ, Stöger I, et al.: New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships. Sci. Rep. 2020; 10(1): 101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKokot M, Długosz M, Deorowicz S: KMC 3: counting and manipulating k-mer statistics. Bioinformatics. 2017; 33(17): 2759–2761. PubMed Abstract \| Publisher Full Text\n\nKrueger F, James F, Ewels P, et al.: TrimGalore: v0. 6.7. Zenodo. 2021. Publisher Full Text Reference Source\n\nManni M, Berkeley MR, Seppey M, et al.: BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol. Biol. Evol. 2021; 38(10): 4647–4654. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMikheenko A, Prjibelski A, Saveliev V, et al.: Versatile genome assembly evaluation with QUAST-LG. Bioinformatics. 2018; 34(13): i142–i150. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMinh BQ, Schmidt HA, Chernomor O, et al.: IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 2020; 37(5): 1530–1534. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOkusu A: Embryogenesis and development of Epimenia babai (Mollusca Neomeniomorpha). Biol. Bull. 2002; 203(1): 87–103. PubMed Abstract \| Publisher Full Text\n\nPryszcz LP, Gabaldón T: Redundans: An assembly pipeline for highly heterozygous genomes. Nucleic Acids Res. 2016; 44(12): e113–e113. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRanallo-Benavidez TR, Jaron KS, Schatz MC: GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 2020; 11(1): 1432. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRitchie H, Jamieson AJ, Piertney SB: Genome size variation in deep-sea amphipods. R. Soc. Open Sci. 2017; 4(9): 170862. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSalvini-Plawen L: Systematic revision of the Epimeniidae (Mollusca: Solenogastres).J. Molluscan Stud.1997; 63(2):131-55. Reference Source\n\nSalvini-Plawen LV, Paar-Gausch I: Three new species of Neomenia (Mollusca: Solenogastres) from the southern hemisphere. N. Z. J. Mar. Freshw. Res. 2004; 38(1): 137–162. Publisher Full Text\n\nSigwart JD, Lindberg DR, Chen C, et al.: Molluscan phylogenomics requires strategically selected genomes. Philos. Trans. R. Soc. B. 2021; 376(1825): 20200161. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSimakov O, Marletaz F, Cho SJ, et al.: Insights into bilaterian evolution from three spiralian genomes. Nature. 2013; 493(7433): 526–531. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSmit AFA, Hubley R: RepeatModeler Open-1.0.2008-2015. Accessed December 29, 2020. Reference Source\n\nSong H, Wang Y, Shao H, et al.: Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting. Proc. Natl. Acad. Sci. 2023; 120(40): e2302361120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTodt C, Wanninger A: Of tests, trochs, shells, and spicules: Development of the basal mollusk Wirenia argentea (Solenogastres) and its bearing on the evolution of trochozoan larval key features. Front. Zool. 2010; 7(1): 6–17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTodt C: Aplacophoran mollusks—still obscure and difficult? Am. Malacol. Bull. 2013; 31(1): 181–187. Publisher Full Text\n\nVarney RM, Speiser DI, McDougall C, et al.: The iron-responsive genome of the chiton Acanthopleura granulata. Genome Biol. Evol. 2021; 13(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVarney RM, Yap-Chiongco MK, Mikkelsen NT, et al.: Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora). F1000Res. 2022; 11: 555. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang Y, Wang M, Li J, et al.: A chromosome-level genome assembly of a deep-sea symbiotic Aplacophora mollusc Chaetoderma sp. Sci. Data. 2024; 11(1): 133. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWick RR: Porechop (Version 0.2.1) [Computer software].2018. Reference Source\n\nYap-Chiongco MK, Bergmeier FS, Roberts NG, et al.: Phylogenomic reconstruction of Solenogastres (Mollusca, Aplacophora) informs hypotheses on body size evolution. Mol. Phylogenet. Evol. 2024; 194(108029): 108029. PubMed Abstract \| Publisher Full Text\n\nYap-Chiongco M: Neomenia megatrapezata and Epimenia babai Extended Genome Data. Dataset. figshare. 2024. Publisher Full Text\n\nZimin AV, Puiu D, Luo M-C, et al.: Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res. 2017; 27(5): 787–792. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "273593", "date": "22 May 2024", "name": "Gloria Arriagada", "expertise": [ "Reviewer Expertise virology", "host-pathogen interaction", "mobile elments", "mollusk LTR-retrotransposons" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article entitled “Two draft genomes of enigmatic Solenogastres (Mollusca, Aplacaphora) Epidemia babai and Neomenia megatrapezata” described the genome sequencing of two mollusk form an underrepresented subphylum among the sequenced mollusks. They clearly explain the methodology used for the sequencing and assembling as well as its annotation. Although they provide access to all the information generated, the results are very succinct and only present the statistics and numbers, and do not explain or discuss anything about the annotated genes, as a reader and not been an expert in sequencing I missed that. It was not clear to me how many of the annotated genes are indeed transcribed, since they use transcriptomics also, how many are protein coding genes and where in the physiological or cellular processes are they most represented. Are there repetitive or mobile elements in these genomes? Which fraction of the total genome are they? Are they expressed? I believe a bit of more functional insight of this very relevant genomic information, will make this a more amicable paper for readers interested in both mollusk evolution and functional genomics.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly", "responses": [] }, { "id": "273592", "date": "30 May 2024", "name": "Alice Dennis", "expertise": [ "Reviewer Expertise Evolutionary genetics", "adaptive physiology", "mollusc genomics" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript is very clear and well written. It presents assemblies of two new molluscan genomes, from the highly neglected clade Aculifera. These genomes are the first to be sequenced in the class Solenogastres. These two genomes are of good quality and are well constructed, using hybrid sequencing methods and assembly. The genomes have been annotated using appropriate models and same-species evidence. I found it interesting to see the comparison of genome size estimates based on Feulgen and kmer methods, next to the final assemblies. After annotation, single copy genes were extracted from both assemblies and well as a set of representative lophotrochozoans species. These were used to construct a phylogeny. This demonstrates the value of this genomic resource for future work in taxonomy and beyond.\nI think this work is suitable for indexing as-is. The only place I might ask for a bit more clarification is in the annotation curation. I am curious as to why there might be so many gene models for Epimenia (123,904). You have reduced this to a more reasonable 25,393 by only retaining genes with direct evidence. This is a good approach, but I worry that a few valid things have been excluded, and that this inflated number of genes perhaps reflects some important aspect of the genome (for example some sort of novel repetitive element).\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-318
https://f1000research.com/articles/13-317/v1	23 Apr 24	{ "type": "Study Protocol", "title": "Comparative study between efficacy of topical tofacitinib 2% ointment versus topical clobetasol propionate 0.05% ointment in hand eczema at a tertiary hospital in central India", "authors": [ "Drishti Bhatt", "Dr Adarshlata Singh", "Dr Adarshlata Singh" ], "abstract": "Background Hand eczema is a prevalent dermatological condition that significantly impacts the quality of life of affected individuals. Topical corticosteroids, such as Clobetasol Propionate, are commonly employed for management, but concerns regarding long-term use and potential side effects necessitate exploration of alternative treatments. This study protocol outlines a randomized controlled trial comparing the efficacy of topical Tofacitinib 2% ointment with Clobetasol Propionate 0.05% ointment in managing hand eczema.\n\nMethods The study will be a single-blinded, parallel-group, randomized controlled trial conducted at the Dermatology outpatient department of Acharya Vinoba Bhave Rural Hospital Sawangi Meghe, Wardha, from March 2023 to September 2025. Eligible participants diagnosed with hand eczema will be randomized into two groups: Group 1 will receive Clobetasol Propionate 0.05% ointment, and Group 2 will receive Tofacitinib 2% ointment. The primary outcome measure is the change from baseline in the Hand Eczema Severity Index (HECSI) score, assessed at two weeks and four weeks. Statistical analysis will utilize appropriate parametric and non-parametric tests, with a p-value <0.05 considered significant.\n\nExpected Outcome The study is anticipated to provide insights into the comparative efficacy and safety of Tofacitinib and Clobetasol Propionate in managing hand eczema. A favorable outcome for Tofacitinib could suggest its potential as an alternative or adjunctive therapy, offering a more targeted approach with fewer side effects. The findings may contribute to optimized treatment strategies for hand eczema, improving patient outcomes and guiding future research in dermatological therapeutics.", "keywords": [ "Hand eczema", "Topical Tofacitinib", "Clobetasol Propionate", "Dermatology", "Randomized controlled trial", "Hand Eczema Severity Index (HECSI)" ], "content": "Introduction\n\nHand eczema is a common dermatological condition characterized by inflammation of the skin on the hands, leading to symptoms such as erythema, vesicles, fissures, and pruritus.1 It significantly impacts the quality of life of affected individuals, causing discomfort and functional impairment.2 The management of hand eczema often involves topical corticosteroids, with Clobetasol Propionate being a commonly prescribed agent.3 However, concerns regarding the long-term use of potent corticosteroids, potential side effects, and the need for alternative treatments have prompted exploration into novel therapeutic options.\n\nOne emerging candidate for managing inflammatory skin conditions is Tofacitinib, a Janus kinase (JAK) inhibitor that modulates cytokine signaling and has demonstrated efficacy in conditions like psoriasis.4 Tofacitinib’s mechanism of action, targeting critical pathways involved in skin inflammation, makes it a promising candidate for hand eczema management.\n\nWhile studies have explored the efficacy of topical corticosteroids like Clobetasol Propionate in hand eczema, there needs to be more comparative research evaluating the potential advantages of Tofacitinib over traditional treatments. This study seeks to address this gap by conducting a randomized controlled trial comparing the efficacy and safety of topical Tofacitinib 2% ointment with topical Clobetasol Propionate 0.05% ointment in managing hand eczema.\n\nTo study the efficiency of topically applied tofacitinib 2% ointment in managing hand eczema.\n\n\n\n1. To evaluate the efficacy of topical tofacitinib 2% ointment in hand eczema.\n\n2. To evaluate the efficacy of topically applied clobetasol propionate 0.05% ointment for hand eczema.\n\n3. To compare the effect of topically applied tofacitinib 2% ointment and topically applied clobetasol propionate 0.05% ointment in hand eczema.\n\n4. To study the side effects of topical clobetasol propionate 0.05% ointment and topical Tofacitinib 2% ointment.\n\n\nProtocol\n\nThis research will be conducted as a prospective, randomized, single-blinded, parallel-group, controlled trial to compare the efficacy of topical tofacitinib 2% ointment versus topical clobetasol propionate 0.05% (10-15 g depending on the area affected over 4 weeks Reagent number: 25122-46-7) ointment in the management of hand eczema.\n\nPatients diagnosed with hand eczema attending the outpatient department of Dermatology (DVL) at AVBRH Sawangi Meghe, Wardha, from March 2023 to September 2025, will be eligible for participation.\n\n\n\n1. Patients providing written consent before the initiation of any treatment.\n\n2. Clinically diagnosed cases of hand eczema of all grades as per the Hand Eczema Severity Index (HECSI) score.\n\n3. Age above 18 years.\n\n4. No prior treatment for hand eczema in the past 1 month.\n\n\n\n1. Patients with an active infection at the local site.\n\n2. Patients with leukopenia or anemia.\n\n3. Pregnant or nursing women.\n\n4. Patients on any treatment that may influence the outcomes of the drugs under study.\n\nPatients meeting the inclusion criteria and providing written consent will be assigned to either Group 1 or Group 2 using computer-generated randomization. To minimize bias, age, and gender cross-matching between the groups will be implemented.\n\nGroup 1 (Control): Topical Clobetasol Propionate 0.05% Ointment. Patients in this group will receive topical Clobetasol Propionate 0.05% ointment as their treatment modality for hand eczema. They will be instructed to apply the ointment twice daily over the affected areas. The treatment duration will extend for 4 weeks.\n\nGroup 2 (Experimental): Topical Tofacitinib 2% Ointment. Patients in this group will receive topical Tofacitinib 2% ointment as their treatment modality for hand eczema. Similar to Group 1, they will be instructed to apply the ointment twice daily over the affected areas. The treatment duration will also be 4 weeks.\n\nApplication instructions: Patients in both groups will be educated on properly applying the assigned ointments. They will be instructed to wash their hands before applying a thin layer of the ointment evenly on the affected areas, avoiding contact with eyes and mucous membranes. Patients will be advised not to bandage or cover the treated areas unless directed by the investigator. Additionally, they will be instructed to avoid excessive sun exposure and use sunscreen on treated areas.\n\nFollow-up visits: Participants from both groups will be scheduled for followup visits at 2 weeks and 4 weeks after the initiation of treatment. During these visits, clinical photographs will be taken with the patient’s informed consent, and the Hand Eczema Severity Index (HECSI)5 score will be recorded to assess the efficacy and side effects of the respective interventions.\n\nMonitoring: The study will be monitored to ensure adherence to the assigned interventions, proper data collection, and participant safety. Adverse events, if any, will be documented and reported. Regular communication with participants will be maintained to address any concerns or queries they may have during the study.\n\nAdjustments: Any deviations from the study protocol will be documented, and appropriate measures will be taken to address them. Adjustments will be made in consultation with the Institutional Ethics Committee if necessary.\n\nBlinding: The study will be single-blinded, with the participants unaware of their assigned treatment group. This helps minimize bias in reporting outcomes.\n\nCode break: In a medical emergency or if unblinding becomes necessary for clinical management, a code break procedure will be in place, ensuring that the treating physician can access information about the assigned intervention while keeping the participant blinded.\n\nAdherence monitoring: Participants will be asked to return unused medication at each followup visit to assess adherence. Additionally, self-reported adherence will be recorded during followup assessments. These interventions and allocation procedures aim to systematically evaluate the comparative efficacy and side effects of topical Clobetasol Propionate 0.05% ointment and topical Tofacitinib 2% ointment in managing hand eczema.\n\n\n\n1. Recruitment: The recruitment process will commence at the Dermatology outpatient department (DVL) of AVBRH Sawangi Meghe, Wardha, from March 2023. A designated study coordinator will identify potential participants based on clinical diagnosis and eligibility criteria. Eligible patients will be provided with detailed information about the study, and the purpose, risks, and benefits will be explained.\n\n2. Informed consent: Written and signed informed consent will be obtained from all eligible patients willing to participate in the study. The consent form will include information about the nature of the study, potential risks and benefits, confidentiality assurances, and the voluntary nature of participation.\n\n3. Screening and inclusion/exclusion criteria: Eligible participants will undergo a screening process to confirm their clinical diagnosis and ensure they meet the inclusion criteria while excluding those who meet any exclusion criteria. The study coordinator will collect relevant medical history and conduct a thorough examination to confirm the diagnosis of hand eczema.\n\n4. Baseline assessments: Baseline assessments will include the collection of demographic information, medical history, and baseline Hand Eczema Severity Index (HECSI) scores. Clinical photographs of affected areas will be taken during followup visits for documentation and comparison.\n\n5. Randomization and allocation: After obtaining informed consent and confirming eligibility, participants will be assigned to either Group 1 (Clobetasol Propionate) or Group 2 (Tofacitinib) through computer-generated randomization. Age and gender cross-matching will be performed to ensure balanced groups.\n\n6. Assignment of interventions: Participants will be provided with the assigned treatment (topical Clobetasol Propionate 0.05% ointment or topical Tofacitinib 2% ointment) along with detailed instructions for application.\n\n7. Follow-up appointments: Participants will be scheduled for followup visits at 2 weeks and 4 weeks after the initiation of treatment. The study coordinator will communicate the importance of attending all followup appointments and the need for adherence to the assigned treatment.\n\n8. Monitoring adherence: Adherence to the assigned intervention will be monitored through self-reporting, return of unused medications, and documentation during followup visits.\n\n9. Data collection: Data collection will include clinical assessments, HECSI score recording, and the capture of clinical photographs during each followup visit.\n\n10. Adverse event reporting: Participants will be encouraged to report any adverse events or concerns during the study. Adverse events will be documented, assessed for severity, and reported to the Institutional Ethics Committee as per regulatory requirements.\n\n11. End of study: The study will conclude in September 2025, and participants will be thanked for participating. Final data analysis and interpretation will be conducted, and the study findings will be disseminated through publications and presentations.\n\nEffect of topical tofacitinib for hand eczema = 81.7%\n\nEffect of topical steroid for hand eczema = 68%\n\nClinically significant at (δ) = 25%\n\nSample size = 36\n\nTotal sample size = 72 (36 per group)\n\nThe statistical analysis for this comparative study between topical Tofacitinib 2% ointment and topical Clobetasol Propionate 0.05% ointment in managing hand eczema will encompass a comprehensive approach utilizing appropriate parametric and non-parametric tests. The primary focus will be on the change from the baseline of the Hand Eczema Severity Index (HECSI) score. In the initial stage, descriptive statistics will be employed to summarize the baseline characteristics of participants in both treatment groups. Continuous variables will be presented as mean and standard deviation (or median and interquartile range), while categorical variables will be expressed as frequencies with percentages.\n\nThe comparative analysis will be conducted using an independent t-test or Mann-Whitney U test for the primary outcome—change from baseline in HECSI score. The choice between tests will depend on the data distribution, and statistical significance will be determined with a threshold of p<0.05. After the primary analysis, subgroup analyses may be undertaken to explore potential variations in treatment response based on age, gender, and baseline severity. Safety and adverse events will be summarized, and the incidence rates between the two treatment groups will be compared using Chi-square or Fisher’s exact test.\n\nThe handling of missing data will be addressed, potentially utilizing multiple imputations to enhance the robustness of the results. Sensitivity analyses may be performed to assess the impact of outliers or influential data points on the overall findings.\n\nExploratory analyses will investigate potential relationships between treatment response and additional factors, such as patient demographics or specific characteristics of hand eczema. Statistical software such as R Studio Version 4.3.1 will execute these analyses.\n\n\nDiscussion\n\nHand eczema is a prevalent dermatological condition that substantially burdens affected individuals, impacting their daily lives and often requiring long-term management.6 The choice of topical corticosteroids, such as Clobetasol Propionate, is a conventional approach, but concerns about prolonged use and potential side effects necessitate exploring alternative therapeutic options.7 This study protocol outlines the design of a randomized controlled trial comparing the efficacy of topical Tofacitinib 2% ointment with topical Clobetasol Propionate 0.05% ointment in managing hand eczema.\n\nThe rationale for exploring Tofacitinib lies in its mechanism of action as a Janus kinase (JAK) inhibitor, which modulates intracellular signaling pathways involved in the inflammatory response.8 While Tofacitinib has shown promise in conditions like psoriasis,9 its efficacy and safety in hand eczema remain to be elucidated. The comparison with Clobetasol Propionate, a well-established treatment, will provide valuable insights into the potential advantages of Tofacitinib in terms of efficacy and side effect profiles.\n\nThe study’s methodology, including the use of a single-blinded randomized controlled trial design, rigorous inclusion and exclusion criteria, and standardized outcome measures, enhances the internal validity of the findings. Including a placebo group could have provided additional insights, but ethical considerations and the necessity of active treatment for hand eczema guided the decision to compare two active treatments.\n\nThe choice of the Hand Eczema Severity Index (HECSI) score as the primary outcome measure aligns with its established use in assessing the severity of hand eczema.5 This comprehensive scoring system considers multiple clinical signs and provides a quantifiable measure for evaluating treatment efficacy.\n\nOne potential limitation of this study is its hospital-based nature, which may limit the generalizability of the findings to the broader population. Additionally, the study’s relatively short duration may not capture long-term effects or relapse patterns. However, the study’s strengths, including the robust study design, systematic randomization, and rigorous statistical analyses, contribute to its credibility and potential impact on clinical practice.\n\n\n\n1. The Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (DU) has approved the study protocol date 21/03/23. Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives. We will prioritize the interviewee’s privacy and comfort during the interview process. Reference Number: DMIHER (DU)/IEC/2024/70.\n\nThis study protocol will be published in an indexed journal.\n\nThe study has not yet started; we will start after the published study protocol.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: SPIRIT checklist for ‘Comparative Study Between Efficacy of Topical Tofacitinib 2% Ointment vs Topical Clobetasol Propionate 0.05% Ointment in Hand Eczema in tertiary hospital in central India”, https://doi.org/10.5281/zenodo.10935094. 10\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nThyssen JP, Johansen JD, Linneberg A, et al.: The epidemiology of hand eczema in the general population--prevalence and main findings. Contact Derm. 2010; 62: 75–87. Publisher Full Text\n\nMeding B: Epidemiology of hand eczema in an industrial city. Acta Derm. Venereol. Suppl (Stockh). 1990; 153: 1–43. PubMed Abstract \| Publisher Full Text\n\nDiepgen TL, Agner T, Aberer W, et al.: Management of chronic hand eczema. Contact Derm. 2007; 57: 203–210. Publisher Full Text\n\nPapp KA, Menter A, Strober B, et al.: Efficacy and safety of tofacitinib, an oral Janus kinase inhibitor, in treating psoriasis: a Phase 2b randomized placebo-controlled dose-ranging study. Br. J. Dermatol. 2012; 167: 668–677. PubMed Abstract \| Publisher Full Text\n\nHeld E, Skoet R, Johansen JD, et al.: The hand eczema severity index (HECSI): a scoring system for clinical assessment of hand eczema. A study of inter- and intraobserver reliability. Br. J. Dermatol. 2005; 152: 302–307, 307. PubMed Abstract \| Publisher Full Text\n\nThyssen JP, Linneberg A, Menné T, et al.: The epidemiology of contact allergy in the general population--prevalence and main findings. Contact Derm. 2007; 57: 287–299. PubMed Abstract \| Publisher Full Text\n\nGrant L, Seiding Larsen L, Burrows K, et al.: Development of a Conceptual Model of Chronic Hand Eczema (CHE) Based on Qualitative Interviews with Patients and Expert Dermatologists. Adv. Ther. 2020; 37: 692–706. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDowty ME, Lin TH, Jesson MI, et al.: Janus kinase inhibitors for the treatment of rheumatoid arthritis demonstrate similar profiles of in vitro cytokine receptor inhibition. Pharmacol. Res. Perspect. 2019; 7: e00537. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSonthalia S, Aggarwal P: Oral Tofacitinib: Contemporary Appraisal of Its Role in Dermatology. Indian Dermatol. Online J. 2019; 10: 503–518. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBhatt D: SPIRIT ‘Comparative Study Between Efficacy of Topical Tofacitinib 2% Ointment vs Topical Clobetasol Propionate 0.05% Ointment in Hand Eczema in tertiary hospital in central India’. Zenodo. 2024. Publisher Full Text" }	[ { "id": "290372", "date": "26 Jun 2024", "name": "Francisco José Navarro-Triviño", "expertise": [ "Reviewer Expertise My area of expertise is the world of immune-mediated diseases", "including eczematous-type inflammatory pathology." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComparative clinical trial between topical tofacitinib Vs clobetasol propionate. The main objective is the reduction of HECSI, although I think it should add the change in symptoms such as itching and pain using the NRS scale. It would be interesting if at the end of the first phase of the trial, patients who do not improve with clobetasol propionate receive topical tofacitinib. The follow-up time seems short to me, 4 weeks may be an early cut-off to assess the short-term response to the treatment.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "361112", "date": "24 Jan 2025", "name": "Snehal Shelke", "expertise": [ "Reviewer Expertise My area of expertise is allergic dermatitis like atopy and eczema and infectious diseases like onychomycosis." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComparative clinical trial between topical tofacitinib Vs clobetasol propionate. The reduction in symptoms/signs as well as improvement in QOL can be included as viewed by the primary investigator and as stated by the patient, given that the primary objective is to look for a reduction in the HECSI score only. A follow up at 6 months after completion of initial 4 weeks would be interesting to look for any relapses as only topical therapy is being given and relapse rates of topical JAK STAT inhibitors for eczema is not well known. Given that among topical treatment options, steroids are the mainstay as of now for eczema treatment, it is interesting to think of topically applied JAK STAT inhibitor as an option to decrease the well known long term side effects of topical steroids. It would be of interest to know if, after the 4 week period, the patients are started on any concomitant oral therapy and if so then which mode of topical responds better if used along with oral treatment.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-317
https://f1000research.com/articles/13-316/v1	23 Apr 24	{ "type": "Research Article", "title": "CD24 and Oct4: Cancer stem markers expression correlates with histological subtyping of head and neck squamous cell carcinoma", "authors": [ "Muhammad Kashif", "Sadia Minhas", "Hafiz Muhammad Shahzad", "Muhammad Bilal Pasha", "Faheem Shahzad", "Romeeza Tahir", "Shah Jahan", "Nadeem Afzal", "Sadia Minhas", "Hafiz Muhammad Shahzad", "Muhammad Bilal Pasha", "Faheem Shahzad", "Romeeza Tahir", "Shah Jahan", "Nadeem Afzal" ], "abstract": "Background Head and neck squamous cell carcinoma (HNSCC) encompasses a diverse range of tumors with varying degrees of differentiation. Within tumors, cancer stem cells (CSCs) are believed to play a crucial role in tumor initiation, progression, and resistance to treatment. This study aimed to explore the expression of two CSC markers i.e. CD24 and Oct4, in patients with HNSCC.\n\nMethods The study included 85 patients diagnosed with HNSCC. Immunohistochemistry was used to evaluate the expression of CD24 and Oct4 in tumor tissues obtained from patients with HNSCC. Staining intensity and the proportion of positive tumor cells were analyzed and compared across the various HNSCC grades and histological subtypes.\n\nResults The findings revealed that the mean immunoreactivity score (IRS) for CD24 was significantly higher in non-conventional HNSCC subtypes compared to conventional types (p = 0.019). Additionally, a significant statistical association was observed between the IRS status of CD24 and histological subtypes (p = 0.043). Other demographic, clinical, and histological parameters showed non-significant associations with staining intensity, proportion score (PC), IRS status, and mean IRS (all p values > 0.05).\n\nConclusions These findings indicate that CD24 could potentially serve as a CSC marker for distinguishing between conventional and non-conventional histological types of HNSCC. This suggests that CD24 holds promise as a valuable tool in identifying specific HNSCC subtypes characterized by CSCs.", "keywords": [ "Squamous cell carcinoma", "head and neck squamous cell carcinoma", "OSCC", "cancer stem cells", "CD24", "Oct4", "immunohistochemistry" ], "content": "Introduction\n\nIn the past few years, extensive studies into the molecular processes that control HNSCC have significantly transformed how cancer patients, especially those with metastatic conditions, are treated. New approaches like targeted therapy and immune checkpoint inhibition have emerged and been used for HNSCC patients. Despite these breakthroughs, completely getting rid of or effectively managing HNSCC has remained elusive, as most patients eventually become resistant to treatment. The primary reason behind this resistance and the resulting treatment ineffectiveness is the presence of intratumoral heterogeneity, a crucial aspect of HNSCC. This refers to a mix of cells within the tumor that respond differently to cancer treatment due to varying levels of sensitivity.1\n\nTwo models have been proposed that may explain heterogeneity; the clonal evolution model, and the CSCs model. The term “CSC” refers to a malignant cancer cell having a stem cell characteristic. The CSCs theory claims that merely a small percentage of a tumor’s cells may renew the heterogeneity form, encourage spread, and cause recurrence, is increasing in popularity.2 CSCs typically compensate less than 1% of the total cells in many of these neoplasms, but they can compensate from 27% to 100% of the entire cancer cell population in extremely malignant tumors.3 In the context of HNSCC, it is suggested that CSCs play a role in initiating tumors, advancing their growth, causing metastasis, resisting drugs, and causing reoccurrence.1\n\nA systematic review had reported 13 types of stem cell markers. The most commonly expressed CSC markers are CD44, aldehyde dehydrogenase, and CD133, which are responsible for tumorigenesis, self-renewal, and therapy resistance, whereas NANOG, SOX-2, and OCT-4 are involved in metastasis and invasion. Identification of an accurate panel of CSC markers is the need of the hour as non-specificity of the current markers poses a problem.4\n\nIn a number of cancer cells, the cytoplasmic protein CD24 is linked to the cellular membrane by glycosylphosphatidylinositol. Gynecologic, breast, prostate, bladder, renal, non-small cell carcinomas, and other human malignancies have high levels of CD24 expression.5 This suggests CD24 as an important marker in the diagnosis and prognosis of tumors. Further, it acts as a substitute ligand for platelet and vascular endothelial contact, that makes it easier for malignant cells to spread via circulation. It makes tumor cells prone to proliferating and sticking to fibronectin, collagen, and laminin. The correlations of CD24 with metastatic disease strengthen its significance as a predictive biomarker and a novel CSC marker.6\n\nOkumura et al. (2021) stated that Octamer 3/4 (Oct 3/4) is an essential transcription factor and stem cell marker during human development, and it is also known as the Oct4 transcription factor gene or POU5F1. Studies have suggested presence of Oct 3/4 in both benign and malignant cells that have differentiated from human cells. Investigations have revealed that tumors with intensive Oct4 stem cell marker expression are associated with rapid disease progression, metastasis, and shorter cancer-related survival, as opposed to tumors with moderate to minimal Oct4 expression. Oct4 is confirmed as a target for CSCs and is critical in regulating stem cell self-renewal and maturation, as per Mohiuddin et al. (2020).7,8\n\nCurrently, there is no single biomarker to define the CSC population accurately for HNSCC. Therefore, assessing the expression of CSC markers in HNSCC appears to be the most rational approach for distinguishing high-risk cases of HNSCC from indolent. The aim of this study was to investigate the expression of two CSC markers (CD24 and Oct4), in tissue samples of HNSCC patients.\n\n\nMethods\n\nEach study participant gave their written informed consent. For this cross sectional study, formalin-fixed paraffin-embedded tissue samples from 85 patients diagnosed with HNSCC were collected. The samples were obtained from the Bakhtawar Amin Trust Teaching Hospital Multan, Pakistan. Included patients had different tumor grades: 67 cases classified as well to moderately differentiated SCC and 18 cases as poorly differentiated. Surgical resection was performed on all patients. Further details regarding the demographic, clinical, and histopathological characteristics of the HNSCC patients can be found in Table 1. In order to be eligible for inclusion criteria included confirmed diagnosis of HNSCC and available tissue samples for immunohistochemical analysis. Patients who had received neoadjuvant chemotherapy or radiotherapy were excluded.\n\n* Statistically significant.\n\nImmunohistochemical analysis was conducted on 4 μm-thick sections of the formalin-fixed paraffin-embedded tissue samples. The avidin-biotin-peroxidase complex method was employed for this purpose. Initially, the tissue sections were deparaffinized and rehydrated. Antigen retrieval was performed by boiling the sections in citrate buffer (pH 6.0) for 15 minutes. To minimize nonspecific binding, the sections were then blocked with 10% normal goat serum for 30 minutes at room temperature.\n\nNext, the sections were incubated overnight at 4°C with primary antibodies targeting CD24 (1:100, Abcam) and Oct4 (1:100, Abcam). Following this, the sections were washed with phosphate-buffered saline (PBS) and incubated with a biotinylated secondary antibody (1:200, Vector Laboratories) for 1 hour at room temperature. After another round of PBS washing, the sections were exposed to streptavidin-peroxidase complex (Vector Laboratories) for 30 minutes at room temperature. Subsequently, the sections were washed with PBS and developed using 3,3’-diaminobenzidine (DAB) (Vector Laboratories). Finally, the sections were counterstained with hematoxylin, dehydrated, and mounted using mounting medium.\n\nThe immunohistochemical staining of CD24 and Oct4 was independently assessed by two pathologists who were unaware of the clinical data. The staining intensity and the percentage of positively stained cells were evaluated. To measure the immunoreactivity score (IRS) for HNSCC tissue sections stained with the aforementioned antibodies, a semi-quantitative scale was utilized. The IRS was calculated by multiplying the staining intensity (SI) of tumor cells (0, no staining; 1, weak staining; 2, moderate staining; and 3, strong staining) by a proportion score (PC) based on the percentage of positive tumor cells (0 = negative, 1 < 25%, 2 = 26%-50%, 3 = 51%-80%, 4 = 81%-100%). The resulting PC and SI scores were multiplied, yielding an immunoreactivity score (IRS) ranging from 0 to 12. An IRS score of 9-12 was considered high, while a score of 0-8 was categorized as low.9\n\nStatistical analysis was carried out utilizing SPSS 25.0 (SPPS Inc., Chicago, USA). Mean with standard deviation (SD) or median within the interquartile range was used to express continuous variables, whereas frequency and percentage were employed for categorical variables. To assess the disparities in means among groups, the One-way ANOVA test was employed. Results were regarded as statistically significant if the p-value was equal to or less than 0.05.\n\n\nResults\n\nThe baseline characteristics of patients with HNSCC were assessed, and their comparison was made with the SI, IRS positive or negative status and mean IRS of CD24 and Oct-4 antibodies (Table 1). The study included 85 patients, with 30 patients in the negative/weakly positive (N/WP) SI group and 55 patients in the positive/strongly positive (P/SP) SI group. The analysis yielded that in patients with conventional HNSCC, 35.4% in the N/WP group and 64.6% in the P/SP group had Oct-4 SI (p-value = 1.000). For CD24 SI, 45.6% of patients with conventional HNSCC in the N/WP group and 54.4% in the P/SP group showed staining intensity, yielding a significant p-value of 0.043. Among patients with non-conventional HNSCC, 34% in the N/WP group and 66% in the P/SP group had Oct-4 SI, while for CD24 SI, the percentages were 50% and 50%, respectively. It may be inferred from this finding that SI of CD24 is significantly associated with histological subtyping of HNSCC (Figure 1). While there existed no statistical association of CD24 and Oct-4 staining intensity with that of any other clinical or histological parameters (all p values >0.05).\n\nTable 2 shows a total of 85 patients, with 31 patients in the low (L) IRS group and 54 patients in the high (H) IRS group. In patients with conventional HNSCC, 62% in the low IRS group and 38% in the high IRS group had Oct-4 IRS. For CD24 IRS, 45.6% of patients with conventional HNSCC in the low IRS group and 54.4% in the high IRS group had immunoreactivity (p = 0.064). Among patients with non-conventional HNSCC, 83.3% in the low IRS group and 16.7% in the high IRS group had Oct-4 IRS, while for CD24 IRS, the percentages were 83.3% and 16.7%, respectively.\n\n* Statistically significant.\n\nTable 3 provides a comparison of the mean IRS of Oct-4 and CD24 antibodies with the histological types and grades of HNSCC. The analysis included a total of 79 patients with conventional histological type and 6 patients with non-conventional histological type. In terms of CD24 IRS, the mean score for conventional histological type was 4.50 ± 3.49, with a 95% CI of 6.88-8.45. For non-conventional histological type, the mean IRS of CD24 was 7.67 ± 3.49, with a 95% CI of 1.09-7.23 (p = 0.019): indicating a statistically significant difference in CD24 IRS between the two histological types.\n\n* Statistically significant.\n\nIn summary, the comparison of SI, IRS status and mean IRS of Oct-4 and CD24 antibodies with demographic, clinical and histological parameters of HNSCC did not reveal any statistically significant differences, except for CD24 SI, IRS status and mean IRS in relation to histological type (conventional vs. non-conventional), where a significant difference was observed.\n\n\nDiscussion\n\nAlthough, early stage cases of HNSCC have high cure rates, up to 50% of patients presents with advanced stage and full spectrum of complications of the disease.10 The category of late diagnosed group necessitates reliable diagnostic tool which can help in early diagnosis and treatment of disease. Presently there is a lack of clinically employable predictive indicator of disease. Hence, to look for potential predictors is paramount. The aim of this study was to investigate the expression of two CSC markers i.e. CD24 and Oct4, in different grades of HNSCC. CSCs are thought to be responsible for tumor initiation, progression, metastasis, drug resistance, and recurrence, making them a crucial focus in cancer research and treatment development.2 The findings of this current study shed light on the potential role of CD24 and Oct4 in distinguishing conventional and non-conventional histological types of HNSCC and offer insights into their significance in CSC biology.\n\nStudying the expression profiling of these two CSCs markers is pivotal in understanding the disease nature. In the present study, a statistically significant difference in staining intensity of CD24 was observed in different histological subtypes (conventional and non-conventional types) HNSCC. In this study, the average immunoreactivity score (IRS) for CD24 was significantly high in non-conventional HNSCC subtypes compared to conventional types (p = 0.019). This suggests that CD24 may serve as a potential CSC marker for distinguishing different histological types of HNSCC. The implications of this finding are significant, as it may aid in identifying highly aggressive HNSCC cases characterized by CSCs, enabling more targeted and personalized treatment approaches.\n\nThese findings align with earlier research that has identified CD24 as a potential marker for cancer stem cells (CSCs) in different types of cancer. For instance, in ovarian cancer, CD24 expression correlated with chemoresistance and poor prognosis.11 These findings suggested the role of CD24’s as a CSC marker for different malignancies, warranting further investigation in HNSCC. It has been reported that expression of CD24 in cases of HNSCC with lymph nodal metastasis was high as compared to non-nodal involvement. Further, HNSCC cases with high expression of CD24 had poor overall survival when compared to low expression cases.12 Likewise, Han and colleagues indicated that the CD24 gene and its corresponding protein could potentially function as a diagnostic indicator or a target for treatment in HNSCC. Their study also revealed that CD24 expression was limited to a small subset of cells, underscoring the heterogeneous nature of tumors, and identified the presence of tumor-initiating cell subtypes (CD24+/CD44+) within HNSCC.13 A meta-analysis revealed that increased expression of CD24 has been observed across multiple types of tumors. The stimulation of the CD24/Siglec-10 pathway has been proven to enhance immune evasion by inhibiting the functionality of cytotoxic T cells and impeding macrophage-driven phagocytosis within tumors. The researchers also noted the absence of a uniform approach to determine CD24 positivity, as certain studies use flow cytometry while others rely on immunohistochemical assessment, leading to considerable variability.14 Zimmerer et al. conducted an in vitro study on OSCC cell lines and reported that almost 30% of tumor cells showed positive expression for CD24. They further reported that in terms of growing therapies based on personalized medicine, CD24 might be a potential target for modulating tumor angiogenesis or eliminating CSCs and thus tumor growth, progression, and metastasis.15\n\nOn the other hand, Oct4, a critical transcription factor and stem cell marker, has been implicated in tumor progression, metastasis, and shorter cancer-related survival. However, in the current study, no statistically significant associations was observed between Oct4 SI or IRS and the clinical and histological parameters of HNSCC (p > 0.05). This might indicate that the role of Oct4 in HNSCC progression and prognosis could be more complex, involving various molecular pathways and interactions. Regarding the relevancy of Oct4 in HNSCC, a study in 2020 was conducted on large cohort of 348 HNSCC patients to investigate its expression potential and impact on patient prognosis that revealed non satisfactory expression in any case of HNSCC which supports findings of the present study.16 Although multiple researchers reported Oct4 association with tumorigenicity, invasion and metastasis but in HNSCC the data is still lacking.17 Different properties of Oct4 isoforms could be the potential cause of confusion and controversies in its behavior in multiple cancer types.\n\nThe findings on Oct4 are consistent with some previous studies, while conflicting results have been reported in others. Mohiuddin et al. (2020) suggested high Oct4 expression in colorectal cancer association with advanced tumor stage and poor survival, suggesting a potential prognostic role. Conversely, in hepatocellular carcinoma.8 Oct4 expression was not significantly correlated with clinicopathological features or prognosis.18 These discrepancies may be attributed to tumor-specific differences in Oct4’s functional role and cellular context. Therefore, further research is warranted to elucidate Oct4’s precise role in the context of HNSCC.\n\nComparing the results of this study with previously reported data on CD24 and Oct4 expression in HNSCC may provide further insights into their relevance as CSC markers and potential prognostic indicators. A systematic review by Singh et al. (2021) identified CD44, aldehyde dehydrogenase, and CD133 as the most commonly expressed CSC markers in HNSCC, responsible for tumorigenesis, self-renewal, and therapy resistance. Meanwhile, NANOG, SOX-2, and OCT-4 were involved in metastasis and invasion.4 The identification of an accurate panel of CSC markers is essential to address the non-specificity of currently used markers and to improve understanding of CSC biology in HNSCC.\n\nIt is important to note that CSC markers are often expressed heterogeneously within tumors, and their expression levels may vary based on tumor stage, location, and patient demographics. Therefore, comprehensive meta-analyses and larger-scale studies involving diverse patient populations would be beneficial to establish a clearer understanding of CD24 and Oct4’s clinical significance in HNSCC.\n\n\nConclusions\n\nIn summary, this study provides valuable insights into the potential role of CD24 as a CSC marker for distinguishing conventional and non-conventional histological types of HNSCC. The findings suggested that CD24 could serve as a valuable tool in identifying specific HNSCC subtypes characterized by CSCs. However, further research is needed to validate these findings and explore the complex interactions between CSC markers and tumor biology in HNSCC. Understanding the roles of both CD24 and Oct4 in HNSCC may contribute to the development of targeted therapies and improved prognostic strategies for this aggressive malignancy. Future studies should aim to investigate larger patient cohorts and include a broader panel of CSC markers to elucidate the underlying molecular mechanisms and clinical implications of CSCs in HNSCC.\n\n\nEthics and consent\n\nThe ethical and technical approval to perform this study was granted by the Ethical Review Committee and the Advanced Studies & Research Board (No.UHS/Edu/126-16/1226, Dated: 17-06-2016) University of Health Sciences, Lahore, Pakistan. This study also strictly adheres to the guidelines given in Helsinki Declaration of World Medical Association. Each study participant gave their written informed consent. Consent to publish the details has been obtained from all individuals and all efforts were made to anonymize individual’s data.", "appendix": "Data availability\n\nHarvard Dataverse: CD24 Oct4 Immunohistochemical Expression in HNSCC. https://doi.org/10.7910/DVN/QGX2E3. 19\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nThis work is supported by the University of Health Sciences (UHS) Lahore and Higher Education Commission (HEC) of Pakistan.\n\n\nReferences\n\nChen D, Wang CY: Targeting cancer stem cells in squamous cell carcinoma. Precis. Clin. Med. 2019 Sep; 2(3): 152–165. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLechner M, Liu J, Masterson L, et al.: HPV-associated oropharyngeal cancer: epidemiology, molecular biology and clinical management. Nat. Rev. Clin. Oncol. 2022 May; 19(5): 306–327. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPimolbutr K, Lim WT, Leeson R, et al.: Prognosis of oral epithelial dysplasia in individuals with and without oral lichen planus. Oral Dis. 2023 Jan 17; 30: 504–517. Publisher Full Text\n\nSingh P, Augustine D, Rao RS, et al.: Role of cancer stem cells in head-and-neck squamous cell carcinoma - A systematic review. J. Carcinog. 2021 Sep 23; 20: 12. Publisher Full Text\n\nAltevogt P, Sammar M, Hüser L, et al.: Novel insights into the function of CD24: A driving force in cancer. Int. J. Cancer. 2021 Feb 1; 148(3): 546–559. PubMed Abstract \| Publisher Full Text\n\nKim S, Kim D, Cho SW, et al.: Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 2014 Jun; 24(6): 1012–1019. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOkumura-Nakanishi S, Saito M, Niwa H, et al.: Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells. J. Biol. Chem. 2005 Feb 18; 280(7): 5307–5317. Publisher Full Text\n\nMohiuddin IS, Wei SJ, Kang MH: Role of OCT4 in cancer stem-like cells and chemotherapy resistance. Biochim. Biophys. Acta Mol. Basis Dis. 2020 Apr 1; 1866(4): 165432. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoxberg M, Götz C, Haidari S, et al.: Immunohistochemical expression of CD44 in oral squamous cell carcinoma in relation to histomorphological parameters and clinicopathological factors. Histopathology. 2018 Oct; 73(4): 559–572. PubMed Abstract \| Publisher Full Text\n\nAfify SM, Seno M: Differentiation Potential of Cancer Stem Cells In Vitro. Methods in Cancer Stem Cell Biology. Springer; 2023. Publisher Full Text\n\nKwon MJ, Han J, Seo JH, et al.: CD24 Overexpression Is Associated with Poor Prognosis in Luminal A and Triple-Negative Breast Cancer. PLoS One. 2015 Oct 7; 10(10): e0139112. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSzafarowski T, Sierdziński J, Ludwig N, et al.: Assessment of cancer stem cell marker expression in primary head and neck squamous cell carcinoma shows prognostic value for aldehyde dehydrogenase (ALDH1A1). Eur. J. Pharmacol. 2020 Jan 15; 867: 172837. PubMed Abstract \| Publisher Full Text\n\nHan J, Kioi M, Chu WS, et al.: Identification of potential therapeutic targets in human head & neck squamous cell carcinoma. Head Neck Oncol. 2009 Jul 14; 1: 27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPanagiotou E, Syrigos NK, Charpidou A, et al.: CD24. A Novel Target for Cancer Immunotherapy. J. Pers. Med. 2022 Jul 28; 12(8): 1235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZimmerer RM, Ludwig N, Kampmann A, et al.: CD24+ tumor-initiating cells from oral squamous cell carcinoma induce initial angiogenesis in vivo. Microvasc. Res. 2017 Jul; 112: 101–108. PubMed Abstract \| Publisher Full Text\n\nPedregal-Mallo D, Hermida-Prado F, Granda-Díaz R, et al.: Prognostic Significance of the Pluripotency Factors NANOG, SOX2, and OCT4 in Head and Neck Squamous Cell Carcinomas. Cancers (Basel). 2020 Jul 4; 12(7): 1794. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFu TY, Hsieh IC, Cheng JT, et al.: Association of OCT4, SOX2, and NANOG expression with oral squamous cell carcinoma progression. J. Oral Pathol. Med. 2016 Feb; 45(2): 89–95. Publisher Full Text\n\nLiang C, Xu Y, Ge H, et al.: Clinicopathological and prognostic significance of OCT4 in patients with hepatocellular carcinoma: a meta-analysis. Onco Targets Ther. 2017 Dec 21; 11: 47–57. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKashif M: CD24 Oct4 Immunohistochemical Expression in HNSCC. [Dataset]. Harvard Dataverse. 2024; V1. Publisher Full Text" }	[ { "id": "301583", "date": "31 Jul 2024", "name": "V K Varsha", "expertise": [ "Reviewer Expertise I could understand every aspect of this study because i have done research on Oral cancer stem cells in OSCC" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nLack of Specificity in References:\nThe text refers to studies and reviews without providing specific details about them. For example, \"extensive studies,\" \"a systematic review,\" and references to Okumura et al. (2021) and Mohiuddin et al. (2020) are mentioned without elaborating on their findings, sample sizes, or methodologies. The introduction of intratumoral heterogeneity and the CSC models is somewhat abrupt. Providing a smoother transition and more background information on these concepts would enhance understanding. The significance of CD24 and Oct4 as CSC markers is discussed, but the text lacks details on why these particular markers were chosen for the study over others Some points are repeated, such as the role of CSCs in drug resistance and metastasis. Streamlining these sections would improve readability. The text includes statements that require citations but are not properly referenced. For instance, the sentence \"Two models have been proposed that may explain heterogeneity; the clonal evolution model, and the CSCs model\" lacks a citation. The term \"CSCs\" is used without first defining it as \"cancer stem cells,\" which might confuse readers unfamiliar with the abbreviation. The transition from discussing general CSC markers to specific markers like CD24 and Oct4 is abrupt. Introducing these markers earlier and providing a rationale for focusing on them would improve coherence The logical flow of the text could be improved. For example, the significance of CSC markers could be discussed in one section, followed by specific markers and their roles, and then leading into the aim of the study The results section is dense and difficult to follow. Breaking it down into sub-sections with clear headings (e.g., \"Baseline Characteristics,\" \"Staining Intensity,\" \"Statistical Analysis\") would improve clarity. The overall logical flow of the text could be improved. The methodology, results, and discussion should be clearly delineated with appropriate subheadings to guide the reader through the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-316
https://f1000research.com/articles/13-313/v1	23 Apr 24	{ "type": "Research Article", "title": "Development, validity and reliability of the systematic screening for handwriting difficulties tool ", "authors": [ "Faiçal Farhat", "Achraf Ammar", "Mohamed Moncef Kammoun", "Nourhen Mezghani", "Khaled Trabelsi", "Haitham Jahrami", "Adnene Gharbi", "Haithem Rebai", "Wassim Moalla", "Fatma Kammoun", "Chahnez Triki", "Bouwien Smits-Engelsman", "Faiçal Farhat", "Mohamed Moncef Kammoun", "Nourhen Mezghani", "Khaled Trabelsi", "Haitham Jahrami", "Adnene Gharbi", "Haithem Rebai", "Wassim Moalla", "Fatma Kammoun", "Chahnez Triki", "Bouwien Smits-Engelsman" ], "abstract": "Background The purpose of this study was to develop an Arabic handwriting screening test and establish its psychometric properties.\n\nMethods Handwriting quality was evaluated using seven criteria from the Systematic Screening for Handwriting Difficulties Arabic (SOS-ARB) and writing speed were measured by counting the number of letters produced in 5 minutes. Construct validity was evaluated using hypothesis testing (learning disabilities, sex and age differences). Convergent validity was examined using data from 106 children with dysgraphia who were also administered the French version of the “Concise Assessment Methods of Children’s Handwriting” (BHK). Intrarater, interrater, and test-retest reliability were established for total and item scores.\n\nResults Handwriting test data were collected from 1274 children (6–10 years) in regular education, of whom 194 were diagnosed with Learning Disabilities (LD). The SOS-ARB scores differed between children with and without LD (F (1, 1273) = 330.90, p <.001, η2 = 0.209), males and females, and different age groups. In addition, significant differences in writing speed were shown between children with and without LD (F (1, 1273) = 60.26, p <0.001, η2 = 0.046), between females and males (F (1, 1273) = 7.57, p =0.01, η2 = 0.006), and between the different age groups (F (4, 1270) = 21.762, p <0.001, η2 = 0.065). A correlation coefficient of 0.72 for the quality score between the SOS-ARB and BHK confirmed convergent validity. Intrarater and interrater reliability were excellent in terms of quality scores (ICC coefficients = 0.988 and 0.972, respectively) and letter speed (ICC coefficients = 0.993 and 0.990, respectively). The quality score and letter speed had excellent and good test-retest reliability (ICC co-efficient = 0.968 and 0.784, respectively).\n\nConclusions Results indicate that the SOS-ARB is a valid and reliable tool for scoring Arabic handwriting abilities in elementary school children.", "keywords": [ "Handwriting difficulties", "dysgraphia", "assessment tools", "legibility", "letter speed", "children", "reliability", "validity" ], "content": "Introduction\n\nHandwriting is a fundamental skill for children to learn in elementary school and is indispensable for their contribution to the classroom environment.1 In fact, in many countries, handwriting is the primary tool for knowledge transmission and student evaluation.2 Certainly, different processing subskills, such as morphological awareness, phonological processing and orthographic knowledge, contribute to the development of writing abilities, and their importance remains across elementary school years.3 Furthermore, cognitive and fine motor skills are both implicated in the complex writing acquisition process.4 If fundamental skills, such as fine motor skills, are not assured, text writing can be decreased.5\n\nHandwriting abilities in other languages, such as Chinese,6 Dutch7 and French,8 have been investigated. Although several studies have examined Arabic writing, research on handwriting quality has received little attention.7 Arabic orthography has a Semitic alphabetic writing structure that has complex and unique attributes.9 Moreover, slow-writing children could have problems with rapid adoption of orthographic knowledge rather than a problem in writing speed.10 Indeed, poor ortho-graphic knowledge is more often a larger constraint than motor skills are in children with handwriting difficulties. Nevertheless, specific Arabic orthography features negatively affect writing acquisition in this Semitic language.11 Consequently, these ortho-graphic features constitute a supplementary visual load in word recognition and influence writing acquisition.12\n\nIn primary school, handwriting is critical to academic success.13 Thus, not mastering this activity can create serious challenges for children during the primary phases of learning.14 Previous studies have shown that handwriting problems, particularly the inability to automatically write legible letters at a suitable speed, may be the primary indication of inadequate development of composition skills.15 Dysgraphia is characterized by poor handwriting quality and speed.16 Handwriting difficulties have been found in children with neurodevelopmental disorders, such as dyslexia,17 specific language impairment,18 attention deficit hyperactivity disorder19 and developmental coordination disorder.20,21\n\nHandwriting is a major cause of problems in school-related skills. However, early remediation has been shown to reduce the critical implications of handwriting problems during school careers.22–25 Occupational therapy frequently supports improvements in handwriting skills. Therefore, it is crucial to develop a language-adapted tool to find students with handwriting problems and develop adaptive strategies and interventions.26 To evaluate students’ handwriting performance, several handwriting evaluation methods have been developed27; examples include the Evaluation Tool of Children’s Handwriting–Manuscript (ETCH-M),7 the Minnesota Handwriting Assessment (MHA),28 the Test of Handwriting Skills–Revised (THS-R),29 the Print Tool,30 the Detailed Assessment of Speed of Handwriting (DASH),27 the Concise Evaluation Scale for Children’s Handwriting (BHK) and the Systematic detection of writing problems (SOS-NL).31\n\nThe SOS-NL demonstrated high validity in identifying children with and without handwriting difficulties. The SOS-NL was developed to support educators and therapists in identifying children writing difficulties who require handwriting remediation. This screening tool consists of the seven most sensitive items from the BHK.32 It is therefore much shorter and easier to score. The SOS measures handwriting legibility and speed. Legibility was assessed by evaluating letter formation, letter fluency, letter size, regularity of letter size, spacing between words, alignment, and joins (for cursive writing). Speed is evaluated as letters written within 5 minutes. The SOS is an easy-to-use test and requires only a blank page, pen and timer, making it feasible for use in daily practice.31 SOS has been adapted in other languages33 such as Dutch, Flemish, and German with Latin script but not yet to Arabic writing systems.\n\nArabic-written language have distinct traits and formats based on their origin and evolution.14 The handwriting difficulties appear to be more severe, as Arabic letters are defined by their unique form and intricate multiple-stroke sequences and directions.34 Therefore, words vary in terms of their levels of graphic complexity, demanding that high levels of fine graphomotor skills and motor control abilities are required to make the pen stroke trajectory.35\n\nAs a result of rapid growth of technology, handwriting evaluation has progressed from paper and pencil tasks to computerized assessments, which provide a more scientific and standardized handwriting evaluation. In fact, Falk et al.36 established a computer-based Minnesota Handwriting Assessment to examine handwriting speed and quality. However, similar studies on Arabic handwriting are limited. Currently, no standardized tools have been used to evaluate children’s Arabic handwriting performance, thus data on validity and reliability of outcomes are lacking.9 To accommodate these problems an existing evaluation method, the SOS-NL was adapted, studied, and validated for the SOS-Arabic Handwriting Test (SOS-ARB).\n\nThe purpose of the present study was to examine the construct validity of the SOS-ARB in different ways. Hypothesis testing was used by comparing groups with expected lower scores and higher scores both on handwriting quality and number of letters written. It was hypothesized that children with learning difficulties would score poorer than typically developing children, boys would score poorer than girls and younger children would score poorer than older children. Next, convergent validity was evaluated by comparing the results of the SOS-ARB score of a text written in Arabic to those on the BHK of a text written in French in a group of children with dysgraphia. Correlations between these results were expected to be moderate.\n\nLastly, we investigated whether the SOS-ARB is a reliable tool by means of intrarater, interrater and test-retest analyses in Arabic handwriting scripts.\n\n\nMethods\n\nThe study examined children aged between 6 and 10 years whose native language was Arabic. The children were selected from 17 elementary schools. For this random sample, children were recruited from areas with different degrees of urbanization in Tunisia. In Tunisia, in cooperation with the medical school center, children with learning difficulties (LD) attend mainstream primary schools and receive extra hours of support per week from their teachers. A total of 1300 participants were included, including a random sample of 1096 children without LD and 204 children with LD. The exclusion criteria included mental retardation, sensory disability, physical disability, or severe trauma. Twenty-six children who did not meet the inclusion criteria were excluded from the study, leaving a total of 1274 children (1080 children without LD and 194 children with LD).\n\nIn addition, another 106 children with dysgraphia were selected who were diagnosed by the clinical observation of attending physicians and were selected from the medical school center to participate in this study. Dysgraphia was defined by a score at or below 29 on the French adaptation of the BHK.8\n\nThe protocol and study design were approved, on January 27, 2021, by the Ethical Committee of the University Hospital of Sfax, Tunisia (CPP SUD N° 0300/2021), in accordance with the Code of Ethics of the World Medical Association (Declaration of Helsinki). After a full explanation of the procedure and prior to testing, all the parents provided written consent and signed child assent forms.\n\nTo assure content validity, the SOS was adapted for Arabic use by a diverse group of handwriting experts. The group included neurodevelopmental pediatricians, physical therapists, occupational therapists, speech and language therapists, teachers and pedagogues. Individual members’ comments and suggestions were collected. Based on these suggestions, the Arabic handwritten text has been revised.\n\nThe children were tested as a group in their classrooms. The examiners described procedures to the children. All the children (with and without LD) provided written Arabic text for 5 minutes. In addition, 106 children with dysgraphia provided Arabic and French text separated by one-hour rest.\n\nTo evaluate test-retest reliability, the Arabic text was copied twice by 226 children without LD and 117 children with LD, with an interval of two weeks. These writers were chosen randomly.\n\nThe SOS-ARB and BHK were administered by three trained occupational therapists. These examiners received instruction sessions for 10 hours for both the BHK and SOS-ARB tests. Each examiner practiced scoring 10 copies with the SOS-ARB and 10 copies with the BHK, and ratings were discussed to limit differences and consistency before scoring the participants’ evaluation.\n\nThe BHK\n\nThe BHK test is a standardized norm-referenced instrument used in individual clinical settings and classical school settings. Handwriting quality was assessed using 13 dysgraphia-specific handwriting criteria. These criteria are evaluated on an ordinal scale of 0 to 5, with a high score suggesting poor handwriting. A child with an overall score greater than 28 (the 10th percentile) was classified as dysgraphic. The writing speed was calculated by counting the number of letters produced within five minutes, including letter corrections. The interrater reliability was between 0.82 and 0.93 for writing speed and between 0.42 and 0.63 for writing quality.37 The correlation between the BHK and the De Ajurlaguerra Dysgraphia Scale38 is reported to be 0.78.37,39\n\nThe SOS\n\nThe SOS is a normative test used to identify writing difficulties. It can be used for school-aged children (from the end of the first to the sixth grade) who have a certain level of handwriting proficiency.\n\nThe total number of letters written within five minutes was used to determine writing speed. Handwriting quality was scored on seven characteristics: letter form, writing fluency, connecting strokes, letter height, regularity of letter height, space between words and straightness. These SOS items were used for the SOS-ARB, with lower scores indicating better performance. An assessment with the SOS takes approximately 10 min. The validity and reliability of the tool were found to be good (ICC 0.66–0.88).40 The international guidelines for DCD have recommended the SOS to detect writing problems in children with DCD.41,42\n\nThe SOS-ARB\n\nThe SOS-ARB is based on item descriptions and scores of the SOS but uses a different text. The instructions and administration have not been changed. For the SOS-ARB, the text was constructed to be appropriate for children in terms of its content and linguistic level while considering the phonological, morphological, syntactic and semantic structure of the language. The first paragraph was selected with words and sentences written during the preschool period, after which the text became increasingly complex. The text includes 29 Arabic letters. The text used verbs, nouns, inflectional and derivational forms and terms requiring specific orthographic knowledge thus assuring that the content was appropriate to screen for handwriting problems in this age bracket.\n\nThe handwriting task was to replicate this standard text for 5 minutes (or at least the first five sentences for slow writers) on an unlined A4 piece of paper. The children were asked to copy the text as quickly and accurately as possible.\n\nThe first five sentences were used to assess handwriting quality based on the seven criteria of the SOS, in which 0 signifies the item’s absence and 1 represents its presence. The total score could vary from 0 to 35 points, with a high score indicating poor handwriting quality. Writing speed was calculated as the number of characters (i.e., letters as well as punctuation marks) written per minute.\n\nThe Kolmogorov–Smirnov test was used to determine the normality of the distribution of all the variables. The mean (M) and standard deviation (SD) were used to represent the data, while categorical variables are shown as the frequency and score. Univariate analysis of variance with 3 between subject factors (learning level, sex and age) was used to examine the effect on writing quality and speed. Pearson correlation coefficients were used to assess the convergent validity between the SOS-ARB and BHK scores.\n\nFor reliability, the scores between the two measurements were evaluated using the intraclass correlation coefficient (ICC) and the corresponding 95% confidence interval. To assess the intrarater, interrater, and test-retest reliability of the total quality score and writing speed (number of characters), we used the ICC (two-way mixed effects model, single measures). An ICC of 0.3-0.5 indicates lower reliability; 0.5-0.7 indicates moderate reliability; 0.7-0.9 indicates high reliability; and 0.9-1.0 indicates excellent reliability.43 Kappa statistics were used to assess intrarater, interrater, and test-retest agreement for item scores. Kappa values range from -1 to +1, with the following categories: -1 for perfect disagreement, 0 for chance agreement, 0-0.2 for poor agreement, 0.21-0.4 for fair agreement, 0.41-0.60 for moderate agreement, 0.61-0.80 for good agreement, and 0.81-1 for very good agreement.44\n\nThe standard error of measurement (SEM) and the smallest detectable change (SDC) were calculated. The SEM was determined by dividing standard deviation of the difference by the square root of two Sd’s. To calculate the SDC (95%), the standard deviation of the difference was multiplied by the 1.96. The systematic proportional bias was visually examined using Bland–Altman plots between the time points and limits of agreement (2 SDs). The significance level was set at p < 0.05. All the statistical analyses were performed using SPSS 28.\n\n\nResults\n\nThe demographic data are shown in Table 1. Children were classified by grade and age.\n\nA total of 515 males (47.7%) and 565 females (52.3%) were without LD, while 108 males (55.7) and 86 females (44.3%) were with LD.\n\nThe main results concerning the handwriting performance of the children with and without LD in grades 1 to 5 are presented in Table 2. Table 2 shows the quality scores and letter speeds corresponding to age, sex, and group (with and without learning difficulties) based on the Arabic handwritten text results.\n\na A high score corresponds to poor handwriting quality.\n\nb Letter speed is the number of characters (letters as well as punctuation marks) produced in 5 min.\n\nHandwriting quality scores: The univariate analysis of variance results are summarized in Table 3, which shows the differences according to learning level (NoLD/LD), age and sex. The analysis indicated significant differences in handwriting quality scores between children with and without LD (F (1, 1273) = 330.90, p < 0.001, η2 = 0.209). A significant main effect of sex (F (1, 1273) = 6.91, p < 0.01, η2 = 0.005) and age (F (4, 1270) = 23.04, p < 0.001) was shown for the total scores. Figure 1 illustrates the differences in handwriting quality between age groups for boys and girls. Figure 2 shows the differences in age groups for children with and without LD, all in the hypothesized directions. As expected, the handwriting score on each subtest increased with age (Figure 1). The post hoc analysis of the quality handwriting score for the total children found that quality scores differ between Grade 1 and Grade 2. There was no improvement between Grade 2 and Grade 3, Grade 3 and Grade 4 or Grade 4 and Grade 5. Likewise, post hoc results showed an increase in writing quality from second to fourth grade and improvement from third to fifth grade (Table 4).\n\nLD = Learning Difficulties.\n\nBoys had significantly poorer performance than girls but with small effect size (p = 0.01 Cohen d = 0.14).\n\nThe analysis also revealed that the difference in quality score between the NoLD and LD groups was large (partial η2 = 0.21; Cohen d = 1.03). The probability that a randomly chosen Arabic writer with poor handwriting will have a higher score (worse) than a randomly chosen learner without poor handwriting was 77%, indicating good discriminative validity. Importantly, no significant first or second order interactions emerged.\n\nHandwriting speed scores: Significant differences were found in letter speed between children with and without LD (F (1, 1273) = 60.26, p < 0.001, η2 = 0.046), between boys and girls (F (1, 1273) = 7.57, p = 0.01, η2 = 0.006), and between the different age groups (F (4, 1270) = 21.62, p < 0.001, η2 = 0.065). The effect sizes for the differences between age groups were moderate for letter speed. Figure 3 shows that the letter speed increased, with age. Girls had significantly greater writing speeds (31 letters more in 5 minutes) than boys. Figure 4 also shows the differences in letter speed (mean difference = -98.99 letters, p < 0.001) between children with and without LD. However, the interaction between age and learning level group was significant (F (4, 1270) = 3.84, p < 0.01) indicating that there was a small difference in speed development (Partial η2 = 0.003; Table 3) between children with and without LD, which made the gap larger as children became older. No other first or second order interactions emerged.\n\nLD = Learning Difficulties.\n\nA correlation was found between age, handwriting quality and speed score for children with LD (quality, r = -0.48; speed, r = 0.61) and without LD with (quality, r = -0.34; speed, r = 0.47).\n\nThe results of 105 children (61 males, 44 females) with writing problems between 8 and 10 years of age (mean age 8.97 years, SD = 0.81) were used to compare the BHK and SOS-ARB scores. The Pearson correlation coefficient between total BHK and the SOS-ARB score was 0.72 (p < 0.001) for the quality score.\n\nA total of 343 participants—226 children without LD and 117 children with LD—were selected from the different age groups for the reliability analysis. The intraclass correlation coefficient (ICC) and kappa coefficient statistics are reported in Table 5.\n\nFor intrarater reliability, the written text was evaluated a second time by the same rater after two weeks. The intrarater reliability was excellent for quality (ICC coefficient = 0.988 (0.985 – 0.990)) and letter speed (ICC coefficient = 0.993 (0.991 – 0.994)). The quality score per item (Kappa coefficients) demonstrated good to very good intrarater reliability (see Table 5). The Bland–Altman plots of the intrarater reliability quality score revealed that the systematic error for the mean value between the two test occasions was 0.24 points, and the limits of agreement (d ±1.96 SD) were 3.17 and -2.69 points (see Figure 5). With respect to writing letter speed, the results indicated a systematic error of 0.72 letters for the mean value between the two test sessions, and the limits of agreement (d ±1.96 SD) were 2.68 and -1.24 letters (Table 6).\n\nFor interrater reliability, the written text was evaluated a second time by another rater. The results are reported in Table 5. The ICCs indicated excellent interrater reliability for quality score and letter speed. The total Arabic handwriting quality score and writing speed were excellent (range from 0.965 to 0.992). The items of the quality score (with kappa coefficients ranging between 0.534 and 0.745) showed moderate to good interrater reliability (Table 5). The Bland–Altman plots for the interrater reliability quality score showed that the mean score had a systematic error of -0.79 points between the two tests, and the limits of agreement (d ± 1.96 SD) were 3.75 and -5.34 points (see Figure 6). Like-wise, the systematic error for the mean writing letter speed between the two test occasions was 5.32 points, and the limits of agreement (d ± 1.96 SD) were 7.28 and 3.36 letters (Table 6).\n\nFor test-retest reliability the selected group of children repeated the SOS-ARB after 2 weeks. As shown in Table 5, the ICC of the test-retest reliability coefficient was excellent for quality 0.968, and good for the writing speed (0.784). Test-retest reliability at the item level was moderate to good, with kappa coefficients ranging from 0.466 to 0.662. The Bland–Altman plots for the test-retest reliability quality score showed that the systematic error for the mean score between the two test occasions was -0.61 points, and the limits of agreement (d ± 1.96 SD) were 4.27 and -5.5 points (see Figure 7). In addition, the systematic error for the mean letter speed between the two test occasions was 3 letters, and the limits of agreement (d ± 1.96 SD) were 1 to 5 letters (Table 6).\n\n\nDiscussion\n\nHandwriting is an important and complex skill. A valid and reliable evaluation is required to identify children with handwriting difficulties. No standardized tool for handwriting assessment for Arabic in available. The aim of this study was to develop the SOS-Arabic handwriting test (SOS-ARB) and to establish aspects of validity and reliability.\n\nTo have content validity, the SOS-ARB must include the distinctive characteristics of the Arabic orthography. Indeed, much emphasis was placed on developing writing texts with content suitable for the children’s grade level using a team of experts. All the 29 letters needed to be present in various forms (initial, middle or final) in the text. Similarly, the scoring system must reflect Arabic’s distinctive characteristics, including letter construction and spatial organization. Our findings showed that the Arabic version of the SOS test is feasible in terms of instructions, assessment times, and different tasks. The SOS-ARB appears to be appropriate for evaluating children in grades one through five.\n\nIn this study, the letter speed was lower for children with LD than for those without LD. Likewise, children with LD had higher total quality scores, indicating poor quality writing, thus confirming discrimination properties of the SOS-ABR. These outcomes were in accordance with other findings in which the SOS was used to differentiate between students with and without handwriting difficulties.40 Another study highlighted a significant difference in the BHK scale score between twenty-nine children with writing difficulties and twenty children without writing difficulties in the second and third grades.45 Importantly, children with LD have a higher prevalence of reading disorders, and difficulties in reading could affect writing speed.46\n\nOur results showed that comparisons between children with and without LD revealed that there was a significant interaction effect between age group and letter speed. Thus, handwriting development differs for children with LD. Children with LD may require special help at younger ages to avoid the widening of the gap. Our results showed that writing speed was more related to age then for quality. Moreover, a higher correlation was found between age and letter speed (r = 0.61) for children with LD than for children without LD (r = 0.47). However, writing speed can be the result of multiple factors, including motivation, attention and fatigue.47\n\nOur findings showed that writing quality and letter speed improved from first to fifth grade. These findings are consistent with the development of handwriting abilities in other languages. Moreover, the evolution of handwriting performance was not linear. The present study showed that quality scores differ between Grade 1 and Grade 2. There was no improvement between Grade 2 and Grade 3, Grade 3 and Grade 4 or Grade 4 and Grade 5, demonstrating an important improvement in handwriting quality during the first year of learning followed by an absence of large evolution of the quality in the next Grades.48 These results, however, differ from those of another study in English language which significant progress was shown between Grades 2 and 3, following a stable period throughout Grade 4, and a slight increase between Grades 5 and 6.49 These variances could be attributed to curricular disparities in the scheduling and teaching of handwriting in different countries.50 Similarly, our results revealed an increase in writing quality from second to fourth Grade and improvement from third to fifth Grade. These findings are consistent with previous research showing that children in fourth grade with an Arabic native language evaluate their handwriting measured performance better than children in second grade do.9 Indeed, the age disparities observed in our study showed that the SOS-Arabic may be sensitive enough to developmental changes in handwriting during the early primary school years.\n\nThe current study showed that girls wrote more legibly than boys. These results were compatible with the findings of previous literature reviews.9 This sex disparity could be explained by girls’ earlier acquisition of motor control, particularly in activities demanding visual-motor coordination and tracing.51 Moreover, in girls the left hemisphere matures faster. This could explain their superiority in the verbal domain necessary for reading and transcribing a text, which may also explain part of differences in copying a text.52\n\nMoreover, we also found sex disparities in terms of letter speed. These conclusions were concordant with prior research findings. In this context, in a Dutch-speaking sample, findings showed an important disparity in favor of girls.53 Furthermore, previous studies have shown significant sex differences in writing speed for Flemisch40 and Arabic45 handwritten texts, whereas in other studies, no sex difference was noted in the Arabic handwriting performance.9\n\nThe findings also showed good concurrent validity of the SOS-ARB with the BHK test using French text. A correlation of 0.72 in quality scores between both tests confirmed convergent validity, which is consistent with the reported coefficient of 0.70 between the BHK and the test SOS40 between the scores of both tests in Dutch.\n\nThe results of this study showed that the SOS-ARB has excellent intrarater, interrater and test-retest reliability for quality score and letter speed. The SOS-ARB is a reliable tool for measuring handwriting ability in children. The excellent interrater reliability of the items indicates that the interpretation and administration of the item scores are robust. The SOS-ARB is well standardized and provides stable outcomes over time. However, the interrater reliability was based on data from only three trained testers. Indeed, in this study, the reason for the excellent interrater reliability was that the raters received ten hours of training and practiced with 10 copies of children with and without LD.\n\nThe intrarater, interrater, and test-retest reliability of the items varied between moderate and very good. The moderate test-retest reliability observed for several item scores could be explained by fluctuations in handwriting style according to motivation, attention level, sense of achievement and goal of attainment in the writing task.54 However, the children were asked to copy the text twice in 2 weeks. This could have decreased their motivation and attention in the retest without any concrete goal of attainment or sense of achievement.\n\nThe SOS-ARB was administered to children with and without handwriting difficulties and could provide an outcome measure for interventions aimed at improving handwriting skills. Previous research has shown that the orthographic properties of written language influence word length, allographic choice, letter complexity, and letter connections.55 Moreover, handwriting legibility is influenced by children’s copying strategy (whole words or letter-by-letter).34 Subsequently, children could be trained to compose fluently connected handwriting, and spacing of letters and words. In fact, the interaction of the multiple unique aspects of the Arabic writing system may not limit the overall legibility of handwriting but rather favor flowing and continuous movements.\n\nThe analysis of the psychometric properties of the SOS-ARB yielded promising results; however, expanding the study to include other Arabic-speaking countries is needed in further studies. This study showed that the SOS-ARB can be useful for assessing Arabic handwriting. Additional investigations are needed to determine the predictive validity of the SOS-ARB score, collect reference norms in different Arabic-speaking countries and determine a clear cut-off point for poor handwriting ability or dygraphia based on this tool.\n\nIn addition, Tunisian children are confronted with concurrent precocious graphic systems (Arabic and Latin writing), which include two distinct graphic structures that could provoke interference between the two different scripts and could have a substantial impact on the development of handwriting abilities. Hence, it is important to compare scripts used by children in different academic systems.\n\nThe SOS-Arabic could also be used in other groups of children known to have a high incidence of poor handwriting such as attention-deficit/hyperactivity disorder, learning disability, dyslexia or developmental coordination disorder. In this context, the SOS-ARB may also be an excellent tool for occupational therapists, in addition to educators. The SOS-ARB permits identifying children with difficulties in Arabic handwriting as starting point for handwriting intervention programs.\n\n\nConclusion\n\nThis study showed that the SOS-ARB is a valid test for assessing handwriting ability in elementary school. During its development, it was important to consider the unique orthography of Arabic-speaking children. Data in other Arabic-speaking countries could be acquired and investigated to examine the generalizability of the SOS-ARB.\n\nThe SOS-ARB results obtained in the present study indicate excellent inter- and intrarater reliability and high test-retest reliability. A comparison with the BHK confirmed the convergent validity of the SOS-ARB quality writing score.\n\nThe structural validity and reliability of the SOS-ARB were the first steps in providing insight into the psychometric properties of the test, which will help with the identification of children with handwriting difficulties in Arabic-speaking countries.\n\n\nEthics and consent\n\nThe protocol and study design were approved, on January 27, 2021, by the Ethical Committee of the University Hospital of Sfax, Tunisia (CPP SUD N° 0300/2021), in accordance with the Code of Ethics of the World Medical Association (Declaration of Helsinki).\n\nAfter a full explanation of the procedure and prior to testing, all the parents provided written consent and signed child assent forms.", "appendix": "Data availability\n\nZenodo: Development, validity and reliability of the systematic screening for handwriting difficulties tool. https://zenodo.org/doi/10.5281/zenodo.10880839. 56\n\nThis project contains the following underlying data:\n\n1. Data of 1274 participants in the RCT titled Development, validity and reliability of the systematic screening for handwriting difficulties tool.\n\n2. Data guidelines in the RCT titled Development, validity and reliability of the systematic screening for handwriting difficulties tool.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe acknowledge the support of parents, children, and management of the participating schools.\n\n\nReferences\n\nRosenblum S: Development, reliability, and validity of the Handwriting Proficiency Screening Questionnaire (HPSQ). Am. J. Occup. Ther. 2008; 62(3): 298–307. PubMed Abstract \| Publisher Full Text\n\nCahill SM: Where Does Handwriting Fit In: Strategies to Support Academic Achievement. Interv. Sch. Clin. 2009; 44(4): 223–228. Publisher Full Text\n\nTaha H, Saiegh-Haddad E: Morphology and spelling in Arabic: Development and interface. J. Psycholinguist. Res. 2017; 46(1): 27–38. PubMed Abstract \| Publisher Full Text\n\nRichards TL, Berninger VW, Stock P, et al.: Differences between good and poor child writers on fMRI contrasts for writing newly taught and highly practiced letter forms. Read. Writ. 2011; 24(5): 493–516. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeverly ST: The importance of handwriting speed in adult writing. Dev. Neuropsychol. 2006; 29(1): 197–216. PubMed Abstract \| Publisher Full Text\n\nPoon K, Li-Tsang C, Weiss T, et al.: The effect of a computerized visual perception and visual-motor integration training program on improving Chinese hand-writing of children with handwriting difficulties. Res. Dev. Disabil. 2010; 31(6): 1552–1560. PubMed Abstract \| Publisher Full Text\n\nAmundson SJ: Evaluation Tool of Children’s Handwriting: ETCH examiner’s manual. OT KIDS; 1995.\n\nCharles M, Soppelsa R, Albaret J: Échelle d’évaluation rapide de l’écriture chez l’enfant. EAP, Éditions et applications psychologiques; 2004.\n\nSalameh-Matar A, Basal N, Nashef-Tali B, et al.: Development and validity of the Arabic Handwriting Assessment for elementary school students. Br. J. Occup. Ther. 2016; 79(4): 212–219. Publisher Full Text\n\nSumner E, Connelly V, Barnett AL: The influence of spelling ability on hand-writing production: children with and without dyslexia. J. Exp. Psychol. Learn. Mem. Cogn. 2014; 40(5): 1441–1447. PubMed Abstract \| Publisher Full Text\n\nMahfoudhi A, Everatt J, Elbeheri G: Introduction to the special issue on literacy in Arabic. Read. Writ. 2011; 24(9): 1011–1018. Publisher Full Text\n\nAsaad H, Eviatar Z: The effects of orthographic complexity and diglossia on letter naming in Arabic: A developmental study. Writ. Syst. Res. 2013; 5(2): 156–168. Publisher Full Text\n\nMaldarelli JE, Kahrs BA, Hunt SC, et al.: Development of early hand-writing: Visual-motor control during letter copying. Dev. Psychol. 2015; 51(7): 879–888. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTaha H, Khateb A: Resolving the orthographic ambiguity during visual word recognition in Arabic: an event-related potential investigation. Front. Hum. Neurosci. 2013; 7: 821.\n\nBerninger VW, Rutberg JE, Abbott RD, et al.: Tier 1 and Tier 2 early intervention for handwriting and composing. J. Sch. Psychol. 2006; 44(1): 3–30. Publisher Full Text\n\nGargot T, Asselborn T, Pellerin H, et al.: Acquisition of handwriting in children with and without dysgraphia: A computational approach. PLoS One. 2020; 15(9): e0237575. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPhelps J, Stempel L: The identification of dyslexic handwriting through grapho-analysis. Development of Graphic Skills: Research, Perspectives, and Educational Impli-cations. London: Academic Press; 1991; pp. 191–203.\n\nDockrell JE, Lindsay G, Connelly V, et al.: Constraints in the production of written text in children with specific language impairments. Except. Child. 2007; 73(2): 147–164. Publisher Full Text\n\nTucha O, Lange KW: The effect of conscious control on handwriting in children with attention deficit hyperactivity disorder. J. Atten. 2005; 9(1): 323–332. PubMed Abstract \| Publisher Full Text\n\nGeuze R: Motor impairment in DCD and activities of daily living In: Sugden D; Chambers M. editors. Children with developmental coordination disorder. 2005; pp. 19–46.\n\nSmits-Engelsman BC, Niemeijer AS, van Galen GP : Fine motor deficiencies in children diagnosed as DCD based on poor grapho-motor ability. Hum. Mov. Sci. 2001; 20(1-2): 161, 182–182. PubMed Abstract \| Publisher Full Text\n\nEngel-Yeger B, Nagauker-Yanuv L, Rosenblum S: Handwriting performance, self-reports, and perceived self-efficacy among children with dysgraphia. Am. J. Occup. Ther. 2009; 63(2): 182–192. PubMed Abstract \| Publisher Full Text\n\nBiotteau M, Danna J, Baudou É, et al.: Developmental coordination disorder and dysgraphia: signs and symptoms, diagnosis, and rehabilitation. Neuropsychiatr. Dis. Treat. 2019; 15: 1873–1885. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJongmans MJ, Linthorst-Bakker E, Westenberg Y, et al.: Use of a task-oriented self-instruction method to support children in primary school with poor handwriting quality and speed. Hum. Mov. Sci. 2003; 22(4-5): 549–566. PubMed Abstract \| Publisher Full Text\n\nTaras H, Brennan J, Gilbert A, et al.: Effectiveness of occupational therapy strategies for teaching handwriting skills to kindergarten children. J. Occup. Ther. Sch. Early Interv. 2011; 4(3-4): 236–246. Publisher Full Text\n\nGerde HK, Foster TD, Skibbe LE: Beyond the pencil: Expanding the occupa-tional therapists’ role in helping young children to develop writing skills. Open J. Occup. Ther. 2014; 2(1): 5.\n\nFrancis A, Wallen M, Bundy A: Comparison of the properties of the Handwriting Speed Test (HST) and Detailed Assessment of Speed of Handwriting (DASH): An exploratory study. Phys. Occup. 2017; 37(2): 155–169.\n\nReisman J: Minnesota handwriting assessment. Psychological Corporation; 1999.\n\nMilone MN: Test of handwriting skills, revised. Academic Therapy Publications; 2007.\n\nOlsen JZ, Knapton EF, Fine EH: Handwriting without tears: Handwriting without tears.2008.\n\nSmits-Engelsman B, van Bommel-Rutgers I , Van Waelvelde H: Systematische Op-sporing Schrijfproblemen. SOS-2–NL.2014.\n\nHamstra-Bletz E, De Bie J, Den Brinker B: Beknopte beoordelingsmethode voor kinderhandschriften: Experimentele versie [The concise assessment scale for children’s handwriting: Experimental version]. City: Lisse: Swets & Zeitlinger.1987.\n\nFranken AM, Harris SR: Teachers’ Perceptions of Handwriting Legibility Versus the German Systematic Screening for Motoric-Handwriting Difficulties (SEMS). OTJR (Thorofare N J). 2021 Oct; 41(4): 251–258. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhoury-Metanis A, Asadi IA, Khateb A: The contribution of basic linguistic skills to handwriting among fifth-grade Arabic-speaking children. Writ. Syst. Res. 2018; 10(2): 95–110. Publisher Full Text\n\nGosse C, Carbonnelle S, De Vleeschouwer C, et al.: Specifying the graphic characteristics of words that influence children’s handwriting. Read. Writ. 2018; 31(5): 1181–1207. Publisher Full Text\n\nFalk TH, Tam C, Schellnus H, et al.: On the development of a computer-based handwriting assessment tool to objectively quantify handwriting proficiency in children. Comput. Methods Prog. Biomed. 2011; 104(3): e102–e111. PubMed Abstract \| Publisher Full Text\n\nLoizzo A, Zaccaria V, Caravale B, et al.: Validation of the Concise Assessment Scale for Children’s Handwriting (BHK) in an Italian Population. Children. 2023; 10(2): 223. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDe Ajurlaguerra J, Auzias M, Coumes F, et al.: L’écriture de l’enfant: L’evolution de l’écriture et ses difficultés.[Children’s handwriting: The development of handwriting and problems in handwriting.]. Paris: Delachaux et Niestlé; 1979. Google Scholar.\n\nHamstra-Bletz L, Blöte AW: A longitudinal study on dysgraphic handwriting in primary school. J. Learn. Disabil. 1993; 26(10): 689–699. PubMed Abstract \| Publisher Full Text\n\nVan Waelvelde H, Hellinckx T, Peersman W, et al.: SOS: a screening instrument to identify children with handwriting impairments. Phys. Occup. 2012; 32(3): 306–319.\n\nBieber E, Smits-Engelsman BC, Sgandurra G, et al.: Manual function outcome measures in children with developmental coordination disorder (DCD): Systematic review. Res. Dev. Disabil. 2016; 55: 114–131. PubMed Abstract \| Publisher Full Text\n\nBlank R, Barnett AL, Cairney J, et al.: International clinical practice recommendations on the definition, diagnosis, assessment, intervention, and psychosocial aspects of developmental coordination disorder. Dev. Med. Child Neurol. 2019; 61(3): 242–285. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHinkle Dennis E, Wiersma W, Jurs Stephen G: Applied Statistics for the Behavioral Sciences. City: Houghton Mifflin College Div.; 1998.\n\nAltmann D: Practical statistics for medical research. City: London, Chapman and Hall; 1991.\n\nVolman M, van Schendel BM , Jongmans MJ: Handwriting difficulties in primary school children: A search for underlying mechanisms. Am. J. Occup. Ther. 2006; 60(4): 451–460. PubMed Abstract \| Publisher Full Text\n\nOvervelde A, Hulstijn W: Handwriting development in grade 2 and grade 3 primary school children with normal, at risk, or dysgraphic characteristics. Res. Dev. Disabil. 2011; 32(2): 540–548. PubMed Abstract \| Publisher Full Text\n\nGraham S, Weintraub N: A review of handwriting research: Progress and prospects from 1980 to 1994. Educ. Psychol. Rev. 1996; 8(1): 7–87. Publisher Full Text\n\nKarlsdottir R, Stefansson T: Problems in developing functional handwriting. Percept. Mot. Skills. 2002; 94(2): 623–662. Publisher Full Text\n\nMojet JW: Characteristics of the developing handwriting skill in elementary education. Development of graphic skills. 1991; pp. 53–75.\n\nMatta Abizeid C, Tabsh Nakib A, Younès Harb C, et al.: Handwriting in lebanese bigraphic children: standardization of the bhk scale. J. Occup. Ther. Sch. Early Interv. 2017; 10(4): 420–435.\n\nFlatters I, Hill LJ, Williams JH, et al.: Manual control age and sex differences in 4 to 11 year old children. PLoS One. 2014; 9(2): e88692. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNikolaenko N: Sex differences and activity of the left and right brain hemispheres. J. Evol. Biochem. Physiol. 2005; 41(6): 689–699. Publisher Full Text\n\nSimons J, Probst M: Reliability of the detailed assessment of speed of handwriting on Flemish children. Pediatr. Phys. Ther. 2014; 26(3): 318–324. PubMed Abstract \| Publisher Full Text\n\nKaplan A, Lichtinger E, Gorodetsky M: Achievement goal orientations and self-regulation in writing: An integrative perspective. J. Educ. Psychol. 2009; 101(1): 51–69. Publisher Full Text\n\nKandel S, Valdois S: Syllables as functional units in a copying task. Lang. Cognitive. Proc. 2006; 21(4): 432–452. Publisher Full Text\n\nFarhat F: Data of 1274 participants in the RCT titled Development, validity and reliability of the systematic screening for handwriting difficulties tool. [Dataset]. Zenodo. 2024. (Last Visit: Mars 26, 2024). Publisher Full Text" }	[ { "id": "270486", "date": "30 May 2024", "name": "Linda Greta Dui", "expertise": [ "Reviewer Expertise machine learning an technological tools for specific learnin gisorders" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study provides the validation of the adaptation to the Arabic language of a handwriting test. More details could be provided about the development of the test.\nReading the introduction, it is not fully clear if the main aim of the SOS questionnaire is to assess quality with or without accounting for orthography (pure dysgraphia or dysorthographia?) One of the hypotheses is that males would perform worse than girls. This is a fact in literature, but it should be introduced better.\nIn the Data Collection paragraph, it is not clear if your sample size was dimensioned using statistical power techniques, or which is the rationale behind the choice of your sample.\nThe Measures section would benefit from a common structure between paragraphs. E.g., scoring method, thresholds (these details are missing in the SOS paragraph). BHK: it is not clear if a child is dysgraphic if scoring above 28 (as in the Measures paragraph) or below 29 (as in the Participants paragraph), or if it is a difference in the French adaptation. SOS-ARB: please, report how many letters has the Arabic alphabet in the sentence \"The text includes 29 Arabic letters .... OUT OF ??\"\nStatistical analysis You are assuming that variables are normal, but please specify.\nAre males and females matched in your sample?\nBe consistent: NoLD or TD\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "270493", "date": "06 Jun 2024", "name": "Denise Lesley Franzsen", "expertise": [ "Reviewer Expertise Rehabilitation", "Research methods", "Occupational Therapy", "Standardized assessments", "Handwriting" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDevelopment, validity and reliability of the systematic screening for handwriting difficulties tool\n\nIs the work clearly and accurately presented and does it cite current literature?\nSome revision to provide more clarity is required but relevant and recent literature is cited. Some texts are not recent but are appropriate to the study since handwriting assessments cited and used for development of the current assessment were published in the late 1990s and early 2000s.\nIs the study design appropriate and does the work have academic merit?\nThe study design covers all expected psychometric tests for confirming the validity and reliability of a newly developed assessment. Although there is an existing Arabic Handwriting Assessment (A‑HAT) as indicated in the article this newly developed SOS-ARB is a shorter more easily administered assessment suit to screening and identifying dysgraphia amongst learners writing Arabic. The study has merit since it includes a large sample size and has considered all appropriate variables when assessing handwriting.\nAre sufficient details of methods and analysis provided to allow replication by others?\nSome methods need clarity – see comments.\nIf applicable, is the statistical analysis and its interpretation appropriate?\nAll is in line with test psychometrics with normal distribution of the data being established prior to analysis and both statistical significance and effect sizes reported. Interpretation is in line with that for psychometric properties of new assessments.\nAre all the source data underlying the results available to ensure full reproducibility?\nYes\nAre the conclusions drawn adequately supported by the results?\nYes\nComments In the introduction introduce the concept of the need for a quicker assessment that is easily scored but do not indicate longer standardized Arabic version of handwriting assessments exist. Reword hypothesis – poorer does not seem appropriate here. It is not clear if all children write in both Arabic and Latin scripts. Why was a second sample of 106 children (105 in results) with dysgraphia were selected (did the others write in Arabic only) – it would seem they completed two assessments for establishing concurrent validity between the BHK and SOS-ARB scores. Need to clarify that this was a separate sample who wrote in both Arabic and Latin text. Were selected appears twice in the sentence about these children. To evaluate test-retest reliability, indicate children were chosen randomly from the existing school based sample of 1274 children. None of the tables or figure indicate the sample size. When comparing scores for boys and girls did this include children with and without LD. Would be useful in identifying which sample the results represent. It may not be necessary to include the SOS as a Measure – rather include this information under the development of the SOS-ARB or in the introduction. Some statistical analysis gives interpretation of scores and methods of calculation. This is not done consistently so could be removed. Effect size (Cohen d) reported in the results is not mentioned in this section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-313
https://f1000research.com/articles/12-1070/v1	31 Aug 23	{ "type": "Brief Report", "title": "Validation and in vivo characterization of research antibodies for Moesin, CD44, Midkine, and sFRP-1.", "authors": [ "Suzanne Doolen", "Riham Ayoubi", "Carl Laflamme", "Ranjita Betarbet", "Elizabeth Zoeller", "Sean-Paul G. Williams", "Haian Fu", "Allan I. Levey", "S. J. Sukoff Rizzo", "Suzanne Doolen", "Riham Ayoubi", "Carl Laflamme", "Ranjita Betarbet", "Elizabeth Zoeller", "Sean-Paul G. Williams", "Haian Fu", "Allan I. Levey" ], "abstract": "Background: A major goal of the Target Enablement to Accelerate Therapy Development for Alzheimer’s disease (TREAT-AD) program is to develop and identify high-quality tools to test target or mechanistic hypotheses. As part of this initiative, it is important that commercial reagents including research antibodies being used to interrogate drug targets have confirmed validation data in knock-out cell lines. Ideally, these antibodies should also have utility for both in vitro and in vivo studies such that the levels of target proteins in target tissues can be quantified. Methods: We evaluated commercial antibodies against TREAT-AD protein targets Moesin (Uniprot ID: P26038), CD44 (Uniprot ID: P16070), Midkine (Uniprot ID: P21741) and Secreted frizzled-related protein 1, referred to as “sFRP-1” (sFRP-1; Uniprot ID: Q8N474). Moesin, Midkine and sFRP-1, that were confirmed as selective based on data in knock-out cell lines. Western blot analysis was used to compare protein levels in brain homogenates from a mouse model with AD-relevant pathology (5XFAD) versus age-matched C57BL/6J control mice.\n\nResults: Anti-Moesin ab52490 reacted in mouse brain homogenate with a predicted molecular weight of 68 kDa. Moesin protein expression was 2.8 times higher in 5xFAD compared to WT. Anti-CD44 ab189524 reacted with a band at the predicted size of 82 kDa. CD44 protein expression was 1.9 times higher in 5xFAD compared to WT. Anti-Midkine AF7769 reacted with a band ~16 kDa and a 17.8 times greater expression in 5xFAD compared to WT. Anti-sFRP-1 ab267466 reacted with a band at 35 kDa as predicted. sFRP-1 protein expression was 11.9 times greater in 5xFAD compared to WT. Conclusions: These data confirm the utility of these selective commercially available antibodies against Moesin, CD44, Midkine, and sFRP-1 for in vivo studies in mice and provide insight into the use of 5XFAD mice for in vivo target engagement studies for these target proteins.", "keywords": [ "Alzheimer’s disease", "Moesin", "sFRP-1", "Midkine", "antibody characterization", "Western blot", "mice", "5xFAD" ], "content": "Introduction\n\nAlzheimer’s Disease (AD) is a debilitating neurodegenerative disorder affecting an estimated 6.7 million Americans age 65 years and older with no clear understanding of the disease mechanism (‘2023 Alzheimer’s disease facts and figures’ 2023). Leading mechanistic hypotheses, such as the amyloid and tau hypotheses, have yet to generate fully efficacious therapies that can prevent or stop AD. As part of a national effort to develop therapeutics and biomarkers for AD, the Accelerated Medicines Partnership for Alzheimer’s Disease (AMP-AD) Consortium has been leveraging unbiased molecular profiling data at the genomic, transcriptomic, proteomic and metabolomic levels to further understanding of AD pathogenesis. Recent studies as part of AMP-AD have used a tandem mass tag mass spectrometry (TMT-MS) approach of postmortem brain tissues to reveal new AD-related protein co-expression modules (Seyfried et al. 2017; Johnson et al. 2020). These protein modules were strongly correlated with higher neuropathological burden and worse cognitive outcomes (Seyfried et al. 2017; Johnson et al. 2020). One such module referred to as Module 4 or “M4” included Moesin and CD44 and had the strongest correlation with higher neuropathological burden and worse cognitive outcomes (Seyfried et al. 2017; Johnson et al. 2020). M4 was enriched in microglial and astrocytic proteins and contains proteins involved in response to inflammation. Another novel AD-associated module, M42 or the matrisome module, had a significant correlation with global pathology and is a source of promising therapeutic targets and biomarkers for AD. M42, which was not present in RNA networks, contained several proteins that have previously been identified by TMT-MS and shown to be correlated with amyloid-beta deposition in brain as well as with Midkine and sFRP-1 (Higginbotham et al. 2020; Ping et al. 2018; Bai et al. 2020; Johnson et al. 2018, 2022).\n\nAlthough the quality of research antibodies has been long been an issue (Weller 2018), technical, economic and sociological challenges obstacles impede proper antibody characterization. The recent democratization of the CRISPR-Cas9 technology allows the generation of ideal isogenic controls for proper antibody characterization (Laflamme et al. 2019, 2021). We have characterized commercial antibodies against Moesin (Alshafie et al. 2023), Midkine (Ayoubi et al. 2023a), sFRP-1 (Ayoubi et al. 2023b). As commercial research antibodies become available and validated in commercially available human knock-out cell lines, it is essential to extend the characterization of these antibodies in murine tissues to enable their use in AD-mouse models.\n\nThe 5xFAD mouse is a well-characterized transgenic model that manifests Aβ plaque deposition as early as 4-6 months of age (Jawhar et al. 2012; Oakley et al. 2006). Here we have characterized the expression of the TREAT-AD target proteins Moesin, CD44, Midkine and sFRP-1 in the 5xFAD mouse model in comparison to age-matched non-transgenic C57BL/6J controls. This allows not only for confirmation of the presence and/or changes in the protein level of target proteins but these antibodies also serve as tools for future in vivo target engagement studies as we evaluate the potential of novel therapeutic agents to modulate disease.\n\n\nMethods\n\nIn vivo studies were in line with NIH Guide for The Care and Use of Laboratory Animals (Council 2011) and followed the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines (Kilkenny et al. 2010; Doolen & Rizzo 2023b). Prior to study initiation (April 2023) all in vivo procedures were reviewed approved by the University of Pittsburgh Institutional Animal Care and Use Committee (IACUC). All efforts were made to ameliorate harm to the animals by adherence to the 3 Rs alternatives; replacement, reduction and refinement (Tannenbaum and Bennett 2015).\n\nAdult male and female 5xFAD (JAX MMRRC Stock #034840; B6.Cg-Tg (APPSwFlLon,PSEN1M146LL286V)6799Vas/Mmjax) and C57BL/6J (JAX stock #000664) were used for these studies. These 5XFAD mice are congenic on the C57BL/6J substrain and were received directly from the Jackson laboratory which maintains a genetic stability and specific pathogen-free biosecurity program, and provides appropriate assurances and genotyping protocols (www.jax.org). Subjects were 7-12 weeks upon arrival to the University of Pittsburgh animal facility and were group-housed within sex (up to 4 per cage) in a dedicated mouse housing room with a 12hr:12hr light:dark cycle (lights on at 7:00am). The University of Pittsburgh animal facility is a specific pathogen-free facility that is fully accredited by the American Association for Accreditation of Laboratory Animal Care (AAALAC). An Animal Welfare Assurance is on file with OPRR-NIH. Subjects were maintained in the dedicated mouse housing facility with ad libitum food and water until the intended age of the experiments which was pre-determined based on our previous published characterization of the 5XFAD mouse model (Oblak et al. 2021). Specifically, 5XFAD mice and controls were aged to 6-9 months which is an age in which 5XFAD mice demonstrate significant AD relevant pathophysiology including amyloid plaque deposition in brain and neuroinflammation, relative to C57BL/6J controls (Oblak et al. 2021) Tissue samples were collected during the light cycle. (All efforts were undertaken to ameliorate animal suffering including appropriate methods of anaesthesia for terminal tissue collection.\n\nThe total number of animals used for all experiments were n= 4 5XFAD and n=4 C57BL/6J. These studies were initially conducted with minimal sample sizes (n=3-4) in line with historical published data for 5XFAD mice showing robust phenotypes of AD-related pathologies (Oblak et al. 2021) and in line with protocols from the MODEL-AD consortium (ADKnowledgeportal.synapse.org).\n\nWestern blots were reproduced and confirmed from initial pilot data, under blinded conditions. The experimenter was not aware of the group allocation during the experiment and data analysis. A staff member who serves the role of a colony manager that was not involved directly with the experiment coded the samples as A and B. The staff member provided the unblind code after the data were analyzed by the experimenter and reviewed for quality control by the supervisor. No samples were excluded from this study.\n\nFor terminal tissue collection, mice were anesthetized with isoflurane to the surgical plane of anesthesia, and brains were collected following decapitation. The brain was extracted and rinsed in ice-cold PBS, cerebellum was removed, and the cortex was bisected into left and right hemispheres then snap frozen and stored at -80 °C until use. Each hemibrain was weighed and then immersed in 1 ml/100 mg tissue homogenization buffer (THB; 2 mM Tris (pH 7.4), 250 mM sucrose 0.5 mM EDTA 0.5 mM EGTA) supplemented with 1X Pierce Protease Inhibitor (Thermo Scientific #A32953) and 1x Phosphatase Inhibitor Cocktail 2 (Sigma-Aldrich #P5726, St. Louis, MO). The tissue was homogenized for 20 sec on ice with a Benchmark D1000 hand-held homogenizer beginning at medium and increasing to high speed. Total protein concentration of the resulting homogenate was measured using a Bradford assay (Bradford 1976). Briefly, 5 μl of homogenate diluted 10× in PBS was added to a 96-well plate. Pierce™ Coomassie Plus (Bradford) Assay Reagent (Life Technologies, Chicago, IL, USA; 250 μl) was added to each well and the plate was read at 595 nm using a SprectraMax i3x (Molecular devices) with SoftMax Pro V7.0.2. The protein concentration was calculated by comparing to a standard curve generated by adding varying known concentrations of Albumin Standard (0, 125, 250, 500, 750, 1000, 1500 and 2000 μl/ml; (Thermo Scientific #23210, Rockford, IL, USA) in duplicate to wells.\n\nHomogenate from N=4 individual 5XFAD subjects and homogenate from N=4 individual C57BL/6J subjects, which served as WT controls, were included on each gel. Equal amounts of protein (25 μg) samples were prepared in 1x loading buffer (4x: 4 ml 100% glycerol, 2.4 ml 1M Tris/HCl (pH 6.8), 0.8 g SDS, 4 mg bromophenol blue, 3.1 ml H2O, 0.5 ml beta-mercaptoethanol) and incubated at 95 °C for 5 min. Samples were separated with SDS-polyacrylamide gel electrophoresis (4–15% Mini-PROTEAN® TGX™ Precast Protein Gels, 10-well, 30 μl, Bio-rad #4561083) using 120 V for 60 min, then transferred onto a nitrocellulose membrane using a Trans-Blot SD Semi-Dry Electrophoretic transfer cell (Bio-rad #170-3940) at 25 V for 30 min. Non-specific binding was blocked using EveryBlot Blocking Buffer (Bio-rad #12010020) for 5 min at room temperature with gentle rocking. Primary antibodies were prepared in EveryBlot Blocking buffer at the dilutions indicated in Table 1. Blots were immersed in primary antibody solutions overnight at 4 °C with gentle rocking. Membranes were then washed with 1X TBST (3 × 5 min) and immersed in 1:1000 fluorescent secondary antibody (Moesin, CD44 and sFRP-1, StarBright blue 700 goat anti-rabbit IgG, Bio-rad #12004161; Midkine, IRDye 800CW Donkey anti-Goat IgG, Licor, Lincoln, NE, USA) and 1:2000 hFAB™ Rhodamine Anti-GAPDH Antibody (Bio-rad #12004167) for 1 h at room temperature. Membranes were then washed (2 × 5 min in 1X TBST; 2 × 5 min in 1X TBS) then scanned with a Bio-rad ChemiDoc MP Imaging System. Pixel intensity was quantified using ImageJ, the public domain NIH Image program (available at http://rsb.info.nih.gov/nih-image/). Statistical analyses and graphing were performed using GraphPad Prism Version 9.3.1 (San Diego, CA).\n\n\nResults\n\nWe have characterized most commercially available antibodies against Moesin (Alshafie et al. 2023), Midkine (Ayoubi et al. 2023a), sFRP-1 (Ayoubi et al. 2023b) and CD44 (Ayoubi et al. 2021) using human WT and knockout cell lines for three research applications, including Western blot. For this study, we selected antibodies based on the following criteria: i) high antibody selectivity by WB based on our previous antibody characterization studies, ii) predicted reactivity with mouse based on the internal validation from the manufacturer, iii) band at the expected size by Western blot using mouse brain lysate (Figure 2) and iv) antibody clonality as we prioritize renewable reagents such as mouse monoclonal or rabbit recombinant antibodies. We selected the recombinant anti-Moesin ab52490, the recombinant anti-CD44 ab189524 and the recombinant anti-sFRP-1 ab267466 antibodies as they met our criteria. However, none of the previously characterized Midkine antibodies was expected to react with mouse Midkine. By searching on antibody manufacturers’ website, we identified the polyclonal antibody AF7769 from Bio-techne generated to specifically detect mouse Midkine. We validated AF7769 as we have done previously (Ayoubi et al. 2023a) (Figure 1). AF7769 met our selection criteria and was further selected for the downstream experiments. The underlying data for this study has been uploaded to Zenodo (Doolen & Rizzo 2023a).\n\nLysates of HAP1 (WT and MDK KO) were prepared, and ~30 μg of protein was processed for Western blot with the Midkine antibody. The Ponceau stained transfers of each blot are presented to show equal loading of WT and KO media and protein transfer efficiency from the acrylamide gels to the nitrocellulose membrane.\n\nWe next used the selected antibodies on protein extracts from cortex of 9-month aged 5xFAD mouse brain homogenates and compared to age-matched C57BL/6J controls. Our immunoblotting results depicting their reactivity in mouse brain homogenate are shown in Figure 2. The antibody source information and the fold change in protein levels in 5xFAD are in Table 1. Anti-Moesin ab52490 reacted in mouse brain homogenate with a predicted molecular weight of 68 kDa and its expression was 2.8 times higher in 5xFAD compared to WT mouse brain (Figure 2A). Anti-CD44 ab189524 reacted with a band at the predicted size of 82 kDa and its expression was 1.9 times higher in 5xFAD compared to WT mouse brain (Figure 2B). Anti-Midkine AF7769 reacted with a band ~16 kDa and a 17.8 times greater expression in 5xFAD compared to WT mouse brain (Figure 2C). Anti-sFRP-1 ab267466 reacted with a band at 35 kDa as predicted and its expression was 11.9 times greater in 5xFAD compared to WT mouse brain (Figure 2D). Interestingly, both Midkine and sFRP-1 are secreted proteins and could still be identified in crude protein extracts from homogenates, prepared as described above.\n\nRepresentative Western blots (left) and quantification (right). (A) Anti-Moesin; (Abcam #ab52490) reacted in mouse brain homogenate with a predicted molecular weight of 68 kDa and 2.8 times greater expression in 5XFAD relative to WT. (B) Anti-CD44 (Abcam #ab189524) reacted with a band at the predicted size of 82 kDa and 1.9 times greater expression in 5XFAD relative to WT. (C) Anti-Midkine (R&D Systems #AF7769) reacted with a band ~16 kDa with 17.8 times greater expression in 5XFAD relative to WT. (D) Anti-sFRP-1 (Abcam #ab267466) reacted with a band at 35 kDa as predicted with 11.9 times greater expression in 5xFAD relative to WT. Brightness and contrast were adjusted in figure for visualization purposes and were applied equally to entire blot. P<0.05, P<0.01, P<0.001, **P<0.0001 by t-test.\n\n\nDiscussion\n\nValidated reagents are important tools for studying underlying biological mechanisms that may contribute to disease and are a critical component of rigorously interrogating potential novel therapeutic targets for AD. Contrastingly, reagents such as antibodies that are not rigorously characterized could lead to spurious, irreproducible data and significant waste of resources. The present studies extend the characterization of antibodies that have been validated in knock-out cell lines to western blots to confirm their utility for in vivo studies. Given the evidence reporting that postmortem brain tissue from AD patients have elevated levels of Moesin, CD44, Midkine, and sFRP-1 relative to case controls, we selected an AD mouse model to evaluate these antibodies. As predicted, 5XFAD mice at an age at which significant amyloid plaque deposition is present (Oblak et al. 2021, 2022), demonstrated increases in Moesin, CD44, Midkine, and sFRPR1, relative to age- and sex- matched non-transgenic controls. These data confirm the utility of these specific antibodies as validated reagents for western blotting of brain tissue, and also highlight the presence of these target proteins in a mouse model of amyloidosis. Taken together, the present studies provide an approach for confirming and extending the validation of antibodies from in vitro tissue preparations to in vivo assays and also provide insight into the utility of the 5XFAD mouse model for studying Moesin, CD44, Midkine, and sFRP-1.", "appendix": "Data availability\n\nZenodo: in vivo characterization of research antibodies for Moesin, CD44, Midkine, and sFRP-1. https://doi.org/10.5281/zenodo.8043971 (Doolen & Rizzo 2023a).\n\nZenodo: ARRIVE checklist for ‘Validation and in vivo characterization of research antibodies for Moesin, CD44, Midkine, and sFRP-1.’ https://doi.org/10.5281/zenodo.8160965 (Doolen & Rizzo 2023b).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nAn earlier version of this article can be found on Open Lab Notebooks (https://openlabnotebooks.org/in-vivo-characterization-of-antibodies-directed-against-treat-ad-target-proteins-in-mouse-model-of-ad-pathology/).\n\n\nReferences\n\n2023 Alzheimer’s disease facts and figures: Alzheimers Dement.2023.\n\nAlshafie W, Ayoubi R, Fotouhi M, et al.: The identification of high-performing antibodies for Moesin for use in Western Blot, immunoprecipitation, and immunofluorescence. F1000Res. 2023; 12.\n\nAyoubi R, Southern K, Laflamme C, et al.: The identification of high-performing antibodies for Midkine for use in Western blot and immunoprecipitation. F1000Res. 2023a; 12.\n\nAyoubi R, Southern K, Laflamme C, et al.: The identification of high-performing antibodies for Secreted frizzled-related protein 1 (sFRP-1) for use in Western Blot and immunoprecipitation. F1000Res. 2023b; 12. Publisher Full Text\n\nAyoubi R, Alshafie W, McPherson PS, et al.: Antibody Characterization Report for CD44 antigen.2021. Publisher Full Text\n\nBai B, Wang X, Li Y, et al.: Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression. Neuron. 2020; 105: 975–991.e7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBradford MM: A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976; 72: 248–254. PubMed Abstract \| Publisher Full Text\n\nCouncil, National Research: Guide for the Care and Use of Laboratory Animals. Eighth ed.Washington, DC: The National Academies Press; 2011.\n\nDoolen S, Rizzo SJS: in vivo characterization of research antibodies for Moesin, CD44, Midkine, and sFRP-1. [Dataset]. Zenodo. 2023a. Publisher Full Text\n\nDoolen S, Rizzo SJS: ARRIVE checklist Doolen 2023. Zenodo. 2023b. Publisher Full Text\n\nHigginbotham L, Ping L, Dammer EB, et al.: Integrated proteomics reveals brain-based cerebrospinal fluid biomarkers in asymptomatic and symptomatic Alzheimer’s disease. Sci. Adv. 2020; 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJawhar S, Trawicka A, Jenneckens C, et al.: Motor deficits, neuron loss, and reduced anxiety coinciding with axonal degeneration and intraneuronal Abeta aggregation in the 5XFAD mouse model of Alzheimer’s disease. Neurobiol. Aging. 2012; 33(196): e29–e40.\n\nJohnson ECB, Carter EK, Dammer EB, et al.: Large-scale deep multi-layer analysis of Alzheimer’s disease brain reveals strong proteomic disease-related changes not observed at the RNA level. Nat. Neurosci. 2022; 25: 213–225. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJohnson ECB, Dammer EB, Duong DM, et al.: Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation. Nat. Med. 2020; 26: 769–780. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJohnson ECB, Dammer EB, Duong DM, et al.: Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease. Mol. Neurodegener. 2018; 13: 52. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKilkenny C, Browne WJ, Cuthill IC, et al.: Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research. PLoS Biol. 2010; 8: e1000412. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLaflamme C, Edwards AM, Bandrowski AE, et al.: Opinion: Independent third-party entities as a model for validation of commercial antibodies. New Biotechnol. 2021; 65: 1–8. PubMed Abstract \| Publisher Full Text\n\nLaflamme C, McKeever PM, Kumar R, et al.: Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. elife. 2019; 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOakley H, Cole SL, Logan S, et al.: Intraneuronal beta-amyloid aggregates, neurodegeneration, and neuron loss in transgenic mice with five familial Alzheimer’s disease mutations: potential factors in amyloid plaque formation. J. Neurosci. 2006; 26: 10129–10140. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOblak AL, Cope ZA, Quinney SK, et al.: Prophylactic evaluation of verubecestat on disease- and symptom-modifying effects in 5XFAD mice. Alzheimers Dement (N Y). 2022; 8: e12317.\n\nOblak AL, Lin PB, Kotredes KP, et al.: Comprehensive Evaluation of the 5XFAD Mouse Model for Preclinical Testing Applications: A MODEL-AD Study. Front. Aging Neurosci. 2021; 13: 713726. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPing L, Duong DM, Yin L, et al.: Global quantitative analysis of the human brain proteome in Alzheimer’s and Parkinson’s Disease. Sci. Data. 2018; 5: 180036. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSeyfried NT, Dammer EB, Swarup V, et al.: A Multi-network Approach Identifies Protein-Specific Co-expression in Asymptomatic and Symptomatic Alzheimer’s Disease. Cell Syst. 2017; 4: 60–72.e4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTannenbaum J, Bennett BT: Russell and Burch’s 3Rs then and now: the need for clarity in definition and purpose. J. Am. Assoc. Lab. Anim. Sci. 2015; 54: 120–132. PubMed Abstract\n\nWeller MG: Ten Basic Rules of Antibody Validation. Anal. Chem. Insights. 2018; 13: 1177390118757462." }	[ { "id": "236011", "date": "15 Feb 2024", "name": "Sarah C Hopp", "expertise": [ "Reviewer Expertise Microglia in Alzheimer's disease" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe work is clear and concise with consideration of the previous work that highlight the significance of validating the antibodies of interest.\nIt would be helpful to have more information on the functions of the four different proteins targeted by the different antibodies, and what the changes in expression in the 5XFAD brain lysate might mean biologically.\n\nThe authors should be commended for their clear and reproducible methods with appropriate levels of detail, particularly the methods for selecting the antibodies. However, some details from the methods were missing: Which sex of 5XFAD and WT mice were used for the Western blotting experiment in Figure 2? There are noted sex differences in pathology between sexes, so knowing which mice are males and females could be helpful. The methods for Figure 1 are missing. Were the cell lysates and Western blots prepared in the same way as the brain lysate? What were the methods for the Ponceau? How was MDK KO confirmed in the HAP1 cells? Where were the HAP1 cells obtained from? How were they grown? What t-test was run on the data in Figure 2?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11386", "date": "20 Jun 2024", "name": "Suzanne Doolen", "role": "Author Response", "response": "The work is clear and concise with consideration of the previous work that highlight the significance of validating the antibodies of interest. It would be helpful to have more information on the functions of the four different proteins targeted by the different antibodies, and what the changes in expression in the 5XFAD brain lysate might mean biologically. The authors should be commended for their clear and reproducible methods with appropriate levels of detail, particularly the methods for selecting the antibodies. RESPONSE: Thank you to the reviewers for this acknowledgement. However, some details from the methods were missing: RESPONSE: we appreciate the feedback and have added points for clarity as suggested. Which sex of 5XFAD and WT mice were used for the Western blotting experiment in Figure 2? There are noted sex differences in pathology between sexes, so knowing which mice are males and females could be helpful. RESPONSE: As described in the second paragraph in the methods section both male and female 5XFAD mice were used for these studies. For clarity we have now revised the western blots methods to state: “Homogenate from N=2 male and N=2 female 9-month aged 5XFAD subjects and homogenate from N=4 age-matched individual male C57BL/6J subjects”. We have also added this detail in the results section. There were no differences at this age between male and female 5XFAD mice for these proteins and although only male WT were used as the age-match control (due to females being used as breeders), based on previous studies in 9 month aged WT mice there was no effect of sex in these proteins. The methods for Figure 1 are missing. Were the cell lysates and Western blots prepared in the same way as the brain lysate? What were the methods for the Ponceau? How was MDK KO confirmed in the HAP1 cells? Where were the HAP1 cells obtained from? How were they grown? RESPONSE: The cell lysates and brain homogenates had different preparations for the western blots. The details for the cell culture westerns have now been added as follows: Wild type (WT) and MDK knockout (KO) HAP1 cells were obtained from Horizon Discovery. Cell lines were prepared by first washing 3× with PBS then starved for ~18 hrs. Culture media were collected and centrifuged for 10 min at 500 × g to eliminate cells and larger contaminants, then for 10 min at 4500 × g to eliminate smaller contaminants.Culture media were initially concentrated using Amicon Ultra-15 Centrifugal Filter Units (MilliporeSigma cat. number UFC9010) by centrifuging at 4000 × g for 15 min. The resulting 500 μl of the concentrated media were centrifuged again at 4000 × g for 15 min using Amicon Ultra- 0.5 Centrifugal Filter Units (MilliporeSigma cat. number UFC5010) to 200 μl.~30μg of protein was loaded and processed for Western blot using the Midkine antibody (AF7769). Western blot was performed using a large 10-20% gradient polyacrylamide gel and transferred on a nitrocellulose membrane. Proteins on the blot were visualized with Ponceau staining which is scanned to show together with the Western blot. The blot was blocked with 5% milk for 1 hr, and the Midkine antibody (AF7769) was incubated overnight at 4°C with 5% bovine serum albumin in TBS with 0.1% Tween 20 (TBST). Following three washes with TBST, the peroxidase conjugated secondary antibody was incubated on the membrane at a dilution of ~0.2 μg/ml in TBST with 5% milk for 1 hr at room temperature followed by three more washes with TBST. The membrane was incubated with ECL from Pierce (cat. number 32106) prior to detection with HyBlot CL autoradiography films from Denville (cat. number 1159T41).The MDK KO cell line can be confirmed based on the results of the Western blot, as the Midkine signal appears in the lane loaded with the WT cells but disappears in lane loaded with the MDK KO cells. Predicted band size: ~16 kDa. What t-test was run on the data in Figure 2? RESPONSE: An unpaired t-test was performed using Graphpad Prism Software Version 9.3.1 for Windows. These details have now been added in the figure legend and the methods." } ] }, { "id": "249991", "date": "22 Mar 2024", "name": "Michelle Erickson", "expertise": [ "Reviewer Expertise Blood-brain barrier", "Alzheimer's disease", "aging", "inflammation", "neurotoxicology", "pharmacology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article evaluates specific antibodies for proteins upregulated in 5xFAD mouse brain, as found by Western blotting. Results are straightforward and potentially useful to the reserach community. Specific comments are below:\n1. A human knockout cell line is used to validate antibody specificity. As this study specifically focuses on mice, it would be important to understand whether specificity is also observed in mouse knockout cells.\n2. 5xFAD mice can show sex-specific differences in AD-associated pathological changes. Group allocation of males and females should be clarified.\n3. Western blotting done here is only semi-quantitative. The increases reflect changes in antibody signal rather than protein expression.\n4. The underlying data in Zenodo aren't appropriately labeled. It's unclear what blot goes with what antibody or what the lanes are. Also, the blots appear to have 12 lanes whereas only 8 are shown in the figure. What are the other 4 lanes?\n\n5. Showing the full blots and clearly indicating what is thought to be the specific band is important, and ideally should be included in the main body of the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11387", "date": "23 Oct 2024", "name": "Suzanne Doolen", "role": "Author Response", "response": "This article evaluates specific antibodies for proteins upregulated in 5xFAD mouse brain, as found by Western blotting. Results are straightforward and potentially useful to the research community. Specific comments are below: A human knockout cell line is used to validate antibody specificity. As this study specifically focuses on mice, it would be important to understand whether specificity is also observed in mouse knockout cells. RESPONSE: We acknowledge the importance of ensuring specificity and cross- reactivity, especially when working with antibodies across species. To address this concern, we conducted Western blot (WB) experiments using human knockout (KO) cell lines and identified several specific antibodies in WB for all four proteins. The antibodies selected in this study were those predicted by the manufacturers to bind to the corresponding murine proteins. We further confirmed specificity in WB by comparing the band sizes between human and murine proteins. It's important to note that for all four proteins, the human and murine proteins are expected to exhibit very similar molecular weights. 2. 5xFAD mice can show sex-specific differences in AD-associated pathological changes. Group allocation of males and females should be clarified. RESPONSE: We have now clarified that both male and female 5XFAD were used (n=2 per sex) for these studies in several places including methods and results. Western blotting done here is only semi-quantitative. The increases reflect changes in antibody signal rather than protein expression. RESPONSE: Thank you for this important point. We have added this to the discussion. The underlying data in Zenodo aren't appropriately labeled. It's unclear what blot goes with what antibody or what the lanes are. Also, the blots appear to have 12 lanes whereas only 8 are shown in the figure. What are the other 4 lanes? RESPONSE: We have now updated the Zenodo notebook and added a file https://zenodo.org/search?q=parent.id%3A8043970&f=allversions%3Atrue&l=list&p=1&s=10&sort=version that shows the additional lanes were other animal models in our lab as we were surveying other strains in addition to 5XFAD for these experiments and wanted to maximize all lanes on the gel that were not other 5XFAD mice. Specifically, this was the SAA mouse model (JAX strain# 034711) which had not yet been fully characterized (Lanes 10-13) and Lanes 14 and 15 were n=2 19 month aged WT mice. We chose to only include 5XFAD in the publication given their extensive characterization and their age-matched WT controls. Since the SAA mouse model did not have full characterization data yet (e.g. amyloid and/or tau, etc.) and we only had n=2 19-month aged WT mice and no 19-month aged 5XFAD to compare to we did not include these in the publication. Showing the full blots and clearly indicating what is thought to be the specific band is important, and ideally should be included in the main body of the manuscript. RESPONSE: This has now been updated in the Zenodo notebook https://zenodo.org/search?q=parent.id%3A8043970&f=allversions%3Atrue&l=list&p=1&s=10&sort=version” that shows the specific bands which is in addition to what is shown in Figure 2." } ] } ]	1	https://f1000research.com/articles/12-1070
https://f1000research.com/articles/12-547/v1	25 May 23	{ "type": "Research Article", "title": "Association of COVID-19 symptoms and functional status of the COVID-19 survivors in a tertiary health care center in a developing country", "authors": [ "Mohammad Tariqul Islam", "Afsana Mahjabin", "Md Mahbubul Islam", "Anika Tasnim", "Fahmida Afroz Khan", "Iffat Islam Khan", "Abdul Alim", "Moshiur Rahman Khasru", "Taslim Uddin", "Afsana Mahjabin", "Md Mahbubul Islam", "Anika Tasnim", "Fahmida Afroz Khan", "Iffat Islam Khan", "Abdul Alim", "Moshiur Rahman Khasru", "Taslim Uddin" ], "abstract": "Background: The COVID-19 pandemic has affected people globally, causing widespread illness and functional limitations. Methods: This cross-sectional study aimed to investigate the association between COVID-19 symptoms and the functional status of COVID-19 survivors at Bangabandhu Sheikh Mujib Medical University (BSMMU) in Bangladesh. A total of 244 COVID-19 survivors were enrolled in the study, and their symptoms and functional status were assessed using standardized questionnaires. The post-COVID-19 functional status scale (PCFS) was used to assess the entire range of functional outcomes. Results: Among the participants 57.4% were male and 42.6% were female. The mean (SD) age of the patients was 44.6 ±14.7 years where 37.7% were from the 20-35 years age group. The mean duration of suffering from COVID-19 was 15.9 ±6.1 days where 61.5 % of the patients had a duration of suffering of 11-20 days. Out of the 244 patients, 40 patients had no functional limitation (grade 0 functional status in the PCFS scale) while 100 had negligible functional limitation and 14 had severe functional limitation. We found patients who were suffering from multi-symptoms were statistically significant with PCFS scale grade 4, whereas grade 1 was found to be statistically significant with only respiratory distress. There was a significant association between the duration of COVID-19 symptoms and post-COVID-19 functional status for patients who experienced symptoms for 14 days or more (p<0.05). Conclusions: Considering the negative impact of COVID-19 symptoms on functional status, comprehensive care and support are required for COVID-19 survivors.", "keywords": [ "COVID-19 Symptoms", "Functional Status", "Tertiary health care center", "Bangladesh", "Developing country" ], "content": "Introduction\n\nThe COVID-19 pandemic has swept across the globe, affecting millions of people in 231 countries, areas, and territories and overwhelming healthcare systems. Bangladesh is one of the countries that has been severely affected by the pandemic, with 2.37 million cases and 29,445 deaths reported up to 26th March, 2023 (Worldometer). Coronaviruses are a family of enveloped viruses known as Coronaviridae. They are large, positive single-stranded RNA viruses that can be transmitted from human to human through respiratory secretions.1\n\nCOVID-19 is characterized by a range of clinical symptoms that appear 2-14 days after exposure to the virus, such as fever, cough, nasal congestion, fatigue, dyspnea, and severe chest symptoms consistent with pneumonia.2,3 The most common COVID-19 symptoms were fever (83%–98%), dry cough (57%–82%), and dyspnea (18%–55%), with a median duration of 5–8 days after the infection. Anosmia also presented in the early stages of the disease in the absence of other symptoms.3\n\nIt is expected that COVID-19 will have a noteworthy impact on physical, cognitive, mental, and social health, even among patients with mild illness.1 Previous studies on the long-term consequences of severe acute respiratory distress syndrome (ARDS) have shown negative effects on pulmonary function and overall health status that can persist for several years after the onset of the disease.4 A large proportion of patients experience fatigue, which reduces both physical and mental performance.5\n\nAccording to the World Health Organization (WHO), quality of life (QOL) refers to an individual’s perception of their position in life within the context of the cultural and value systems they live in and their goals, expectations, standards, and concerns.6 Standard indicators of QOL include wealth, employment, physical and mental health, education, environment, leisure and recreational activities, social connections, religious beliefs, safety, security, and freedom. In patients who have recovered from COVID-19, their mental health may require a long-term recovery process, which can significantly impact their overall quality of life.1,7\n\nA study found that general, respiratory, and gastrointestinal symptoms were associated with an increased risk of death due to COVID-19. Additionally, pre-existing conditions such as diabetes, cardiovascular diseases, and respiratory disease had a statistically significant association with the hospitalization of patients.3 Another study noted that many COVID-19 hospital survivors face adverse effects even six months after hospital discharge in terms of the level of physical activity and functional level decline in older adults.8\n\nFunctional capacity refers to an individual’s maximal ability to perform daily activities across various domains of life, such as physical, psychological, social, and spiritual. Meanwhile, functional performance refers to the actual activities that individuals carry out during their daily lives.1\n\nBangladesh is a developing country that has been severely affected by the pandemic, with thousands of cases and deaths reported.9 With the given number of COVID-19 survivors and their associated disabilities and financial constraints, their quality of life in terms of functional status in Bangladesh is negatively impacted.9,10 Like other low resource countries, in Bangladesh the healthcare system is underdeveloped where rehabilitation is not a health priority, and so COVID-19 survivors added an extra burden over healthcare delivery system.10\n\nWhile many individuals have been able to recover from the disease, it is essential to understand the impact that COVID-19 can have on survivors’ functional status. This study aims to investigate the association between COVID-19 symptoms and functional status among COVID-19 survivors in a tertiary healthcare center in Bangladesh. By examining the functional status of survivors, this study seeks to shed light on the impact of COVID-19 on the physical, mental, and social wellbeing of those who have contracted the virus. These findings emphasize the importance of providing a comprehensive care and support to COVID-19 survivors beyond the acute phase of the illness to improve their functional outcomes and quality of life. Hence, an attempt was made to determine the association between COVID-19 symptoms and functional status among COVID-19 survivors in a tertiary health care center in a developing country.\n\n\nMethods\n\nThe study received ethical clearance from the Institutional Review Board (IRB) of BSMMU (memo no: BSMMU/2020/9236, date of approval: 19-10-2020). Written informed consent was obtained from each participant prior to the commencement of the interview after assuring complete anonymity and no disclosure of their personal information. Participants with no education provided fingerprints on the consent form after receiving sufficient verbal explanation. This cross-sectional study was conducted in accordance with the Declaration of Helsinki (as revised in 2013) and no invasive procedure was involved.\n\nThe Post-COVID-19 functional status scale (PCFS) was used to cover the entire range of functional outcomes by focusing on limitations in usual duties/activities either at home/at work/study, as well as changes in lifestyle.11 The PCFS scale is a widely used tool to assess the functional limitations of COVID patients. It consists of five grades ranging from 0 (no functional limitation) to 4 (severe functional limitation). PCFS “0” denotes the complete absence of symptoms, and the individual is able to engage in all activities they could before to contracting COVID-19. PCFS “1” shows no symptoms when at rest, but there are restrictions on activities that call for strenuous physical effort or intense mental focus. PCFS “2” suggests symptoms while at rest, although the individual is capable of taking care of themselves. PCFS “3” denotes the requirement for some assistance with daily tasks like cooking, cleaning, or shopping. PCFS “4” denotes the requirement for assistance with daily living tasks like dressing or bathing.11 The PCFS scale is used to measure how COVID-19 will affect a person’s everyday functioning over the long run, and it can assist medical practitioners in determining whether the patient needs ongoing care and support. Researchers looking on the long-term impacts of COVID-19 on people and populations can also benefit from it.\n\nThis cross-sectional study was conducted from November 2020 to October 2021 in the Department of Physical Medicine & Rehabilitation at BSMMU. A total of 244 patients were selected according to the inclusion and exclusion criteria from the post-COVID-19 follow-up clinic under the Department of Medicine at BSMMU.\n\nSample size for this study was determined during protocol submission of IRB ethical clearance by using the formula n = z2pq/d2 = 382 (where n = sample size, z = 1.96 at 95% confidence level, p= prevalence of fatigue12 as post COVID-19 complication 53%, q = 1-p). Patients between the ages 18 and 90 years, irrespective of sex, who provided informed written consent and tested positive for COVID-19 through RT PCR test were included. Notably, those who had a history of major depressive illness, schizophrenia, mental retardation, or were on medication for psychiatric illness were excluded from the study due to their unique psychological profiles.\n\nThe interviews took place in the post-COVID-19 follow-up clinic where attendants were allowed to accompany participants during interview sessions. The hospital staff and medical personnel cooperated to ensure the success of the session. Wearing masks and maintaining a six-foot distance, both the participants and research assistants prioritized safety. The interview lasted for less than 30 minutes and the participants were assured of their right to withdraw themselves at any time without providing an explanation. They were informed that their participation was voluntary, and there were no incentives offered for their participation.\n\nData were collected by using a semi-structured questionnaire based on COVID-19 symptoms and complications through face-to-face interviews with trained research assistants. Participants were asked about sociodemographic variables and personal habits, alongside the duration of their COVID-19 attack, symptoms experienced during COVID-19 attack, co-morbidities, post COVID-19 complications and their quality of life, as evaluated by PCFS scale.\n\nData were analyzed using SPSS version 26. Continuous variables are provided with the appropriate mean and standard deviation. In categorical variables, frequency is shown. A Chi-square test was used to compare categorical variables amongst participants with varying degrees of functional impairment. A p value < 0.05 was regarded as statistically significant.\n\n\nResults\n\nWithin the specified time frame, a total of 280 participants agreed to participate in the study. However, 36 participants were subsequently excluded for various reasons. Specifically, 20 of them did not present their COVID-19 test result during the interview, 12 withdrew from the study due to time constraints or feeling unwell during the interview, and 4 were missing data. Among the 244 participants, 57.4 percent were male and 42.6 percent were female. The mean (SD) age of the patients was 44.6 (±14.7) years, where 37.7 percent were from 20-35 years age group. Again, the majority of the patients have above secondary level education (82), work as a service holder (56.6%) and came from nuclear family (67.2%). 63.9 percent of the patients had a monthly family income between 31000-60000 BDT. The mean duration of suffering, on the basis of how long patients had COVID-19 symptoms, was 15.9 (±6.1) days where 61.5 percent of the patients had a duration of 11-20 days (Table 1).\n\nOut of the 244 patients, 40 (16.4%) patients had no functional limitation (grade 0 functional status in PCFS scale) while 100 (40.9%) had negligible functional limitation and 14 (5.7%) had severe functional limitation (Figure 1).\n\nThis study revealed that grade 0 was found to be statistically significant with fever, cough, respiratory distress, weakness or numbness of limbs, joint pain and skin rash or discoloration of fingers and toes. Grade 1 was found to be statistically significant (p < 0.001) with only respiratory distress and Grade 2 with weakness or numbness of limbs (p < 0.001). Grade 3 was found to be statistically significant (p < 0.001) with fever, cough, loss of taste, respiratory distress, and sore throat. Grade 3 was also found to be statistically significant (p < 0.05) with weakness or numbness of limbs and skin rash or discoloration of fingers and toes. Grade 4 was found to be statistically significant at p < 0.001 level with the symptoms of fever, fatigue, chest pain, and skin rash or discoloration of fingers and toes, whereas loss of taste, respiratory distress, sore throat, weakness or numbness of limbs were found statistically significant at p < 0.05 level (Table 2).\n\n* p < 0.05.\n\n** p < 0.001.\n\nPatients with symptoms lasting 14 days or more had a higher percentage of functional limitations. The statistical analysis of the data revealed that there was a significant association between the duration of COVID-19 symptoms and post-COVID-19 functional status for patients who experienced symptoms for 14 days or more. Specifically, there was a statistically significant difference in the proportion of patients with grade 1, grade 3, and grade 4 functional status compared to those with symptoms lasting less than 14 days, with p-values of less than 0.05. However, for patients with symptoms lasting less than 14 days, there was no statistically significant association with post-COVID-19 functional status. Overall, these findings suggest that a longer duration of COVID-19 symptoms is associated with a higher risk of functional limitations in post-COVID-19 recovery (Table 3).\n\n* p < 0.05.\n\n** p < 0.001.\n\n\nDiscussion\n\nIn the current study, the mean age of the patients was 44.6 years, with a standard deviation of 14.7 years. More specifically, a significant proportion (37.7%) of the patients belonged to the 20-35 years age group. This age group was considered to be relatively less vulnerable to COVID-19, and the high representation of this group might suggest a higher prevalence of the virus in the younger population of the studied area. The average age of the patients was found in earlier investigations to be 33.09 ± 12.09 years and 38.48±16.20 years old respectively.9,13\n\nThere are differences in the clinical and demographic traits of COVID-19 individuals in a given population. Male patients make up 57.4% of the total population, with female patients making up the remaining 42.6%. These results were in line with some earlier research and global trends6,13–15 which represented both developed and developing nations. Additionally, 56.6% of patients were service users, and 82% of patients had education beyond the secondary level. According to these statistics, COVID-19 may have impacted individuals from a variety of backgrounds, including those with higher levels of education and professional positions. In addition, 67% of participants were from nuclear households, compared to 37% from joint families. Regarding economic status, a significant proportion of the patients (63.9%) had a monthly family income between 31000-60000 BDT; they faced an extra burden during the pandemic for treatment due to out-of-pocket expenditure, which was about two thirds of total health expenditure in Bangladesh.16 Previous reports also showed that “vulnerable non-poor” families in Bangladesh have a monthly income between 35,000-70,000 BDT.\n\nThe mean duration of suffering from COVID-19 was 15.9 days, with a standard deviation of 6.1. days. The bulk of the patients (61.5%) experienced illness for 11 to 20 days. This finding may point to a relatively mild form of disease in the population under study because it was in line with the normal COVID-19 duration. In contrast, Jradi et al.’s study reported a longer (35.31 ± 18.75) mean duration than the results of the current investigation.15 This long duration might be due to the impairment in physical activities, the long duration of confinement and the extreme doubt during the COVID-19 disease had generated remarkable mental and attitude disorders.17\n\nOut of the 244 patients, 40 (16.4%) had no functional limitation (grade 0), while 100 (40.9%) had negligible functional limitation (grade 1 or 2). This suggests that a significant proportion of the patients had some degree of functional limitation, but it was not severe enough to affect their daily activities. On the other hand, 14 (5.7%) of the patients had severe functional limitation (grade 4). This indicates that a small proportion of patients had significant functional limitations that restricted their ability to perform daily activities. It is important to note that the statement does not provide information about the remaining 90 (36.9%) patients. Similar results were mentioned by Machado et al.13 In similar study, Hussein et al., reported that most of participants (63.1%) had a trivial limitation in activities after recovery from COVID-19 (Grade 1), 14.1% had slight (Grade 2), 2.5% had moderate (Grade 3), and only 0.5% had severe functional limitation (Grade 4). However one fifth of the participants had no functional limitations (Grade 0).15 Another study conducted by Pant et al. showed negligible functional limitation (PCFS grade 1) among nearly one fourth (27.3%) of the patients, 13 (12.3%) patients had slight functional limitation (PCFS grade 2), and a negligible portion of the patients had moderate (PCFS grade 3) and severe functional limitations (PCFS grade 4).14\n\nThe present study describes the relationship between the functional status of patients and various symptoms they experienced. According to the statement, grade 0 functional status was statistically significant with fever, cough, respiratory distress, weakness or numbness of limbs, joint pain, and skin rash or discoloration of fingers and toes. This suggests that patients with grade 0 functional status were less likely to experience these symptoms compared to patients with higher functional status grades. Grade 1 functional status was found to be statistically significant with only respiratory distress, and grade 2 was found to be statistically significant with weakness or numbness of limbs. This indicates that patients with higher functional status grades were more likely to experience these symptoms compared to patients with lower functional status grades. Grade 3 functional status was statistically significant with fever, cough, loss of taste, respiratory distress, sore throat, weakness or numbness of limbs, and skin rash or discoloration of finger toes. Similarly, grade 4 functional status was statistically significant with fever, fatigue, loss of taste, respiratory distress, sore throat, weakness or numbness of limbs, chest pain, and skin rash or discoloration of fingers and toes. This suggests that patients with higher functional status grades were more likely to experience these symptoms compared to patients with lower functional status grades.\n\nIn a notable fraction of COVID-19 survivors, persistent symptoms have been linked to a progression toward low functional status.18 A higher percentage of people in a different study by Machado et al., who present a symptom-based COVID-19 diagnosis and have a lower functional level, such as living alone, have symptoms.14 Among individuals who had symptoms for at least 14 days, there was a significant correlation between the length of COVID-19 symptoms and post-COVID-19 functional status ((p<0.05)). Longer symptom duration was linked to worse functional status in a research by Huang et al., including decreased mobility and greater fatigue, discomfort, and depressive illness.19 The limitations of this study were firstly, the study used a convenience sampling technique, which may limit the generalizability of the findings. Secondly, the study relied on self-reported information, which may be subject to recall bias. Finally, the study was conducted in a single tertiary healthcare center, which may limit the generalizability of the findings to other settings.\n\n\nConclusion\n\nThis research will provide valuable insights into the association between COVID-19 symptoms and functional status of survivors in a developing country. The findings will be useful in developing effective rehabilitation programs for COVID-19 survivors and improving their quality of life.", "appendix": "Data availability\n\nData cannot be made publicly available due to patient privacy concerns and the need to protect the confidentiality of research participants as specified on the consent form. The ethical committee has requested not to breach the confidentiality of the data and that the data should not be made publicly available.\n\nTo apply for access to the data, please contact the corresponding author (tariqulpmr@bsmmu.edu.bd). Applicants must maintain confidentiality, and there should be a reasonable cause to utilize these data only for research purposes. De-identified underlying data will be provided to approved applicants.\n\n\nReferences\n\nSarap R, Shinde DM, Mahajan DP: Evaluation of Quality of Life, Fatigue Severity and Functional Status in Post Covid-19 Patients - Cross Over Longitudinal Study. Int J Heal Sci Res. 2022; 12(9): 49–56. Publisher Full Text\n\nPal M, Berhanu G, Desalegn C, et al.: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2): An Update. Cureus. 2020; 2(3): 1–9. Publisher Full Text\n\nTavakolifard N, Moeini M, Haddadpoor A, et al.: Clinical symptoms of COVID-19 and their association with disease outcome. Adv Biomed Res. 2022; 11(1): 2.\n\nNgai JC, Ko FW, Ng SS, et al.: The long-term impact of severe acute respiratory syndrome on pulmonary function, exercise capacity and health status. Respirology. 2010; 15(3): 543–550. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMandal S, Barnett J, Brill SE, et al.: Long-COVID’: A cross-sectional study of persisting symptoms, biomarker and imaging abnormalities following hospitalisation for COVID-19. Thorax. 2021; 76(4): 396–398.\n\nYanti B, Asril AR, Hajar S: The relationship between disease severity and functional status of post-covid-19 patients in Banda Aceh, Indonesia. J Ners. 2022; 17(2): 176–182. Publisher Full Text\n\nHolmes EA, O’Connor RC, Perry VH, et al.: Multidisciplinary research priorities for the COVID-19 pandemic: a call for action for mental health science. Lancet Psychiatry. 2020; 7(6): 547–560. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShanbehzadeh S, Zanjari N, Yassin M, et al.: Association between long COVID, functional activity, and health-related quality of life in older adults. BMC Geriatr. 2023; 23(1): 11–40. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUddin T, Islam MT, Rahim HR, et al.: Rehabilitation Perspectives of COVID-19 Pandemic in Bangladesh. J Bangladesh Coll Physicians Surg. 2020; (May): 76–81. Publisher Full Text\n\nUddin T, Siddiq AB, Islam MT: International Journal of Physical Medicine and Rehabilitation Strategies to Adapt COVID-19 Impacted Low Resource Rehabilitation Services. Int J Phys Med Rehabil. 2020; 8(3): 1–2.\n\nKlok FA, Boon GJAM, Barco S, et al.: The post-COVID-19 functional status scale: A tool to measure functional status over time after COVID-19. Eur Respir J. 2020; 56(1): 10–12. Publisher Full Text\n\nWise J: Covid-19: Symptoms are common after acute phase of disease, Italian study shows. BMJ. 2020; 370: m2804. Publisher Full Text\n\nMachado FVC, Meys R, Delbressine JM, et al.: Construct validity of the Post-COVID-19 Functional Status Scale in adult subjects with COVID-19. Health Qual Life Outcomes. 2021; 19(1): 10–40. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPant P, Joshi A, Basnet B, et al.: Prevalence of functional limitation in COVID-19 recovered patients using the post COVID-19 functional status scale. J Nepal Med Assoc. 2021; 59(233): 7–11. Publisher Full Text\n\nJradi H: Post-COVID-19 functional status: Relation to age, smoking, hospitalization, and previous comorbidities. Ann Thorac Med. 2017; 13(3): 156–162.\n\nOut-of-pocket spending on treatment rises further\|undefined: [cited 2023 Apr 13]. Reference Source\n\nJawad MJ, Abbas MM, Jawad MJ, et al.: Mental Health and Psychosocial Considerations Post Covid-19 Outbreak. Wiad Lek. 2021; 74(12): 3156–3159. PubMed Abstract \| Publisher Full Text\n\nGoërtz YMJ, Van Herck M, Delbressine JM, et al.: Persistent symptoms 3 months after a SARS-CoV-2 infection: The post-COVID-19 syndrome? ERJ Open Res. 2020; 6(4): 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHuang L, Yao Q, Gu X, et al.: 1-year outcomes in hospital survivors with COVID-19: a longitudinal cohort study. Lancet. 2021 Aug 28; 398(10302): 747–758. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "175341", "date": "14 Nov 2023", "name": "Parisa Rezaeifar", "expertise": [ "Reviewer Expertise Pulmonary disease and intensive care medicine" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThere are some noticeably problems in this article\nDuration of the convalescence period for patients is not considered in this article, I mean that how long it takes to assess patients and include in this study after resolving Covid 19. As we expect the first days after discharge, disability and function status may be worse than the following days and months and evaluation in different time lags for patients causes bias in this study.\n\nIt seems to me that results part needs more evaluation and revision, for example the association between age groups and functional status or predictive factors and their correlation on functional status such as gender, occupation and … (multivariable analysis) is not considered. In this way we have less information about the identifying effective factors on functional status.\n\nIn discussion part, the results are repeated. It needs revision.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "11087", "date": "13 Apr 2024", "name": "Mohammad Tariqul Islam", "role": "Author Response", "response": "1. Duration of the convalescence period for patients is not considered in this article, I mean how long it takes to assess patients and include in this study after resolving Covid 19. As we expect the first days after discharge, disability and function status may be worse than the following days and months, and evaluation in different time lags for patients causes bias in this study. Answer: We recognize the significance of the convalescence period in assessing functional status post-COVID-19. Unfortunately, our study did not specifically track the duration from discharge to evaluation. Future studies should consider this factor to better understand the trajectory of functional recovery and minimize potential bias. 2. It seems to me that the results part needs more evaluation and revision, for example, the association between age groups and functional status or predictive factors and their correlation on functional status such as gender, occupation, and … (multivariable analysis) is not considered. In this way, we have less information about the identifying effective factors on functional status. Answer: Our initial study design focused on descriptive statistics due to the sample size. We recommend further research with larger cohorts to enable comprehensive multivariable analysis, which could provide deeper insights into the factors affecting functional status post-COVID-19. 3. In the discussion part, the results are repeated. It needs revision. Answer: We have edited the discussion part accordingly. (mailed to editor with corrected word file)" } ] } ]	1	https://f1000research.com/articles/12-547
https://f1000research.com/articles/11-459/v2	12 Sep 22	{ "type": "Research Article", "title": "Effects of modified twin block appliance in growing Class II high angle cases: A cephalometric study", "authors": [ "Kanistika Jha", "Manoj Adhikari", "Kanistika Jha" ], "abstract": "Background: Class II malocclusions represent anteroposterior dysplasia usually resulting from mandibular retrusion. Along with a retropositioned mandible, it can be associated with either upward or backward jaw rotation. High angle cases are often associated with a short ramal height, steeper mandibular plane, and large gonial angle. Twin block is a commonly used myofunctional appliance that incorporates bite planes that direct the occlusal forces in a more favorable direction for correction of the retrognathic mandible. We aimed to evaluate skeletal, dental, and soft tissue changes following modified twin block appliance therapy in high-angle cases. Methods: A cephalometric study was performed on 15 growing (10-14 years) high angle (Frankfort mandibular angle 28-35°) Class II Division I malocclusion patients undergoing twin block therapy. Skeletal, dental, and soft tissue changes were evaluated by cephalometric analysis using Dolphin software. Results: Pre- and post-treatment changes in cephalograms were assessed by analysis of variance and paired t-test. Significant changes in the position of the mandible (angle between Sella-Nasion-Point B [SNB] increased by 3.9 degrees, P=0.02), Wits appraisal (decreased by 1.54in mm, P=0.04), maxillo-mandibular relationship (angle between Point A-Nasion-Point B [ANB] decreased by 3.73 degrees, P=0.02) were observed. Soft tissue changes like the nasolabial angle were also significant, increasing by 3.8 degrees (P=0.04) and lower lip relation to E-line (reduction in lower lip protrusion) by 2 mm (P=0.04). Vertical parameters showed non-significant changes, like the Frankfort mandibular angle (FMA) increased by 0.07 degrees, (P=0.67), the angle between Sella-Nasion and Gonion-Gnathion (SN-Go-Gn) increased by 0.33 degrees, (P=0.67), Y-axis increased by 0.2 degrees, (P=0.32). The upper incisor inclination decreased non-significantly from 5.60±1.24 to 4.20±0.86 degrees, (P=0.31) and lower incisor increased non-significantly from 100.13±2.23 to 101.80 ±1.37 degrees, (P=0.08). Conclusions: Modified twin block appliance can be used to successfully treat Class II Division I high angle cases with good vertical control.", "keywords": [ "Class-II", "high angel cases", "vertical growers", "twin block", "modified twin block", "cephalometry", "digitization", "pubertal growth phase" ], "content": "Introduction\n\nClass II malocclusions represent anteroposterior dysplasia that may result from maxillary protrusion, mandibular retrusion, or a combination of both, but the most common cause is mandibular retrusion.1 Along with a retropositioned mandible, it can be associated with either upward or backward jaw rotation.2 High angle cases are often associated with a short ramal height, steeper mandibular plane, and large gonial angle and anterior attachment of masseter muscle relative to the occlusal plane. According to Pepicelli, the vertical growers have a flaccid and weak type of muscle pattern with reduced bite force along with a long facial pattern.3 The basic treatment objective of Class II vertical dysplasia in growing children would alter the amount and direction of jaw growth. According to Graber, the basic objective of the functional appliance is to train the musculature to assist in optimal dentofacial development by eliminating abnormal muscle functions.4 Anderson V activator,5 high posterior bite blocks,6 and magnetic appliances7 had shown promising results in directing the growth of vertical dysplasia. Twin Block is one of the commonly used myofunctional appliances which incorporates the bite planes that direct the occlusal forces in a more favorable direction for correction of the retrognathic mandible.8 Clark has also described a modified version of the twin block appliance for high-angle cases.9 Therefore, this study aimed to evaluate the cephalometric changes with a modified twin block appliance in growing Class II high angle cases.\n\n\nMethods\n\nA total of 15 growing children with skeletal Class II Division I malocclusion within the age group of 10 to14 years, and falling under cervical vertebral maturation index (CVMI) stage 3 and 4 with Frankfort Mandibular Plane angle (28-35 degrees) were enrolled.\n\nPretreatment diagnostic records were taken, analyzed and a treatment plan was established with a twin block appliance. The bite registration was taken 2 to 3 mm beyond the freeway space (average 7 mm in premolar region) and at 3-4 mm interincisal opening. The twin block was fabricated with an increased posterior bite block as per Clark’s protocol for vertical growers with heat-cured acrylic materials. The inclined plane was modified with a mean value of 65 degrees and the posterior bite plate was kept intact, covering up to the last erupted molars, and no trimming was done. A mid-palatal expansion screw was incorporated for expansion in the upper arch. A long labial bow (stainless steel 0.7 inch) in the upper arch and a delta clasp on upper first molars and lower first premolars were incorporated for retention. Incisal capping was done to prevent the lower incisor proclination.\n\nAll patients were followed up after 24 hours for any discomforts and then every four weeks interval (Clark’s protocol10). The questionnaires regarding pain in the muscles of mastication and temporomandibular joint (TMJ) area, difficulties with the appliance, duration of wearing were recorded. The expansion schedule was started after 10 days and consisted of one turn twice a week. The duration of the appearance of pterygoid response was recorded.\n\nThe treatment with the twin block was divided into stages. During the six to eight months study period, most subjects completed their active phase with the achievement of Class I molar relationship. The sagittal correction was maintained with the twin block. In follow-up visits, the appliances were examined for loose fit and discomforts. No trimming was done and the vertical dimension of posterior blocks was kept intact up to the last erupted molars. All the patients adapted well and were able to follow the proper protocol of appliance wear.\n\nStandardized lateral skull radiographs were taken for all patients at 0 months, 6 months and 9 months stages, with the Frankfort horizontal plane parallel to plane and teeth in occlusion. All lateral cephalograms were traced using Dolphin software (Dolphin Imaging 11.95) and analyzed for skeletal, dental, and soft tissue changes after twin block therapy. All cephalograms were traced by a single investigator and checked twice.\n\nEthical approval was obtained from the Institutional Review Committee of College of Medical Sciences Teaching Hospital (COMSTH-IRC), Kathmandu University, Nepal (Reference number COMSTH-IRC/2021-153).\n\nWritten informed consent was obtained from all patients.\n\n\nResults\n\nThe mean age of the patients at the start of treatment was 12 years. Pre-and post-treatment lateral cephalograms were taken and evaluated for skeletal, dental, and soft tissue changes after wearing a twin block appliance therapy for nine months. Cephalometric changes during treatment are shown in Table 1. Figure 1 shows pre-treatment cephalograms, Figure 2 shows post-treatment cephalograms and Figure 3 shows the superimposition of pre-and post-treatment average digitizations. Twin block appliance wearing resulted in rapid skeletal correction as was evident from a statically significant decrease in angle Point A-Nasion-Point B (ANB), from 7.07±1.98 to 3.33±1.23 degrees (P=0.02); the angle of convexity decreased significantly from 9.87±1.5 to 5.13±1.24 degrees (P=0.01). There was a significant change in Wits appraisal, which decreased from 4.87±0.91 to 3.33±0.72 mm (P=0.04). Angle between Sella-Nasion-Point B (SNB) increased significantly from 74.0±1.46 to 77.9±0.77 degrees (P=0.02). There was a non-significant increase in mandibular length from 86.73±3.34 to 87.8±3.32 mm (P=0.1). The total anterior facial height (increased from 101.73±2.86 to 102.13±2.5 mm, P=0.09) and posterior facial height (increased from 57.27±1.53 to 57.40±1.68 mm, P=0.43) did not show significant changes with no significant increase in Frankfort mandibular angle (FMA increased from 30.73±1.48 to 30.80±1.37 degrees, P=0.67); there were no significant changes in Jarback ratio too (63.73±1.71 to 63.20±1.6, P=0.15); the angle between Sella-Nasion and Gonion-Gnathion (SN-Go-Gn) increased non-significantly from 132.27±2.43 to 132.60±2.29 degrees (P=0.67); the Y-axis increased non-significantly from 56.66±1.75 to 56.86±1.95 degrees (P=0.32). The upper incisor inclination decreased non-significantly from 115.27±1.33 to 113.42±1.65(P=0.12) and the lower incisor increased non-significantly from 100.13±2.23 to 101.80±1.37 degrees, (P=0.08). The nasolabial angle increased by 3.8 degrees and the change was statistically significant (P=0.04). The mean pretreatment (stage 0) value of overjet was 9.60±1.35 mm which was statistically significantly (P=0.01) reduced to 3.6±0.91 mm at 9 months (stage IV) of the twin block therapy. The mean overbite before the start of treatment (stage 0) was 6±0.92 mm. This changed to 2.47±0.83 mm at 9 months of twin block therapy. The change was statistically significant (P=0.03).\n\n\nDiscussion\n\nThe study was designed to evaluate the skeletal, dental, and soft tissue changes with a modified twin block appliance in high-angle cases. Growing children of ages 8-14 years in the cervical vertebra maturation index (CVMI) stages 3 and 4 were enrolled. Baccetti and McNamara stated that CVMI stages 3 and 4 represent the optimal treatment timing in dentofacial orthopedics.11 Twin block appliances are patient-friendly, comfortable, designed to be worn for 24-hour periods.12 The increased anterior facial height and high mandibular plane angle in vertical growers, and their response to the twin block appliance were determined in this study. The pre- and post-lateral cephalograms were digitized, and cephalometric parameters were determined with Dolphin software and rechecked manually twice. The main cephalometric parameter for correction of Class II was a significant increase in SNB angle, with insignificant change in the SNA angle indicating no maxillary skeletal change as suggested by Lund and Sandler.13 A slight change in A point post twin block therapy is due to the remodeling of the bone of the anterior maxilla during retraction of upper anterior teeth.14 The appliance was effective in correcting the Class II skeletal discrepancy with change in position and length of the mandible during the pubertal growth spurt.15 Change in overjet and molar correction was due to a combination of skeletal and dentoalveolar changes with predominant skeletal changes.16 The patients were treated during the peak growth spurt, which favored more skeletal changes than dental changes. Dentoalveolar correction was due to proclination of lower incisors and upper incisor retroclination. IMPA increased despite acrylic capping of the lower incisors. Upper incisor inclination was corrected with upper lip musculature force during functional treatment17 and upper labial bow effects.13,15 The high-bite twin block showed vertical control with no change in any vertical facial relationships, mandibular plane angle (FMA), and Jarabak ratio. Posterior bite blocks were kept intact without trimming.18 Vertical control was due to having the acrylic block in the posterior region, which provides disocclusion of the teeth, removing the dental intercuspation, and releasing the mandibular growth, thus improving the Class II relationship.19 So, the vertical dentoalveolar development could be controlled without changing the inclination of the mandibular plane as well as provide an additional increment of mandibular growth to the Class II correction.20 The ratio of total anterior facial height to lower facial height remained the same pre- and post-functional treatment.\n\n\nConclusion\n\nClass II malocclusion in vertical growers is corrected by proclination of lower incisors, retroclination of upper incisors, distal movement of upper molars and/or mesial movement of lower molars, increase in mandibular length, and/or forward movement of the mandible. No significant changes on maxilla or mandible lengthening with good vertical control can be done with a high-bite twin block appliance.\n\n\nData availability\n\nFigshare: Effects of modified twin block appliance in growing Class II high angle cases: A cephalometric study, https://doi.org/10.6084/m9.figshare.19146296.v1.21\n\nThis project contains the following underlying data:\n\n- DATA excel sheet.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgments\n\nWe would like to thank all our patients who were involved in our study.\n\n\nReferences\n\nMoyers RE, Riolo ML, Guire KE, et al.: Differential diagnosis of Class II malocclusions. Am. J. Orthod. 1980; 78(5): 477–494. Publisher Full Text\n\nBjork A, Skieller V: Normal and abnormal growth of the mandible. A synthesis of longitudinal cephalometric implant studies over a period of 25 years. Eur. J. Orthod. 1983; 5: 1–46. Publisher Full Text\n\nPepicelli A, Woods M, Briggs C: The mandibular muscles and their importance in orthodontics: A contemporary review. Am. J. Orthod. Dentofac. Orthop. 2005; 128(6): 774–780. PubMed Abstract \| Publisher Full Text\n\nGraber Graber TM: The “three M’s”: Muscles, malformation, and malocclusion. Am. J. Orthod. 1963; 49(6): 418–450. Publisher Full Text\n\nCasutt C, Pancherz H, Gawora M, et al.: Success rate and efficiency of activator treatment. Eur. J. Orthod. 2007; 29(6): 614–621. PubMed Abstract \| Publisher Full Text\n\nDoshi UH, Bhad WA: Spring-loaded bite-blocks for early correction of skeletal open bite associated with thumb sucking. Am. J. Orthod. Dentofac. Orthop. 2011; 140(1): 115–120. Publisher Full Text\n\nRodrigues L, Jawale B, Jamenis S, et al.: Application of magnets in orthodontics –A review. JSAS. 2020; 2(3): 50–57. Publisher Full Text\n\nClark WJ: The twin block technique. A functional orthopedic appliance system. Am. J. Orthod. Dentofac. Orthop. 1988; 93(1): 1–18. PubMed Abstract \| Publisher Full Text\n\nClark W:New Horizons in Orthodontics. Twin Block Functional Therapy: Applications in Dentofacial Orthopedics. Jaypee Brothers Medical Publishers (P) Ltd.; 2015; p. 361–361.\n\nClark WJ: The twin block technique A functional orthopedic appliance system. Am. J. Orthod. Dentofac. Orthop. 1988 Jan 1; 93(1): 1–8. PubMed Abstract \| Publisher Full Text\n\nBaccetti T, Franchi L, Toth LR, et al.: Treatment timing for Twin-block therapy. Am. J. Orthod. Dentofac. Orthop. 2000; 118(2): 159–170. PubMed Abstract \| Publisher Full Text\n\nClark W: Design and management of Twin Blocks: reflections after 30 years of clinical use. J. Orthod. 2010; 37(3): 209–216. PubMed Abstract \| Publisher Full Text\n\nLund DI, Sandler PJ: The effects of Twin Blocks: a prospective controlled study. Am. J. Orthod. Dentofac. Orthop. 1998; 113(1): 104–110. PubMed Abstract \| Publisher Full Text\n\nSkeletal and dentoalveolar effects of Twin-block and bionator appliances in the treatment of Class II malocclusion: a comparative study - PubMed.[cited 2021 Aug 8].Reference Source\n\nBrien K, Wright J: I. Effectiveness of early orthodontic treatment with the Twin-block appliance: a multicenter, randomized, controlled trial. Part 1: Dental and skeletal effects. Am. J. Orthod. Dentofac. Orthop. 2003; 124(3): 234–243.quiz 339. Publisher Full Text\n\nJena A: Skeletal and dentoalveolar effects of Twinblock and bionator appliances in the treatment of Class II malocclusion: A comparative study.\n\nToth LR, McNamara JA: Treatment effects produced by the twin-block appliance and the FR-2 appliance of Fränkel compared with an untreated Class II sample. Am. J. Orthod. Dentofac. Orthop. 1999; 116(6): 597–609. PubMed Abstract \| Publisher Full Text\n\nVig PS, Vig KW: Hybrid appliances: a component approach to dentofacial orthopedics. Am. J. Orthod. Dentofac. Orthop. 1986; 90(4): 273–285. PubMed Abstract \| Publisher Full Text\n\nAltuna G, Woodside DG: Response of the midface to treatment with increased vertical occlusal forces. Treatment and posttreatment effects in monkeys. Angle Orthod. 1985; 55(3): 251–263. PubMed Abstract\n\nHarvold EP, Vargervik K: Morphogenetic response to activator treatment. Am. J. Orthod. 1971; 60(5): 478–490. Publisher Full Text\n\nAdhikari M: Effects of modified twin block appliance in growing Class II high angle cases: A cephalometric study. figshare. Dataset. 2022. Publisher Full Text" }	[ { "id": "225540", "date": "18 Dec 2023", "name": "Alka Gupta", "expertise": [ "Reviewer Expertise Orthodontics" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study's presentation is clear and scientific. The aim to treat Class II division 1 high angle cases using modified twin block appliance has been meet and successfully treated. The availability of the data ensures complete reproducibility of the results. However, the sample size calculation could be done more scientifically. This will provide a baseline data for the Class II division 1 high angle cases treated by Modified twin block.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "238486", "date": "19 Feb 2024", "name": "Ankit Kumar Shahi", "expertise": [ "Reviewer Expertise Treatment of Class II malocclusion" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI would like to appreciate the author for a commendable work on this article on detailed view over the effects of modified Twin Block on Class II cases. However, there are few questions for better understanding: - 1. What was the rationale for selecting the sample size of 15? and what was the number of males and females in the selected sample? 2. The age group mentioned in abstract is 9-14, However in discussion section its mentioned 8-14 ...Kindly verify if there is any typing error. 3. Please elaborate about the significant changes in the Nasolabial angle as mentioned in the results and also please support it by any literature evidence 4. The article mentions in results and discussion about the good vertical control, however the superimposition provided is showing an increase in the anterior lower facial height with increase in vertical angle.\nThanks, and regards.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11443", "date": "29 Apr 2024", "name": "Manoj Adhikari", "role": "Author Response", "response": "What was the rationale for selecting the sample size of 15? and what was the number of males and females in the selected sample? Author response : This is a pilot study so a sample size was taken as 15. Typically, the twin block appliance is contraindicated in cases with a high-angle presentation. The primary objective of this study is to determine the effectiveness of the twin block appliance in high-angle cases and to assess its impact on skeletal, dental, and soft tissue parameters. Gender is not considered as a variable in this study; however, there were 8 male and 7 female participants. 2. The age group mentioned in abstract is 9-14, However in discussion section its mentioned 8-14 ...Kindly verify if there is any typing error. Author response: The age group included in this study ranges from 10 to 14 years. A typing error in the discussion section has been rectified in version 3 of the article. 3. Please elaborate about the significant changes in the Nasolabial angle as mentioned in the results and also please support it by any literature evidence Author response: The nasolabial angle shows a significant increase in this study, attributed to the retroclination of the upper incisors and the retrusion of the upper lip. Supporting evidence from the literature is provided below. “Khoja A, Fida M, Shaikh A. Cephalometric evaluation of the effects of the Twin Block appliance in subjects with Class II, Division 1 malocclusion amongst different cervical vertebral maturation stages. Dental press journal of orthodontics. 2016 May;21:73-84.” 4. The article mentions in results and discussion about the good vertical control, however the superimposition provided is showing an increase in the anterior lower facial height with increase in vertical angle. Author response: The twin block appliance exerts both horizontal and vertical effects. Vertical dimensional changes primarily result from appliance trimming; however, the blocks remain intact in this study. Therefore, vertical dimension changes may be attributed to mandibular growth rather than appliance action. Additionally, Figures 1, 2, and 3 have been updated in version 3." } ] }, { "id": "225537", "date": "26 Apr 2024", "name": "Rudra Deo kumar", "expertise": [ "Reviewer Expertise Dentistry", "Maxillofacial developmental anomaly", "maxillofacial Trauma", "Maxillofacial Pathology", "Orthognathic Surgery etc." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe current research paper demonstrates potential for indexing. It focuses on the adaptability of the Twin Block appliance, commonly utilized for horizontal jaw growth correction, to effectively address vertical growth patterns when modified accordingly. Emphasizing the necessity of early intervention using myofunctional appliances in treating skeletal malocclusion during a patient's developmental phase, the study underscores the importance of averting extensive Orthognathic surgery later in life.\nNotably, this research encourages clinicians to consider the modified Twin Block appliance as an effective approach for mandibular advancement in high-angle cases while maintaining excellent vertical control. Through comprehensive analysis, significant changes in various anatomical landmarks have been observed, supporting the efficacy of this modified appliance. Consequently, this study serves as a valuable resource for clinicians, offering insights into optimizing the use of myofunctional appliances.\nThe paper's presentation is clear and precise, with thorough citations from current literature. Its robust study design and technically sound methodology make it replicable for other researchers. Moreover, the availability of the source data ensures complete reproducibility of the results. The conclusions drawn are well-founded, and adequately supported by the obtained results, contributing substantively to the field.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	2	https://f1000research.com/articles/11-459
https://f1000research.com/articles/12-1111/v1	06 Sep 23	{ "type": "Study Protocol", "title": "Platelet indices and neutrophil:lymphocyte ratio as a predictive tool in acute sickle cell vaso-occlusive crisis: A study protocol", "authors": [ "Kashish Khurana", "Satish Mahajan", "Satish Mahajan" ], "abstract": "Platelet indices and the neutrophil:lymphocyte ratio are newly emerging indicators of systemic inflammation in chronic diseases, such as hemoglobinopathies. The objectives of this study include estimation of platelet indices and neutrophil:lymphocyte ratio in sickle cell disease (SCD) patients with and without vaso-occlusive crisis. This cross-sectional study will be conducted in the Department of Medicine at a tertiary care teaching hospital situated in the rural area of Wardha district. The participants will include patients of SCD older than 14 years of age attending the sickle cell clinic. We hypothesize the use of neutrophil:lymphocyte ratio (NLR) and platelet indices as clinically significant predictive markers in acute sickle cell vaso-occlusive crisis.", "keywords": [ "Neutrophil:lymphocyte ratio", "Platelet Indices", "Sickle cell disease", "vaso occlusive crisis" ], "content": "Introduction\n\nThe sickle cell disease (SCD)-causing globin gene mutation can be inherited homozygously or compound heterozygously. The hydrophobic amino acid valine replaces the hydrophilic amino acid glutamic acid in the sixth position to produce haemoglobin S (HbS). HbS polymerizes as a result of deoxygenation, and this polymerization is associated with both increased red cell density and cell dehydration. The disease’s acute (painful episodes, acute chest syndrome) and chronic (avascular necrosis, renal insufficiency) consequences are considered to be caused by the thick, rigid, and sickling red cells, which cause vaso-occlusion and reduced blood flow and are associated with these symptoms.1\n\nIn SCD, the complicated interactions between sickled erythrocytes, endothelial cells, leukocytes, platelets, and plasma proteins lead to the vaso-occlusive crisis (VOC). It is generally known that platelets play a part in these interactions. While platelet levels typically rise and are functionally hyperactive in the “steady-state” of sickle cell illness, during a sickle cell crisis, platelet count falls first and then increases, later on, during recovery. Although it is uncommon, acute splenic sequestration, aplastic crisis brought on by parvovirus B19 infection, and fat embolism can all cause thrombocytopenia.2\n\nVaso-occlusive crises are associated with enhanced platelet reactivity and activation, which raises platelet volume and widens platelet distribution. Moreover, patients with sickle cell anaemia who experienced more crises had higher platelet concentrations than other patients. In contrast to wealthy nations, patients in central India, also referred to as the sickle cell belt, sadly experience more severe symptoms, with vaso-occlusive crisis and stroke being the two main clinical manifestations.3 A number of studies done in this region reflect on the severity of SCD related complications.4–6\n\nIn several inflammatory and hemolytic illnesses, mean platelet volume serves as a prognostic indicator. Moreover, higher platelet production will result in larger, more reactive platelets with a larger mean platelet size, hence the MPV readings can be utilised to draw conclusions about disorders causing platelet destruction.3\n\nThe high cost of hydroxyurea therapy for sickle cell anaemia challenges the significant population that hail from tribal and socioeconomically disadvantaged backgrounds. Also, there hasn’t been much research done on the use of platelet counts as prognostic indicators, which might be very helpful, particularly for a nation like India with a significant population of sickle cell sufferers. As a result, the goal of this study is to evaluate the role of platelet indices in the early identification of patients at a higher risk of crisis. If a positive correlation is found, platelet indices may be used as a required investigation in the evaluation of sickle cell patients to predict the possibility of vaso-occlusive crisis and to start hydroxyurea therapy early for better patient outcomes.3\n\n\n\n• To estimate platelet indices in sickle cell disease patients with and without crisis.\n\n• To estimate neutrophil:lymphocyte ratio in SCD patients with and without crisis.\n\n\nProtocol\n\nThe study will be conducted in the Department of Medicine, at a tertiary care teaching hospital Acharya Vinoba Bhave Rural hospital situated in the rural area of Wardha district. The overview of the study has been shown in Figure 1.\n\nThis will be a cross-sectional study.\n\nParticipants\n\nCases of sickle cell disease more than 14 years attending Sickle cell clinic at a tertiary care teaching hospital Acharya Vinoba Bhave Rural hospital situated in the rural area of Wardha district.\n\n\n\n• Known patients of SCD older than 14 years of age\n\n• Newly detected cases of SCD older than 14 years of age\n\n\n\n• Age - less than 14 years\n\n• Patients with other causes of thrombocytopenia\n\n• Liver or renal disease\n\n• Patients with hereditary disorders of large platelets\n\n• Patients on anticoagulants\n\n• Patients on antiplatelet agents\n\nDaniel et al. formula for sample size:\n\nwhere, Z∝22 is the level of significance at 5% i.e. 95% confidence interval = 1.96\n\nn = 70 patients needed in each group\n\nStatistical methods: Chi Square test\n\nStudent t-test\n\nSoftware used: SPSS 27.0 Version\n\n\nMethods\n\nThe following data will be collected for all patients with SCD older than 14 years of age.\n\n1. Age of the patient\n\n2. Thorough history – including family history and previous history of crisis, history of chest pain, medication history\n\n3. Assessing pre-existing comorbidities in patient if any:\n\n• H/O Cancer\n\n• H/O Chronic Kidney disease\n\n• H/O Chronic Liver Disease\n\n4. Complete blood count-platelet count and Platelet indices – MPV (mean platelet volume), PDW (platelet distribution width) & PCT (plateletocrit) (blood sample to be collected on day of admission) and differential leucocyte count (neutrophil, lymphocyte, basophils, monocytes and eosinophils)\n\nComplete blood count with hemoglobin and differential leucocyte count (neutrophil, lymphocytes, eosinophils, basophils and monocytes), platelet count.\n\nMean platelet volume (fl), Platelet distribution width (%), plateletcrit (%).\n\nData collection will be done on demography, comorbidities, platelet count, MPV, PDW and PCT. Serum electrolytes and lipid profile shall also be measured.\n\nThe data will be examined using IBM and SPSS (IBM Corp., Statistics for Windows, version 23.0, Armonk, NY). Continuous variables will be expressed as mean standard deviation, whilst categorical data were expressed as a percentage (SD). If there is a statistically significant difference between the bivariate samples in independent groups, it will be determined using the unpaired sample t-test and the Chi-square test. For all of the aforementioned statistical techniques, a p-value ≤ 0.05 will be considered as statistically significant.\n\nDissemination\n\nThe report will be published in an indexed journal.\n\nStudy status\n\nThe study has not yet started.\n\n\nDiscussion\n\nThe most often performed laboratory test in patients with sickle cell disease is the complete blood counts. Little is known, however, about the frequency of platelet-count abnormalities, clinical correlation of various forms of sickle cell crises, and the prognostic importance of platelet indices in these critically ill patients in the ICU. This is the main reason behind designing this protocol.3\n\nCommon complications include vaso-occlusive crisis and stroke. The main event in pathophysiology of sickle cell crisis is vaso-occlusion with ischemia-reperfusion damage, although the pathophysiology at play is complicated.3 Deoxyhemoglobin S polymerization causes tissue ischemia, which causes both acute and chronic pain. It can also cause damage to any organ in the body including the bones, joints, brain, eyes, liver, kidneys and lungs. SCD activates all cellular components in the blood system.4\n\nAdditionally, aberrant red cells and activated platelets may interact, resulting in vaso-occlusion and aggregation. MPV is a simple way to measure platelet activation and function.3,7\n\nIn illnesses like idiopatic thrombocytopenic purpura, platelet production and/or destruction are accelerated and MPV, a measure of platelet size, is increased. In individuals with coronary heart disease, higher MPV levels have been found to be an independent risk factor for myocardial infarction, as well as for death or recurrent vascular events following myocardial infarction.4\n\nStudies have linked high NLR with clinical outcomes in cardiovascular disease, malignancies, as well as renal disease in SCD NLR has been proposed as marker of inflammation. The transition from steady state to vaso- occlusive crisis (VOC) is facilitated by leukocytes, which are both elevated and active in SCA. By secreting pro-inflammatory mediators and expressing related adhesion molecules, leukocytes increase the adhesiveness of the endothelial cells in the presence of the proper VOC-producing substances, hence intensifying vaso-occlusion and the pain process.5\n\nJust prior to or during VOC, there is a surge in hematopoietic activity in addition to the shift of the marginating leukocytes to the circulation pool. The significant leukocytosis seen in the VOC group as opposed to the steady state non vaso occlusive SCD patients may be caused by this. The tendency of leukocytes to stick to the postcapillary venular endothelium is increased during leukocytosis, which reduces the vessel lumen. Sickled and unsickled RBCs, platelets and leukocytes all have a greater propensity to cling to the arterial wall and to other cells in these patients, which exacerbates this blockage. Contrarily, in these individuals, leukocytosis might be a type of defence against overwhelming infectious pathogens to which SCA patients are sensitive as a result of functional asplenia brought on by repeated splenic infarction. Patients with functional asplenia are more susceptible to severe infections, especially those caused by encapsulated pathogens such as Streptococcus pneumoniae and Hemophilus influenzae.8\n\nIn SCA patients, a high NLR increases the chance of developing VOC and other end-organ damage. In line with John et al., this study discovered that SCA patients had greater NLRs than HbA controls.8 Another study, on the other hand, was unable to show a connection between increased NLR and sickle cell nephropathy, perhaps as a result of the cohort being made up of SCA patients in the steady state.8\n\nIn line with earlier studies, a rebound thrombocytosis may have been the cause of the dramatically higher platelet count in the VOC and steady state group. Due to the compensating feedback impact that anaemia has on the synthesis of erythropoietin, rebound thrombocytosis may coexist with hemolytic anemias and the anaemia caused by chronic diseases. The structural similarity between erythropoietin and thrombopoietin is to blame for this. Additionally, hyposplenism in SCA excludes the spleen’s pooling impact on platelets, which greatly contributes to the high platelet count seen in voc state.8\n\nAlthough there is no statistically significant difference between the steady state and VOC groups in the percentage of haemoglobin S in each red blood cell, it is inversely correlated with HbF levels and inversely proportionate to the degree of polymerization of deoxygenated sickle haemoglobin. However, in all previous studies conducted, NLR was not correlated with HbF.8\n\nThe neutrophil and platelet contributions to the chronic inflammatory state in SCA patients are supported by the positive connection between neutrophil to lymphocyte ratio in these individuals. These ratios may serve as reliable, inexpensive and stable indicators of inflammation. When determining the level of inflammation in SCA patients, the use of these simple indicators may be beneficial and superior to using absolute neutrophil count or platelet count alone.8\n\nThis is due to the fact that these ratios are a little bit more stable and are less susceptible to the physiological, pathological or stressful circumstances that are known to affect platelet and neutrophil counts.8\n\nIEC approval was obtained from Datta Meghe Institute of Medical Sciences and research (Reference number: DMIMS (DU)/IEC/2022/1084).\n\nWritten informed consent will be obtained from the patients and their relatives/parents in case of minor patients.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nPakbaz Z, Wun T: Role of the Hemostatic System on SCD Pathophysiology and Potential Therapeutics. Hematol. Oncol. Clin. North Am. 2014 Apr; 28(2): 355–374. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShome DK, Jaradat A, Mahozi AI, et al.: The platelet count and its implications in sickle cell disease patients admitted for intensive care. Indian J. Crit. Care Med. 2018 Aug; 22(8): 585–590. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStudent AK: Mean Platelet Volume as a Prognostic Indicator in Sickle Cell Anemia. Int. J. Recent Surg. Med. Sci. 2018 Jan; 04(01): 005–009. Publisher Full Text\n\nSerum Lactate to Albumin Ratio as a Prognostic Marker of Sepsis Syndrome\|Annals of the Romanian Society for Cell Biology. [cited 2023 May 30].. http\n\nJadhav U, Babu R, Ghewade B, et al.: Acute chest syndrome, a distinctive manifestation in sickle cell disease – A case study. J. Datta Meghe Inst. Med. Sci. Univ. 2020 Jul 1; 15(3): 492. Publisher Full Text\n\nTaksande A, Jameel PZ, Pujari D, et al.: Variation in pulmonary function tests among children with sickle cell anemia: a systematic review and meta-analysis. Pan. Afr. Med. J. 2021; 39: 140.\n\nCelik T, Unal S, Ekinci O, et al.: Mean Platelet Volume can Predict Cerebrovascular Events in Patients with Sickle Cell Anemia. Pak. J. Med. Sci. 2015; 31(1): 203–208. PubMed Abstract \| Publisher Full Text\n\nAlagbe: Pattern of neutrophil-lymphocyte ratio and platelet-lymphocyte ratio in sickle cell anemia patients at steady state and vaso-occlusive crisis.[cited 2023 May 30]. Reference Source" }	[ { "id": "232202", "date": "24 Jan 2024", "name": "Ashwin P. Patel", "expertise": [ "Reviewer Expertise Hematology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors should address the following queries to increase the clarity of the proposed research. (1) The inclusion and exclusion criteria mentioned in the draft and Figure 1 are different. For example, the figure mentions age < 18 years as an exclusion criterion while the text mentioned < 14 years. (2) Two different versions of SPSS are mentioned in the manuscript. (3) The statistical analysis section needs clarity. The authors mentioned, \" Continuous variables will be expressed as mean standard deviation\". Continuous variables with a normal distribution are expressed as mean and standard deviation while continuous variables with a non-normal distribution are expressed as median and inter-quartile range. (4) The language used the the manuscript creates confusion. Is this project completed or is it to be carried out?\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "11186", "date": "13 Apr 2024", "name": "Kashish Khurana", "role": "Author Response", "response": "1) In the age criteria mentioned in the article, there is a typing mistake and the age criteria in exclusion criteria should be <18 years and not <14 years. It has been rectified in the article. 2) SPSS software version used in the manuscript was version 27.0 and not version 23. That was a typing error. 3) I will rectify the statistical analysis section and will write the following: Continuous variables with a normal distribution are expressed as mean and standard deviation while continuous variables with a non-normal distribution are expressed as median and inter-quartile range. 4) This project is currently in process and is likely to be completed in June 2024." } ] } ]	1	https://f1000research.com/articles/12-1111
https://f1000research.com/articles/12-765/v1	30 Jun 23	{ "type": "Study Protocol", "title": "Effect of foot core exercises vs ankle proprioceptive neuromuscular facilitation on pain, range of motion, and dynamic balance in individuals with plantar fasciitis: a comparative study", "authors": [ "Manali Boob", "Pratik Phansopkar", "Pratik Phansopkar" ], "abstract": "Plantar fasciitis is generally described as an inflammation of the plantar fascia and adjacent tissues around calcaneus tuberosity. Plantar fasciitis onset has been proposed to have an internal mechanical cause, even though this is inadequately recognized. Studies related to alternation in lower-extremity biomechanics that leads to reduced domes of the foot are hypothesized to cause tension in the underlying fascia. Similarly, despite a wealth of anecdotal data suggesting a direct connection between foot mechanism and disability. This condition typically leads to calf muscular stiffness, soreness in the bottom of the feet, decreased range and foot function, strength, and balance impairment. These results in interference with the normal biomechanics of ambulation. A total of (n=66) individuals with plantar fasciitis will be selected for the trial. Subjects will be allocated to Groups A and B at equal allocation with randomization. Group A will undergo foot core exercises, while Group B will undergo ankle proprioceptive neuromuscular facilitation, with both groups receiving conventional treatment. The regimen lasts for 40 minutes, 5 days, for 6 weeks. The outcome measures will be assessed on Foot Functional Index, modified Star Excursion Balance Test (mSEBT), Visual Analogue Scale (VAS), and Weight Bearing Lunge Test (WBLT) be assessed at the initiation and completion of the entire treatment protocol. Prior and after therapeutic intervention results will be analyzed. Based on the comparison of the two treatments' effects on measuring outcomes in individuals with plantar fasciitis, an analysis will be conducted.", "keywords": [ "Plantar fasciitis", "foot core exercises", "ankle proprioceptive neuromuscular facilitation", "foot functional index", "modified star excursion test." ], "content": "Introduction\n\nThe ankle and foot are constituted of twenty-six separate small bones as well as the major bones of the leg.1 The ankle joint creates a connection that enables the lower extremity to connect with the foot.1 Ankle and foot mobility is described in the following three categorical planes: longitudinal, coronal, and axial.2 The sole of the foot comprises three main vaults: a transverse arch, and two longitudinal arches. The muscles, ligaments, tendons, and fascia in the foot support these domes.3 The gastrocnemius and soleus muscles work together to predominantly plantarflex the ankle.4 The plantar layers contain the intrinsic foot muscles in their anatomical alignment.4 The ends of extrinsic foot muscles are connected at the foot distally and the leg proximally, respectively.5 A broad, longitudinally oriented strand that are firmly linked to the sole of the foot is referred to as plantar fascia. The proximally plantar fascia is attached to the calcaneal tuberosity and distally split into five bands for each toe.6\n\nA gradual degenerative irritation of the plantar fascia, which starts at the medial calcaneal tuberosity, as well as the nearby perifascial tissues, results in plantar fasciitis, an inflammatory disorder. The plantar fascia serves a crucial role in accurate foot mechanics.7 The main prevalent source of heel discomfort is plantar fasciitis. This is responsible for around 15% of all foot issues brought to the attention of healthcare practitioners.8 A mechanical model known as the “windlass mechanism” offers a complete justification for the biomechanical components of the foot. Such knowledge is crucial for clinical practice since it could give medical experts a comprehensive grasp of the connection between pathologies and biomechanical factors.9 A history of pain with the first steps in the morning, pain that becomes worse with loading activities and gets better over the day, and palpable soreness in the medial calcaneal tubercle are used to make the diagnosis of this illness. Achilles tendon tightness may cause patients to have decreased ankle dorsiflexion, which might lead to anticipatory overpronation of the ankle.10\n\nTheories of Proprioceptive Neuromuscular Facilitation (PNF) may be beneficial in enhancing postural balance and stability. In the development of a therapeutic relationship, PNF is characterized as a strategy to improve the neuromuscular stimulation of the proprioceptive sense response mechanism. This technique set contains methods that stimulate proprioceptive sense to improve the response of the neurological and muscular systems. PNF is a stretching method that is utilized in the realms of exercise and sports to increase muscular flexibility, strength, and balance as well as joint mobility.11 The technique emphasis of timing in ankle proprioceptive neuromuscular facilitation (PNF) was enhanced to synchronise and strengthen the movement patterns of both the foot's intrinsic and exterior muscles.12\n\nExercises for the foot core were done to maintain proper foot alignment, manage the position of the arch, and activate the proprioceptors on the foot's sole to enhance balance. As a result, earlier gait retraining studies have started to include foot core exercise to lower the risk of injury in individuals when the striking pattern abruptly changes. The towel curls, foot doming, and toe spread, which have been shown to be efficient treatments to develop the arch muscles, might be used to strengthen the foot muscles in order to stabilise the form of the arch.13\n\nVisual analogue scale (VAS) is used to assess the pain, rated from zero to ten. The foot functional index (FFI) questionnaire evaluates physical discomfort, impairments, as well as activity-restricting foot pathologies in everyday functioning.14 The 23 items on the questionnaire are categorized into three subdimensions: pain, activity limitations, and disabilities. It was created in English, and it has official translations for usage in Chinese, German, French, Italian, and Spanish. Because standardisation is crucial when utilising measures of assessment, checklists created in other languages must be translated and their parametric qualities assessed to promote comparability between research.15 Ankle dorsiflexion may be directly monitored with weight bearing lung test. The therapist measured the amount of dorsiflexion in affected limbs while the patient will be in a lunge position. The therapists either employed an inclinometer or a measuring tape to evaluate the numerical outcome. In several disorders, including patellofemoral pain syndrome and overpronation of the foot, which may result in plantar fasciitis, it is well-accepted that inadequate ankle dorsiflexion plays a vital role.16\n\nThe modified Star Excursion Balance Test is among the popular techniques for the clinical examination of dynamic balance (mSEBT). When assessing the likelihood of lower extremity injuries, clinicians frequently employ just one of these diagnostic techniques and one outcome factor. It is well-established that age, sex, and sport may affect dynamic balance scores.17\n\nThe purpose of the study is to compare the effects of foot core exercises and ankle proprioceptive neuromuscular facilitation on pain, range of motion, and dynamic balance in patients with plantar fasciitis. The plantar fascia is subjected to steadily increasing loading stress if these musculatures are weaker and the plantar fascia lacks flexibility, which flattens the longitudinal arch and causes foot eversion. This results in the hip of the afflicted side descending, which causes the hip to rotate inward, and a reduction in the medial joint space of the knee. This may result in plantar fascia overload, muscle imbalance, abnormal gait, and reduced functional performance. Foot core exercises and Proprioceptive neuromuscular facilitation have been shown to be helpful in the reduction of pain, restoring the motion, and regaining muscular strength. There is a lack of literature that emphasizes a comparison between foot core exercises and PNF that helps in improving dynamic state of balance, as well as functional status in patients suffering from plantar fasciitis. As a result, strong evidence is very important in this field.\n\n\nAim and objective\n\n\n\n1) To assess and evaluate the effects of foot core exercises on pain (VAS and FFI), range of motion (WBLT), and dynamic balance (mSEBT) in patients with plantar fasciitis.\n\n2) To assess and evaluate the effects of ankle proprioceptive neuromuscular facilitation on pain (VAS and FFI), range of motion (WBLT), and dynamic balance (mSEBT) in patients with plantar fasciitis.\n\n3) To compare the effects of foot core exercises and ankle proprioceptive neuromuscular facilitation on pain (VAS and FFI), range of motion (WBLT), and dynamic balance (mSEBT) in patients with plantar fasciitis.\n\nTrial Design: single centric two arm parallel, comparative open labelled superiority trial.\n\n\nProtocol\n\nThe study will be conducted at Musculoskeletal Physiotherapy OPD of Acharya Vinoba Bhave Rural Hospital and Musculoskeletal Physiotherapy OPD of Ravi Nair Physiotherapy college, Sawangi (Meghe) Wardha, after receiving approval from ethical committee of Datta Meghe Institute of Higher Education and Research. The participants diagnosed as plantar fasciitis and follows the inclusion criteria will be randomly selected using simple random sampling and divided into Group A and Group B using computer generated list. After explaining the study protocol in detail, written consent will be signed by the participants. The duration of study will be one year. A total of 33 participants will be in each group. The outcome measures are foot functional index, modified star excursion balance test, weight bearing lunge test and visual analogue scale used to assessed pain, range of motion, dynamic balance, disability, and limitations in activities of daily living. Group A patients will be receiving foot core exercises and conventional therapy and group B patients will be receiving ankle proprioceptive neuromuscular facilitation. The outcome measure will be assessed at the base line and after six weeks of intervention Figure 1. Explains the study procedure.\n\n\n\n1) A progressive onset of heel pain lasting three months or more, localized to the medial calcaneal tubercle.\n\n2) Sharp and worsen pain with the first few steps out of bed in morning.\n\n3) Positive windlass test.\n\n4) Both male and female.\n\n5) Age ranging between 40-60.\n\n\n\n1) Patients with type 1 or 2 Diabetes Mellitus, systemic inflammatory arthritis, cancer, active tuberculosis.\n\n2) Arthrosis of the ankle, knee, and hip.\n\n3) Pregnant women.\n\n4) Patients with numbness or tingling with or without provocation in the lower extremity, undiagnosed pain.\n\n5) Patients currently receiving treatment and using steroids within the last six months for the plantar fasciitis.\n\nControl group\n\nGroup A will be given foot core exercises which includes heel raise, toe curls, foot doming, toe spreading, balancing board, and tennis ball roll under foot along with conventional therapy which includes ultrasound, plantar fascia stretching and Achilles stretching. The foot core exercises mentioned in Table 1. which lasts for 30 mins with 10 mins of conventional therapy. The entire protocol lasts for 40 min, five days a week, for six weeks.\n\nExperimental group\n\nGroup B will be given Ankle Proprioceptive Neuromuscular Facilitation (PNF) which includes techniques such as slow reversal (SR), and rhythmic stabilization (RS) along with conventional therapy. The PNF protocol mentioned in Table 2 which last for 30 mins with 10 mins of conventional therapy. The entire protocol lasts for 40 min, five days a week, for six weeks.\n\nPrimary outcomes\n\n\n\n1. Foot Function Index (FFI)\n\nthe Foot Function Index (FFI) was designed to analyze the effect of foot abnormalities on performance in terms of pain, functional limitations, and activity restriction. The internal consistency was between 0.96 and 0.7.15\n\n2. The Modified Star Excursion Balance Test (mSEBT)\n\nThe SEBT (Star Excursion Balance Test) is a multi-dimensional test that includes power, mobility, and postural control. This is a dynamic balancing measurement that poses a substantial challenge to players and healthy and active adults. The evaluation is used to measure functional ability as well as to screen for inadequacies in dynamic balance caused by musculoskeletal disorder. coefficients of variation ranging from 2.0 to 2.9 percent, the mSEBT has been shown to be a valid indicator of dynamic balance.17\n\nSecondary outcome\n\n\n\n1) The Visual Analogue Scale (VAS)\n\nTo determine the intensity of the pain this scale is used. The VAS is a 10 cm line that has two terminals marked with the numbers 0 (“no discomfort”) and 10 (“pain as horrific as it can be”). Ask the patient to rate their current level of discomfort and mark the line accordingly. Using a ruler determine the distance in centimetres between baseline and the current pain mark.18\n\n2) Weight Bearing Lunge Test (WBLT)\n\nAnkle dorsiflexion range is determined with this procedure. In this test with the help of inch tape distance will be measured. Inter-rater ICC values for angles were 0.97 and 0.99. The analysis shows evaluating a dorsiflexion range with this method have great reliability.19\n\nSample size calculation resulted at 5% level of significance considering Z (1-α) value = 1.96 and (1- β) at power of 80% = 0.84 measuring the expected mean difference for superiority (effect side) of (δ) = 2.602 and standard deviation (σ) = 3.24\n\nFormula Using Mean difference\n\nPrimary variable – (Foot Functional Index)\n\nMean. (Pre) result on Foot Functional Index for foot core exercises with conventional physiotherapy = 72.68\n\nMean. (Post)- result on Foot Functional Index for foot core exercises with conventional physiotherapy = 59.67 ± 10.69\n\nDifference (mean ± SD) = 13.01 ± 3.24 (As per reference article)\n\nClinically relevant superiority = 20% = (13.01 *20)/100 = 2.602\n\nMinimum samples required = 25 per group\n\nConsidering 30% drop out = 8\n\nTotal sample size required = 33 per group\n\nAssumptions\n\nRef Article: - Jadhav and Gurudut.20\n\nAll the results will be calculated using SPSS 27 version. Demographic variables (Confounding factors) as per quantitative assessment will be resulted for finding observational values on mean Standard deviation minimum and maximum. Quantitative assessment will be observed on frequency and percentage. The data for inferential statistics, with outcome variables will be tested for normality using Kolmogorov Smirnov Test. A parametric test will be used if the data follows normal distribution. Non-normal data will be attempted for transformation to normality by using mathematical algorithm such as log or exponential function or box cox method. For finding the significance over the mean pre- and post T-paired will be used for analysis if data still persist with non-normal distribution alternative Wilcoxon test will be used for finding the difference for mean significance between the two groups (Inter) un-paired t-test will be used while the Man-Whitney will be used as an alternative t-test for non-normal data Association and analysis for finding the significance of confounding parameters will be evaluated using Chi square test or Fischer Exact Test or using multi-variant analysis.\n\nThe two groups will be compared using inferential statistics for their mean change in the primary variable (Foot functional index and modified star excursion test) between baseline and six weeks. For research participants, random effects will be generalised, treatment group and visit count will be taken into consideration while analysing fixed effects. At the conclusion of the intervention, the effect size over the mean change difference on the primary variable will be assessed and the matching 95% confidence interval (CI) given.\n\nTo predict the difference in effect size between the active and control groups, secondary outcomes (the visual analogue scale and the weight bearing lunge test) will be examined in accordance with the mixed model effect. If the data is distributed normally, the T-test (unpaired) will be performed to determine whether there is a significant difference between the means of the two groups. The data will be transformed into a normal distribution for non-normal distributions using mathematical techniques. If the primary variable's data still exhibits a non-normal distribution, an alternative non-parametric test will be used (Chi square, Mann Whitney, Wilcoxon test).\n\nTo present the research findings at conferences, seminars, community forums etc.\n\nThe study is yet to start.\n\n\nDiscussion\n\nThe purpose of this study to analyse the efficacy of ankle pnf vs standard foot core exercises in enhancing functional capacities, enhancing dynamic balance, increasing joint mobility, and reducing discomfort in individuals who are suffering from plantar fasciitis. Poor foot posture can lead to structural abnormalities throughout the body because it places enormous strain on the lower extremity’s joints and muscles. If this abnormal pressure is not alleviated, it will continue to cause discomfort, fatigue, and musculoskeletal injury. When a person has plantar fasciitis, the fascia becomes inflamed because of excessive intense activity, which causes pain and discomfort when doing weight-bearing activities like walking. When engaging in weight-bearing activities, dynamic balance control can be impacted by pain.21\n\nNumerous studies demonstrate the impact on the reduction of pain, improve joint mobility and foot function, etc. According to Ranbhor et al., foam rolling and calf and plantar fascia stretching both aided with pain relief and joint motion. However, the outcome measure shows boosting effects in the foam rolling than the traditional stretching exercises.22 According to Kaur and Koyal's study, stretching the Achilles tendon produced a significant improvement in the patient's outcome variables, but stretching the calves reduced discomfort and foot function deficit but did not have the same impact.23 According to Kumar et al., low dye taping combined with stretching of the plantar fascia and strengthening of the intrinsic muscles was an effective method for reducing pain and enhancing functional activities. Both groups showed a substantial improvement in all categories, however the people who had low dye taping saw a considerably superior overall improvement. Consequently, low dye tape is an effective intervention method for the treatment of plantar fasciitis patients.24\n\nBy analysing the outcome, we will be evaluating the impact of foot core exercises and ankle pnf on dynamic balance and compare both the intervention in this study. Muscle strength in the fundamental body parts is crucial for maintaining balance. Accurate and efficient exercise of these muscles appears to be of utmost importance since they play a significant function secondary to that of the foot, as well as in relation to the complete kinematic chain.\n\nInstitutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (Deemed to be University) approved this study.\n\nDMIHER (DU)/IEC/2023/804 is the reference number.", "appendix": "Data availability\n\nNot applicable as this is a protocol.\n\nZenodo: SPIRIT Checklist DOI: 10.5281/zenodo.7990088. 25\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nI would like to thank my institution, colleague, and my guide Dr. Pratik Phansopkar.\n\n\nReferences\n\nBrockett CL, Chapman GJ: Biomechanics of the ankle. Orthop. Traumatol. 2016 Jun 1; 30(3): 232–238. Publisher Full Text\n\nHertel J: Functional Anatomy, Pathomechanics, and Pathophysiology of Lateral Ankle Instability. J. Athl. Train. 2002; 37(4): 364–375. PubMed Abstract\n\nGray’s Anatomy - 42nd ed.[cited 2023 Feb 27]. Reference Source\n\nMcKeon PO, Hertel J, Bramble D, et al.: The foot core system: a new paradigm for understanding intrinsic foot muscle function. Br. J. Sports Med. 2015 Mar; 49(5): 290–290. PubMed Abstract \| Publisher Full Text\n\nOrthotics MF: Intrinsic and Extrinsic Foot Musculature. MASS4D® Foot Orthotics; [cited 2023 Feb 27]. Reference Source\n\nPlantar fasciitis: [cited 2023 Jan 23]. Reference Source\n\nBuchanan BK, Kushner D: Plantar Fasciitis. StatPearls. Treasure Island (FL): StatPearls Publishing; 2022 [cited 2023 Jan 15]. Reference Source\n\nMenon NA, Jain J: Plantar fasciitis: A review. Indian J. Pain. 2018 Jan 1; 32(1): 24. Publisher Full Text\n\nBolgla LA, Malone TR: Plantar Fasciitis and the Windlass Mechanism: A Biomechanical Link to Clinical Practice. J. Athl. Train. 2004; 39(1): 77–82. PubMed Abstract\n\nThe epidemiology of plantar fasciitis\|Lower Extremity Review Magazine: 2010 [cited 2023 Jan 23]. Reference Source\n\nVoss DE, Ionta MK, Myers BJ, et al.: Proprioceptive Neuromuscular Facilitation: Patterns and Techniques. Harper & Row; 1985; 370.\n\nPark DJ, Lee KS, Park SY: Effects of Two Foot-Ankle Interventions on Foot Structure, Function, and Balance Ability in Obese People with Pes Planus. Healthcare. 2021 Jun 3; 9(6): 667. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim HJ, Cho J, Lee S: Talonavicular joint mobilization and foot core strengthening in patellofemoral pain syndrome: a single-blind, three-armed randomized controlled trial. BMC Musculoskelet. Disord. 2022 Feb 15; 23: 150. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWhole R, Chitale N, Phansopkar P: A Case Report of Plantar Fasciitis in Diabetic Female Successfully Treated with Physical Therapy. Biosci. Biotechnol. Res. Commun. 2021; 14: 113–115.\n\nMartinez BR, Staboli IM, Kamonseki DH, et al.: Validity and reliability of the Foot Function Index (FFI) questionnaire Brazilian-Portuguese version. Springerplus. 2016 Oct 18; 5(1): 1810. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCejudo A, Sainz de Baranda P, Ayala F, et al.: A simplified version of the weight-bearing ankle lunge test: Description and test–retest reliability. Man. Ther. 2014 Aug 1; 19(4): 355–359. PubMed Abstract \| Publisher Full Text\n\nBulow A, Anderson JE, Leiter JR, et al.: THE MODIFIED STAR EXCURSION BALANCE AND Y-BALANCE TEST RESULTS DIFFER WHEN ASSESSING PHYSICALLY ACTIVE HEALTHY ADOLESCENT FEMALES. Int. J. Sports Phys. Ther. 2019 Apr; 14(2): 192–203. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRatna S: EFFECT OF KINESIO TAPING IN ADJUNCT TO CONVENTIONAL THERAPY IN REDUCING PAIN AND IMPROVING FUNCTIONAL ABILITY IN INDIVIDUALS WITH PLANTAR FASCIITIS A RANDOMIZED CONTROLLED TRIAL. Int. J. Theor. Phys. 2015 Aug 17; 2. Publisher Full Text\n\nBennell K, Talbot R, Wajswelner H, et al.: Intra-rater and inter-rater reliability of a weight-bearing lunge measure of ankle dorsiflexion. Aust. J. Physiother. 1998 Jan 1; 44(3): 175–180. PubMed Abstract \| Publisher Full Text\n\nJadhav A, Gurudut P: Comparative Effectiveness of Gua Sha, Cryostretch, and Positional Release Technique on Tenderness and Function in Subjects with Plantar Fasciitis: a Randomized Clinical Trial. Int. J. Ther. Massage Bodyw. 2023 Mar 1; 16(1): 13–23. Publisher Full Text\n\nLakhwani M, Phansopkar P: Efficacy of Percussive massage Versus Calf Stretching on Pain, Range of Motion, Muscle Strength and Functional Outcomes in Patients with Plantar Fasciitis – A Randomized Control Trial.2021.\n\nRanbhor AR, Prabhakar AJ, Eapen C: Immediate effect of foam roller on pain and ankle range of motion in patients with plantar fasciitis: A randomized controlled trial. Hong Kong Physiother. J. 2021 Jun; 41(01): 25–33. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaur S, Koley S: Efficacy of Calf Stretching and Achilles Tendon Stretching in Reducing Pain and Improving Foot Function Disability in Patients with Plantar Fasciitis.2020; 2.\n\nKumar S, Kumar A, Kaur J: Effect of PNF technique on gait parameters and functional mobility in hemiparetic patients.2012.\n\nBoob MA: SPIRIT checklist. doc (Version v1). Zenodo. 2023. Publisher Full Text" }	[ { "id": "209275", "date": "02 Oct 2023", "name": "Pornpimol Muanjai", "expertise": [ "Reviewer Expertise Exercise", "aging", "physical therapy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIntroduction\nThe rational in term of using these two intervention is still weak. Please provide more the beneficial effects to plantar fasciitis condition.\n\n\"PNF is a stretching method..\" It sounds a bit wrong. Please kindly check or rephrase as it is a kind of neuromuscular facilitation acts as muscle contracting or stretched.\n\nFifth paragraph can be shortened regrading available languages.\n\nPlease explain more why plantar fasciitis affects to balance deficit.\n\nThe study hypothesis should be given.\n\nReferences needs for \"foot core exercises and PNF have been shown to be helpful in...\"\n\nMethods\nPlease provide the ethical approve number for this study.\n\nPlease specify in case bilateral foot involved, which side will be trained and tested.\n\nPlease specify the treatment detail where those received and will be excluded from the study.\n\nWhy those 2 PNF technique were selected in this study? It would be useful to know for the other.\n\nPlease reconsider the foot core exercise program as in the review it was suggested that those 3 exercises were effective treatment for arch correction. Personally, I would suggest to remove the double leg heel raise as single one would be more loading and also the tennis ball rolls which it should be as a part of the conventional treatment for plantar fascia stretching for both groups.\n\nWhat activity VAS will be examined? at rest or walking?\nDiscussion\nIt would be better if the evidence regarding the using these 2 interventions in plantar fasciitis or on those parameters will be more available.\n\nThere was no data to report yet.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "234132", "date": "20 Feb 2024", "name": "Elif Tuğçe Çil", "expertise": [ "Reviewer Expertise Physiotehrapy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThanks to the authors for their efforts. -The terminology of plantar fasciitis should be explained in an up-to-date manner. Because this condition is not only associated with inflammation. -The discussion section should be written by discussing and interpreting the current literature in comparison with your results. -The language of the article contains many grammatical errors and should be corrected. -I did not see any table of your result.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] } ]	1	https://f1000research.com/articles/12-765
https://f1000research.com/articles/12-95/v1	24 Jan 23	{ "type": "Research Article", "title": "Local Multiset Dimension of Amalgamation Graphs", "authors": [ "Ridho Alfarisi", "Liliek Susilowati", "Dafik Dafik", "Savari Prabhu", "Ridho Alfarisi", "Dafik Dafik", "Savari Prabhu" ], "abstract": "\\textbf{Background}: One of the topics of distance in graphs is the resolving set problem. Suppose the set $W=\\{s_1,s_2,…,s_k\\}\\subset V(G)$, the vertex representations of $\\in V(G)$ is $r_m(x\|W)=\\{d(x,s_1),d(x,s_2),…,d(x,s_k)\\}$, where $d(x,s_i)$ is the length of the shortest path of the vertex $x$ and the vertex in $W$ together with their multiplicity. The set $W$ is called a local $m$-resolving set of graphs $G$ if $r_m (v\|W)\\neq r_m (u\|W)$ for $uv\\in E(G)$. The local $m$-resolving set having minimum cardinality is called the local multiset basis and its cardinality is called the local multiset dimension of $G$, denoted by $md_l(G)$. Thus, if $G$ has an infinite local multiset dimension and then we write $md_l (G)=\\infty$. \\\\ \\textbf{Methods}: This research is pure research with exploration design. There are several stages in this research, namely we choose the special graph which is operated by amalgamation and the set of vertices and edges of amalgamation of graphs; determine the set $W\\subset V(G)$; determine the vertex representation of two adjacent vertices in $G$; and prove the theorem.\\\\ \\textbf{Results}: The results of this research are an upper bound of local multiset dimension of the amalgamation of graphs namely $md_l(Amal(G,v,m))\\leq m.md_l(G)$ and their exact value of local multiset dimension of some families of graphs namely $md_l(Amal(P_n,v,m))=1$, $md_l(Amal(K_n,v,m))=\\infty$, $md_l(Amal(W_n,v,m))=m. md_l(W_n)$, $md_l(Amal(F_n,v,m))=m. md_l(F_n)$ for $d(v)=n$, $md_l(Amal(F_n,v,m))=m. \\lfloor\\frac{n}{4}\\rfloor$. \\\\ \\textbf{Conclusions}: We have found the upper bound of a local multiset dimension. There are some graphs which attain the upper bound of local multiset dimension namely wheel graphs\\\\", "keywords": [ "local m-resolving set", "local multiset dimension", "amalgamation graph." ], "content": "Introduction\n\nIn this paper, we study the local multiset dimension of the amalgamation of graphs. One of the topics of distance in graphs is resolving set problems. This topic has many application in science and technology namely in the navigation of robots, chemistry structure, and computer sciences. The application of metric dimension in networks is the navigation of robots. Suppose, we represent a place as a vertex and a connection between place is represented by an edge. The minimum numbers of robots required to locate each vertex in the networks is part of the resolving set problems. More details of this application can be seen.1\n\nSeveral applications of resolving sets in chemistry are the substructures of a chemical compound which can be denoted by a set of functional groups. Moreover, in a chemical structure or molecular graph edges and vertices are known as bonds and atoms, respectively. Furthermore, the sub graphs are simply deliberated as substructures and functional groups. Now after altering the position of functional groups, the formed collections of compounds are distinguished as substructures being similar to each other. Later on using the method of traditional view, we can investigate if any two compounds hold the same functional group at the same point, while in drugs discovery comparative statements contributes a critical part to determine pharmacological activities related to the feature of compounds.2\n\nAll graphs G are simple, finite, and connected. Given that the vertex set V (G) and the edge set E(G), we write G = (V, E). The distance of u and v, denoted by d(u, v) is the length of the shortest path of the vertices u to v. For the set W = {s1, s2, …, sk} ⊂ V (G), the vertex representations of the vertex x to the set W is an ordered k-tuple, r(x\|W) = (d(x, s1), d(x, s2), …, d(x, sk)). The set W is called the resolving set of G if all vertices of G have different vertex representations. The resolving set having minimum cardinality is called basis and its cardinality is called metric dimension of G, denoted by dim(G).3 Okamoto et al.4 introduced the new variant of resolving set problems which is called local resolving set problems. In his paper, this notion is called a local multiset dimension of graphs G. The set W is called a local resolving set if for every xy ∈ E(G), r(x\|W)≠r(y\|W). The local resolving set having minimum cardinality is called local basis and it’s cardinality is called local metric dimension of G and denoted by ldim(G).\n\nSimanjuntak et al.5 defined multiset dimension of graphs G. Suppose the set W=s1s2…sk⊂VG, the vertex representations of a vertex x ∈ V (G) to the set W is the multiset rmxW=dxs1dxs2…dxsk where d(x, si) is the length of the shortest path of the vertex x and the vertex in W together with their multiplicities. The set W is called a m-resolving set if for every xy ∈ E(G), rm(x\|W)≠rm(y\|W). If G has a m-resolving set then an m-resolving set having minimum cardinality is called a multiset basis and it’s cardinality is called the multiset dimension of graphs G and denoted by md(G); otherwise we say that G has an infinite multiset dimension and we write mdG=∞. Alfarisi et al.6 studied the multiset dimension of almost hypercube graphs. Later, Alfarisi et al.7 extended a new notion based on the multiset dimension of G, namely a local multiset dimension. Suppose the set W=s1s2…sk⊂VG, the vertex representations of a vertex x ∈ V (G) to the set W is rm(x\|W) = {d(x, s1), d(x, s2), …, d(x, sk)}. The set W is called a local m-resolving set of G if rm(v\|W)≠rm(u\|W) for uv ∈ E(G). The local m-resolving set having minimum cardinality is called the local multiset basis and it’s cardinality is called the local multiset dimension, denoted by mdl(G): otherwise we say that G has an infinite local multiset dimension and we write mdlG=∞.\n\nWe illustrate this concept in Figure 1. In this case, the m-resolving set is W = {v2, v3, v6}, shown in Figure 1(a). The multiset dimension is md(G) = 3. The representations of v ∈ V (G) with respect to W are all distinct. For the local multiset dimension, we only need to make sure the adjacent vertices have distinct representations. Thus, we could have the local m-resolving set W = {v1}, shown in Figure 1(b). Thus, the local multiset dimension is μl(G) = 1.\n\nWe have some results on the local multiset dimension of some known graphs namely path, star, tree, and cycle and also the local multiset dimension of graph operations namely, cartesian product,7 m-shadow graph.8 Adawiyah et al.9 also studied local multiset dimension of unicyclic graphs. The followings are some results which is used for proving the new results in this study.\n\nLet G be a connected graphs and W ⊂ V (G). If W contains a resolving set of G, then W is a resolving set of G.10\n\nA graph is bipartite if and only if it contains no odd cycle.11\n\nThe local multiset dimension of G is one if and only if G is a bipartite graph.12\n\nIf T is tree graph with order n, then mdl(T) = 1.12\n\nLet Kn be a complete graph with n ≥ 3, we have mdlKn=∞.6\n\nLet (Gi) be a finite collection of graphs and each Gi has a fixed vertex v called a terminal. The amalgamation Amal (Gi, v, m) is formed by taking of all the Gi and identifying their terminal.\n\nFigure 2 is an example of an amalgamation graph with isomorphic and non-isomorphic graph.\n\n\nMethods\n\nThe nature of the methods follows an extrapolative design. There are several stages in this research as follows:\n\n1. Choose the special graph which is operated by amalgamation;\n\n2. Determining the set of vertices and edges of amalgamation of graphs;\n\n3. Determining the set W ⊂ V (G);\n\n4. Determining the vertex representation of two adjacent vertices in G;\n\n5. Proving the theorem.\n\nThe flowchart of this method can be seen in Figure 3.\n\n\nResults\n\nIn this section, we investigated the local multiset dimension of graph amalgamation. We provide an upper bound of local multiset dimension of Amal(G, v, m) and we show that the upper bound is sharp. We also determined the exact value of the local multiset dimension of Amal(G, v, m) for some certain graphs namely path, complete graph, fan graph, and wheel graph. The following theorem provides a sharp upper bound of Amal(G, v, m).\n\nLet m and n be two integers with m ≥ 2 and n ≥ 3. Let G be a connected graph of order n and v be a terminal vertex of G, then mdl (Amal(G, v, m)) ≤ m.mdl(G)\n\nLet\n\nWe show that mdl (Amal(G, v, m)) ≤ m.mdl(G). Let W be the local m-resolving set of G. Amal(G, v, m) has m copies of G, such that S=∪j=1j=mWj. We take identified vertex v ∉ W, thus two adjacent vertices uk,r, uk,s ∈ V (G) have different representation. There are two conditions for uk,r, uk,s ∈ V (G) to terminal vertex.\n\n1. For uk,r, uk,s ∈ V (G) and d (uk,r, v) = d (uk,s, v), then d (uk,r, w) = d (uk,s, w) for w ∈ S − Wk. Thus, rm (uk,r\|S)≠rm (uk,s\|S).\n\n2. For uk,r, uk,s ∈ V (G) and d (uk,r, v)≠d (uk,s, v), then d (uk,r, w)≠d (uk,s, w) for w ∈ S − Wk. Thus, rm (uk,r\|S)≠rm (uk,s\|S).\n\nBased on 1 and 2 that S=∪j=1j=mWj is the local m-resolving set of Amal(G, v, m). Thus, mdl (Amal(G, v, m)) ≤ m.mdl(G). □\n\nIf Amal (Pn, v, m) is an amalgamation of m paths, then mdl (Amal(Pn, v, m)) = 1\n\nLet\n\nSince Pn is bipartite graph, then Amal (Pn, v, m) is bipartite graph. Based on Theorem 0.1 that mdl (Amal(Pn, v, m)) = 1. □\n\nIf Amal (Kn, v, m) is an amalgamation of m complete graphs, then mdlAmalKnvm=∞\n\nLet\n\nFor two adjacent vertices x, y ∈ V ((Kn)k) with k ∈ [1, m] such that we have d(x, u) = d(y, u). Since d(x, u) = d(y, u), then d(x, w) = d(y, w) with w ∈ V (Amal (Kn, v, m)). Thus, rm(x\|W)≠rm(y\|W). □\n\nConsider graph Amal (Wn, v, m) where v is a center vertex of Wn. Let V (Amal (Wn, v, m)) = {v} ∪ {uj, i;1 ≤ j ≤ m and 1 ≤ i ≤ n} such that EAmalWnvm=∪j=1j=mE(Wnj).\n\nLet m and n be two integers with m ≥ 2 and n ≥ 3. Let Wn be a wheel graph of order n + 1 and v ∈ V (Wn) where v is a center vertex of Wn, then mdl (Amal (Wn, v, m)) = m.mdl (Wn).\n\nLet W be a local m-resolvings of Wn and S be a local m-resolving set of Amal (Wn, v, m) Based on Lemma 0.2 that mdl (Amal(Wn, v, m)) ≤ m.mdl (Wn). Furthermore, we will show that mdl (Amal(Wn, v, m)) ≥ m.mdl (Wn). Take any S ⊂ V (Amal (Wn, v, m)) with \|P\|<\|S\|. Suppose \|P\|=\|S\| − 1 = m.\|W\| − 1. There is one copy of Wn, (Wn)k have \|Wk\|− 1, such that we have three condition as follows\n\ni For n ≡ 0(mod4)\n\nLet u(k, l) ∉ P for 1 ≤ l ≤ n or i ≡ 4s − 3 with 1≤s≤n4 and d (uk, 4(s−1)−3, u4(s+1)−3) > 4, then rmuk,4s−1−1Wk=…=rmu4s+1−5Wk=2,2,2,…,2⏟n−44. Since duk,4s−1−1w=…=duk,4s+1−5w for w ∈ P − Wk and rmuk,4s−1−1P=…=rmuk,4s+1−5P, then P is not local m-resolving set of Amal(Wn, v, m).\n\nii For n ≡ 2(mod4)\n\nThere are three possibilities namely 1) uk,1 ∉ P; 2) uk,l ∉ P for 1 < l < n − 1 and 3) uk,n−1 ∈ P.\n\n(a) Let uk,1 ∉ P, then rmuk,1Wk=…=rmuk,3Wk=2,2,2,…,2⏟n4−1. Since duk,1w=…=duk,3w for w ∈ P − Wk and rmuk,1P=…=rmuk,3P, then P is not local m-resolving set of Amal (Wn, v, m).\n\n(b) Let uk,l ∉ P for 1 < l < n − 1 or i ≡ 4s − 3 with 2≤k≤n4−1 and d (uk, 4(s−1)−3, uk, 4(s+1)−3) > 4, then rmuk,4s−1−1Wk=…=rmuk,4s+1−5Wk=2,2,2,…,2⏟n4−1. Since duk,4s−1−1w=…=duk,4s+1−5w for w ∈ P − Wk and rmuk,4s−1−1P=…=rmuk,4s+1−5P, then P is not local m-resolving set of Amal (Wn, v, m).\n\n(c) Let uk,n−1 ∉ P. Since rmuk,n−3Wk=…=rmuk,n−1Wk=2,2,2,…,2⏟n4−1. Since duk,n−3w=…=duk,n−1w for w ∈ P − Wk and rmuk,n−3P=…=rmuk,n−1P, then P is not local m-resolving set of Amal (Wn, v, m).\n\niii For n ≡ 1, 3(mod4)\n\nWe know that mdlWn=∞, so there are two adjacent vertices x, y ∈ V (Wn), rm(x\|Wk) = rm(y\|Wk). Since d(x, v) = d(y, v) and d(x, w) = d(x, w) where w ∈ P − Wk, then rm(x\|P) = rm(y\|P). Thus, mdlAmalWnvm=∞.\n\nBased on i), ii), and iii) that mdl (Amal (Wn, v, m)) = m.mdl (Wn). □\n\nFor further discussion, consider graph Amal (Wn, v, m) where v is not a center vertex of Wn. Let V (Amal (Wn, v, m)) = {v} ∪ {uj;1 ≤ j ≤ m} ∪ {uj, i;1 ≤ j ≤ m and 1 ≤ i ≤ n − 1} such that E (Amal(Wn, v, m)) = {vuj, vuj,1, vuj,n−1}∪{uj, iuj, i+1;1 ≤ i ≤ n−2}∪{ujuj, i;1 ≤ j ≤ m, 1 ≤ i ≤ n−1}.\n\nLet m and n be two integers with m ≥ 2 and n ≥ 3. Let Wn be a wheel graph of order n + 1 and v ∈ V (Wn) where v is not center vertex of Wn, then\n\nWe consider four cases.\n\nFor n ≡ 0(mod 4)\n\nChoose S = {uj,i;1 ≤ j ≤ m, 1 ≤ i ≤ n − 1, i ≡ 0(mod4)} obtained the vertex representation as follows\n\n1. For uk, v ∈ V (Amal (Wn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n2. For uk, uk,l ∈ V ((Wn)k) and l≠0(mod4). Since uk adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1, n − 1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1, n − 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n3. For uk, i ∈ V ((Wn)k) and 1 ≤ i ≤ 3. Since d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk and d (uk,1, w)≠d (uk,2, w) where w ∈ Wk such that rm (uk,1\|S)≠rm (uk,2\|S). Since d (uk,2, w) = d (uk,3, w) where w ∈ S − Wk and d (uk,2, w)≠d (uk,3, w) where w ∈ Wk such that rm (uk,2\|S)≠rm (uk,3\|S).\n\n4. For uk, i ∈ V ((Wn)k) and n − 3 ≤ i ≤ n − 1. Since d (uk,n−1, w)≠d (uk,n−2, w) where w ∈ S − Wk and d (uk,n−1, w)≠d (uk,n−2, w) where w ∈ Wk such that rm (uk,n−1\|S)≠rm (uk,n−2\|S). Since d (uk,n−2, w) = d (uk,n−3, w) where w ∈ S − Wk and d (uk,n−2, w)≠d (uk,n−3, w) where w ∈ Wk such that rm (uk,n−2\|S)≠rm (uk,n−3\|S).\n\n5. For uk, i ∈ V ((Wn)k) where 4l + 1 ≤ i ≤ 4l + 3 and 1≤l≤n−84. Since d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ S − Wk and d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ Wk such that rm (uk,4l+1\|S)≠rm (uk,4l+2\|S). Since d (uk,4l+2, w) = d (uk,4l+3, w) where w ∈ S − Wk and d (uk,4l+2, w)≠d (uk,4l+3, w) where w ∈ Wk such that rm (uk,4l+2\|S)≠rm (uk, 4l+3\|S).\n\nBased on the representation above that every two adjacent vertices has distinct representations such that S is local m-resolving set and mdlAmalWnvm≤m.n4−1. Furthermore, proving that mmdlAmalWnvm≥m.n4−1. Taking any set P ⊂ V (Amal (Wn, v, m)) with \|P\|=m.n4−1−1. Let u(k, l) ∉ P for l ≡ 4s with 1≤s≤n−84 and d (uk, 4(s−1), uk,4(s+1)) > 4, then rmuk,4s−1+2Wk=…=rmu4s+1−2Wk=2,2,2,…,2⏟n−84. Since duk,4s−1+2w=…=duk,4s+1−2w for w ∈ P − Wk and rmuk,4s−1+2P=…=rmuk,4s+1−2P, then P is not local m-resolving set of Amal (Wn, v, m). Thus, mdlAmalWnvm=m.n4−1.\n\nFor n ≡ 1(mod 4)\n\nChoose S = {uj, i;1 ≤ j ≤ m, 1 ≤ i ≤ n − 1, i ≡ 0(mod4)} obtained the vertex representation as follows\n\n1. For uk, v ∈ V (Amal (Wn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n2. For uk, uk,l ∈ V ((Wn)k) and l≠0(mod4). Since uk adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1, n − 1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1, n − 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n3. For uk, i ∈ V ((Wn)k) and 1 ≤ i ≤ 3. Since d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk and d (uk,1, w)≠d (uk,2, w) where w ∈ Wk such that rm (uk,1\|S)≠rm (uk,2\|S). Since d (uk,2, w) = d (uk,3, w) where w ∈ S − Wk and d (uk,2, w)≠d (uk,3, w) where w ∈ Wk such that rm (uk,2\|S)≠rm (uk,3\|S).\n\n4. For uk, i ∈ V ((Wn)k) where 4l + 1 ≤ i ≤ 4l + 3 and 1≤l≤n−54. Since d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ S − Wk and d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ Wk such that rm (uk,4l+1\|S)≠rm (uk,4l+2\|S). Since d (uk,4l+2, w) = d (uk,4l+3, w) where w ∈ S − Wk and d (uk,4l+2, w)≠d (uk,4l+3, w) where w ∈ Wk such that rm (uk,4l+2\|S)≠rm (uk,4l+3\|S).\n\nBased on the representation above that every two adjacent vertices has distinct representation such that S is local m-resolving set and mdlAmalWnvm≤m.n−14. Furthermore, proving that mmdlAmalWnvm≥m.n−14. Taking any set P ⊂ V (Amal (Wn, v, m)) with \|P\|=m.n−14−1. Let u(k, l) ∉ P for l ≡ 4s with 1≤s≤n−54 and d (uk,4(s−1), uk,4(s+1)) > 4, then rmuk,4s−1+2Wk=…=rmu4s+1−2Wk=2,2,2,…,2⏟n−54. Since duk,4s−1+2w=…=duk,4s+1−2w for w ∈ P − Wk and rmuk,4s−1+2P=…=rmuk,4s+1−2P, then P is not local m-resolving set of Amal (Wn, v, m). Thus, mdlAmalWnvm=m.n−14\n\nFor n ≡ 2(mod 4)\n\nChoose S = {uj, i;1 ≤ j ≤ m, 1 ≤ i ≤ n − 1, i ≡ 0(mod4)} obtained the vertex representation as follows\n\n1. For uk, v ∈ V (Amal (Wn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n2. For uk, uk,l ∈ V ((Wn)k) and l≠0(mod4). Since uk adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1, n − 1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1, n − 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n3. For uk,i ∈ V ((Wn)k) and 1 ≤ i ≤ 3. Since d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk and d (uk,1, w)≠d (uk,2, w) where w ∈ Wk such that rm (uk,1\|S)≠rm (uk,2\|S). Since d (uk,2, w) = d (uk,3, w) where w ∈ S − Wk and d (uk,2, w)≠d (uk,3, w) where w ∈ Wk such that rm (uk,2\|S)≠rm (uk,3\|S).\n\n4. For uk, i ∈ V ((Wn)k) where 4l + 1 ≤ i ≤ 4l + 3 and 1≤l≤n−64. Since d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ S − Wk and d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ Wk such that rm (uk,4l+1\|S)≠rm (uk,4l+2\|S). Since d (uk,4l+2, w) = d (uk,4l+3, w) where w ∈ S − Wk and d (uk,4l+2, w)≠d (uk,4l+3, w) where w ∈ Wk such that rm (uk,4l+2\|S)≠rm (uk,4l+3\|S).\n\nBased on the representation above that every two adjacent vertices has distinct representation such that S is local m-resolving set and mdlAmalWnvm≤m.n−24. Furthermore, proving that mmdlAmalWnvm≥m.n−24. Taking any set P ⊂ V (Amal (Wn, v, m)) with \|P\|=m.n−24−1. Let u(k, l) ∉ P for l ≡ 4s with 1≤s≤n−64 and d (uk,4(s−1), uk,4(s+1)) > 4, then rmuk,4s−1+2Wk=…=rmu4s+1−2Wk=2,2,2,…,2⏟n−64. Since duk,4s−1+2w=…=duk,4s+1−2w for w ∈ P − Wk and rmuk,4s−1+2P=…=rmuk,4s+1−2P, then P is not local m-resolving set of Amal (Wn, v, m). Thus, mdlAmalWnvm=m.n−24\n\nFor n ≡ 3(mod 4)\n\nChoose S = {uj, i;1 ≤ j ≤ m, 1 ≤ i ≤ n − 1, i ≡ 0(mod4)} obtained the vertex representation as follows\n\n1. For uk, v ∈ V (Amal (Wn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n2. For uk, uk,l ∈ V ((Wn)k) and l≠0(mod4). Since uk adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1, n − 1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1, n − 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n3. For uk, i ∈ V ((Wn)k) and 1 ≤ i ≤ 3. Since d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk and d (uk,1, w)≠d (uk,2, w) where w ∈ Wk such that rm (uk,1\|S)≠rm (uk,2\|S). Since d (uk,2, w) = d (uk,3, w) where w ∈ S − Wk and d (uk,2, w)≠d (uk,3, w) where w ∈ Wk such that rm (uk,2\|S)≠rm (uk,3\|S).\n\n4. For uk, i ∈ V ((Wn)k) and n − 2 ≤ i ≤ n − 1. Since d (uk,n−1, w)≠d (uk,n−2, w) where w ∈ S − Wk and d (uk,n−1, w)≠d (uk,n−2, w) where w ∈ Wk such that rm (uk,n−1\|S)≠rm (uk,n−2\|S).\n\n5. For uk, i ∈ V ((Wn)k) where 4l + 1 ≤ i ≤ 4l + 3 and 1≤l≤n−74. Since d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ S − Wk and d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ Wk such that rm (uk,4l+1\|S)≠rm (uk,4l+2\|S). Since d (uk,4l+2, w) = d (uk,4l+3, w) where w ∈ S − Wk and d (uk,4l+2, w)≠d (uk,4l+3, w) where w ∈ Wk such that rm (uk,4l+2\|S)≠rm (uk,4l+3\|S).\n\nBased on the representation above that every two adjacent vertices has distinct representations such that S is local m-resolving set and mdlAmalWnvm≤m.n−34. Furthermore, proving that mmdlAmalWnvm≥m.n−34. Taking any set P ⊂ V (Amal (Wn, v, m)) with \|P\|=m.n−34−1. Let u(k, l) ∉ P for l ≡ 4s with 1≤s≤n−74 and d (uk, 4(s−1), uk, 4(s+1)) > 4, then rmuk,4s−1+2Wk=…=rmu4s+1−2Wk=2,2,2,…,2⏟n−74. Since duk,4s−1+2w=…=duk,4s+1−2w for w ∈ P − Wk and rmuk,4s−1+2P=…=rmuk,4s+1−2P, then P is not local m-resolving set of Amal (Wn, v, m). Thus, mdlAmalWnvm=m.n−34. □\n\nConsider graph Amal (Fn, v, m) where v is a center vertex of Fn. Let V (Amal (Fn, v, m)) = {v} ∪ {uj, i;1 ≤ j ≤ mand1 ≤ i ≤ n} such that EAmalFnvm=∪j=1j=mEFnj.\n\nLet m and n be two integers with m ≥ 2 and n ≥ 6. Let Fn be a fan graph of order n + 1 and v ∈ V (Fn) where v is a center vertex of Fn, then mdl (Amal (Fn, v, m)) = m.mdl (Fn)\n\nLet W be a local m-resolvings of Fn and S be a local m-resolving set of Amal (Fn, v, m) Based on Lemma 0.2 that mdl (Amal(Fn, v, m)) ≤ m.mdl (Fn). Furthermore, we will show that mdl (Amal(Fn, v, m)) ≥ m.mdl (Fn). Take any S ⊂ V (Amal (Fn, v, m)) with \|P\|<\|S\|. Suppose \|P\|=\|S\| − 1 = m.\|W\| − 1. There are one copies of Fn, (Fn)k have \|Wk\|− 1, such that we have three condition as follows\n\ni For n ≡ 1(mod4)\n\nThere are three possibilities namely 1) uk,3 ∉ P; 2) uk,l ∉ P for 3 < l < n − 2 and 3) uk,n−2 ∈ P.\n\n(a) Let uk,3 ∉ P. Since uk,1uk,2 ∈ E((Fn)k), then rmuk,1Wk=rmuk,2Wk=2,2,2,…,2⏟n−54. Since d (uk,1, w) = d (uk,2, w) for w ∈ P − Wk and rm (uk,1\|P) = rm (uk,2\|P), then P is not local m-resolving set of Amal (Fn, v, m).\n\n(b) Let uk,l ∉ P for 3 < l < n − 2 or i ≡ 4s − 1 with 2≤s≤n−54 and d (uk, 4(s−1)−1, uk, 4(s+1)−1) > 4, then rmuk,4s−1+1Wk=…=rmuk,4s+1−3Wk=2,2,2,…,2⏟n−54. Since duk,4s−1+1w=…=duk,4s+1−3w for w ∈ P − Wk and rmuk,4s−1+1P=…=rmuk,4s+1−3P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n(c) Let uk,n−2 ∉ P. Since uk,n−1uk, n ∈ E((Fn)k), then rmuk,n−4Wk=…=rmuk,nWk=2,2,2,…,2⏟n−54. Since duk,n−4w=…=duk,nw for w ∈ P − Wk and rmuk,n−4P=…=rmuk,nP, then P is not local m-resolving set of Amal (Fn, v, m).\n\nii For n ≡ 0, 2, 3(mod4)\n\nThere are three possibilities namely 1) uk,1 ∉ P; 2) uk,l ∉ P for 1 < l < n − 1 and 3) uk,n−1 ∈ P for n ≡ 0(mod4), uk,n−1 ∈ P for n ≡ 2(mod4), and uk,n ∈ P for n ≡ 3(mod4).\n\n(a) Let uk,3 ∉ P. Since rmuk,1Wk=…=rmuk,5Wk=2,2,2,…,2⏟n4−1. Since duk,1w=…=duk,5w for w ∈ P − Wk and rmuk,1P=…=rmuk,5P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n(b) Let uk,l ∉ P for 3 < l < n − 2 or i ≡ 4s − 1 with 2≤s≤n4 and d (uk,4(s−1)−1, uk, 4(s+1)−1) > 4, then rmuk,4s−1+1Wk=…=rmuk,4s+1−3Wk=2,2,2,…,2⏟n4−1. Since duk,4s−1+1w=…=duk,4s+1−3w for w ∈ P − Wk and rmuk,4s−1+1P=…=rmuk,4s+1−3P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n(c) Let uk,n−1 ∉ P for n ≡ 0(mod4). Since rmuk,n−3Wk=…=rmuk,nWk=2,2,2,…,2⏟n4−1. Since duk,n−3w=…=duk,nw for w ∈ P − Wk and rmuk,n−3P=…=rmuk,nP, then P is not local m-resolving set of Amal (Fn, v, m).\n\n(d) Let uk,n−1 ∉ P for n ≡ 2(mod4). Since rmuk,n−1Wk=rmuk,nWk=2,2,2,…,2⏟n4−1. Since d (uk,n−1, w) = d (uk,n, w) for w ∈ P − Wk and rm (uk,n−1\|P) = rm (uk,n\|P), then P is not local m-resolving set of Amal (Fn, v, m).\n\n(e) Let uk,n ∉ P for n ≡ 3(mod4). Since rmuk,n−2Wk=…=rmuk,nWk=2,2,2,…,2⏟n4−1. Since duk,n−2w=…=duk,nw for w ∈ P − Wk and rmuk,n−2P=…=rmuk,nP, then P is not local m-resolving set of Amal (Fn, v, m).\n\nBased on i) and ii) that mdl (Amal (Fn, v, m)) = m.mdl (Fn). □\n\nFor further discussion, consider graph Amal (Fn, v, m) where v ∈ V (Fn) with d(v) = 2. Let V (Amal (Fn, v, m)) = {v} ∪ {uj;1 ≤ j ≤ m} ∪ {uj, i;1 ≤ j ≤ mand1 ≤ i ≤ n − 1} such that E (Amal(Fn, v, m)) = {vuj, vuj,1}∪{uj, iuj, i+1;1 ≤ i ≤ n−2}∪{ujuj, i;1 ≤ j ≤ m, 1 ≤ i ≤ n−1}.\n\nLet m and n be two integers with m ≥ 2 and n ≥ 3. Let Fn be a fan graph of order n + 1 and v ∈ V (Fn) where d(v) = 2, then mdlAmalFnvm=m.n4\n\nWe have some condition for the set S as follows\n\na for n ≡ 1, 2, 3(mod4), S = {uj, i;1 ≤ j ≤ m, 1 ≤ i ≤ n − 1, i ≡ 0(mod4)}.\n\nb for n ≡ 0(mod4), S = {uj, i;1 ≤ j ≤ m, 1 ≤ i ≤ n − 1, i ≡ 0(mod4)} ∪ {uj,n−2}.\n\nWe obtained the vertex representation as follows\n\n1. For uk, v ∈ V (Amal (Fn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n2. For uk, uk,l ∈ V ((Fn)k) where l≠0(mod4) and uk,l where l≠n − 2 for n ≡ 0(mod4). Since uk is adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n3. For uk, i ∈ V ((Fn)k) and 1 ≤ i ≤ 3. Since d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk and d (uk,1, w)≠d (uk,2, w) where w ∈ Wk such that rm (uk,1\|S)≠rm (uk,2\|S). Since d (uk,2, w) = d (uk,3, w) where w ∈ S − Wk and d (uk,2, w)≠d (uk,3, w) where w ∈ Wk such that rm (uk,2\|S)≠rm (uk,3\|S).\n\n4. For uk, i ∈ V ((Fn)k) where 4l + 1 ≤ i ≤ 4l + 3 and 1≤l≤n4−1. Since d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ S − Wk and d (uk,4l+1, w)≠d (uk,4l+2, w) where w ∈ Wk such that rm (uk,4l+1\|S)≠rm (uk,4l+2\|S). Since d (uk,4l+2, w) = d (uk,4l+3, w) where w ∈ S − Wk and d (uk,4l+2, w)≠d (uk,4l+3, w) where w ∈ Wk such that rm (uk,4l+2\|S)≠rm (uk,4l+3\|S).\n\n5. For uk, i ∈ V ((Fn)k) where n − 2 ≤ i ≤ n − 1 and n ≡ 3(mod4). Since d (uk,n−1, w) = d (uk,n−2, w) where w ∈ S − Wk and d (uk,n−1, w)≠d (uk,n−2, w) where w ∈ Wk such that rm (uk,n−1\|S)≠rm (uk,n−2\|S).\n\nBased on the representation above that every two adjacent vertices has distinct representations such that S is local m-resolving set and mdlAmalWnvm≤m.n4−1.\n\nFurthermore, we will show that mdlAmalFnvm≥m.n4. Take any S ⊂ V (Amal (Fn, v, m)) with\|P\|<\|S\|. Suppose \|P\|=\|S\|−1=m.n4−1. There are one copies of Fn, (Fn)k have n4−1, such that we have three condition as follows\n\ni For n ≡ 1(mod4)\n\nThere are three possibilities namely 1) uk,l ∉ P for 1 < l < n − 1 and 2) uk,n−1 ∉ P.\n\n(a) Let uk,l ∉ P for 1 < l ≤ n − 1 or l ≡ 4s with 1≤s≤n−54 and d (uk, 4(s−1)+1, uk, 4(s+1)−1) > 4, then rmuk,4s−1+2Wk=…=rmuk,4s+1−2Wk=2,2,2,…,2⏟n−54. Since duk,4s−1+2w=…=duk,4s+1−2w for w ∈ P − Wk and rmuk,4s−1+2P=…=rmuk,4s+1−2P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n(b) Let uk,n−1 ∉ P. Since rmuk,n−3Wk=…=rmuk,n−1Wk=2,2,2,…,2⏟n−54. Since duk,n−3w=…=duk,n−1w for w ∈ P − Wk and rmuk,n−3P=…=rmuk,n−1P, then P is not local m-resolving set of Amal (Fn, v, m).\n\nii For n ≡ 0, 2, 3(mod4)\n\nThere are three possibilities namely 1) uk,l ∉ P for 1 < l < n − 1 and 2) uk,n−1 ∈ P for n ≡ 0(mod4), uk,n−2 ∈ P for n ≡ 2(mod4), and uk,n−3 ∈ P for n ≡ 3(mod4).\n\n(a) Let uk,l ∉ P for 1 < l < n − 1 or l ≡ 4s with 1≤s≤n4−1 and d (uk, 4(s−1)+1, uk, 4(s+1)−1) > 4, then rmuk,4s−1+2Wk=…=rmuk,4s+1−2Wk=2,2,2,…,2⏟n4−1. Since duk,4s−1+2w=…=duk,4s+1−2w for w ∈ P − Wk and rmuk,4s−1+2P=…=rmuk,4s+1−2P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n(b) Let uk,n−1 ∉ P for n ≡ 0(mod4). Since rmuk,n−2Wk=rmuk,n−1Wk=2,2,2,…,2⏟n4−1. Since d (uk,n−2, w) = d (uk,n−1, w) for w ∈ P − Wk and rm (uk,n−2\|P) = rm (uk,n−1\|P), then P is not local m-resolving set of Amal (Fn, v, m).\n\n(c) Let uk,n−2 ∉ P for n ≡ 2(mod4). Since rmuk,n−4Wk=…=rmuk,n−1Wk=2,2,2,…,2⏟n4−1. Since duk,n−4w=…=duk,n−1w for w ∈ P − Wk and rmuk,n−4P=…=rmuk,n−1P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n(d) Let uk,n−3 ∉ P for n ≡ 3(mod4). Since rmuk,n−5Wk=…=rmuk,n−1Wk=2,2,2,…,2⏟n4−1. Since duk,n−5w=…=duk,n−1w for w ∈ P − Wk and rmuk,n−5P=…=rmuk,n−1P, then P is not local m-resolving set of Amal (Fn, v, m).\n\nBased on i) and ii) that mdlAmalFnvm=m.n4. □\n\nLet m and n be two integers with m ≥ 2 and n ≥ 3. Let Fn be a fan graph of order n + 1 and v ∈ V (Fn) where d(v) = 3, then\n\nSince Identified vertex v = uj, p, then we have two part namely uj,1 − uj, p−1 and uj, p+1 − uj, n. We consider two cases as follows\n\nFor 2 ≤ p ≤ 3\n\nFor d (uj,1, uj, p−1) ≤ 2, then the vertices uj,1,…,uj,p−1 don’t need to be resolver. Thus, we focus for d (uj, p+1, uj, n) ≥ 3\n\nFor n − p ≡ 0, 1, 2(mod4)\n\nChoose S = {uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p} obtained the vertex representation as follows\n\n1. For uk,l ∈ V (Amal (Fn, v, m)) and 1 ≤ l ≤ p − 1, d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk such that rm (uk,1\|S − Wk)≠rm (uk,2\|S − Wk). Since d (uk,1, w) = d (uk,2, w) where w ∈ Wk such that rm (uk,1\|Wk)≠rm (uk,2\|Wk). Thus, rm (uk,1\|S)≠rm (uk,2\|S).\n\n2. For uk, v ∈ V (Amal (Fn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n3. For uk, uk,l ∈ V ((Fn)k) where l≠p (mod4) and uk,l where l≠n − 2 for n − p ≡ 2(mod4). Since uk adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n4. For uk, i ∈ V ((Fn)k) and p + 1 ≤ i ≤ p + 3. Since d (uk, p+1, w)≠d (uk, p+2, w) where w ∈ S − Wk and d (uk, p+1, w)≠d (uk, p+2, w) where w ∈ Wk such that rm (uk, p+1\|S)≠rm (uk, p+2\|S). Since d (uk, p+2, w) = d (uk, p+3, w) where w ∈ S − Wk and d (uk, p+2, w)≠d (uk, p+3, w) where w ∈ Wk such that rm (uk, p+2\|S)≠rm (uk, p+3\|S).\n\n5. For uk, i ∈ V ((Fn)k) where p + 4l + 1 ≤ i ≤ p + 4l + 3 and 1≤l≤n4−1. Since d (uk, p+4l+1, w)≠d (uk, p+4l+2, w) where w ∈ S − Wk and d (uk, p+4l+1, w)≠d (uk, p+4l+2, w) where w ∈ Wk such that rm (uk, p+4l+1\|S)≠rm (uk, p+4l+2\|S). Since d (uk, p+4l+2, w) = d (uk, p+4l+3, w) where w ∈ S − Wk and d (uk, p+4l+2, w)≠d (uk, p+4l+3, w) where w ∈ Wk such that rm (uk, p+4l+2\|S)≠rm (uk, p+4l+3\|S).\n\nBased on the representation above that every two adjacent vertices have distinct representations such that S is local m-resolving set and mdlAmalFnvm≤m.p4+n−p4.\n\nFurthermore, we will show that mdlAmalFnvm≥m.p4+n−p4. Take any S ⊂ V (Amal (Fn, v, m)) with \|P\|<\|S\|. Suppose \|P\|=\|S\|−1=m.p4+n−p4−1. There is one copy of Fn, (Fn)k have m.p4+n−p4−1. Let uk,l ∉ P for p + 1 < l ≤ n − 1 or l ≡ p + 4s with 1≤s≤n−p4 and d (uk, p+4(s−1)+1, uk, p+4(s+1)−1) > 4, then rmuk,p+4s−1+2Wk=…=rmuk,p+4s+1−2Wk=2,2,2,…,2⏟n−p4−1. Since duk,p+4s−1+2w=…=duk,p+4s+1−2w for w ∈ P − Wk and rmuk,p+4s−1+2P=…=rmuk,p+4s+1−2P, then P is not local m-resolving set of Amal (Fn, v, m). Thus, mdlAmalFnvm=m.p4+n−p4.\n\nFor n − p ≡ 3(mod4)\n\nChoose S = {uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p} ∪ {uj,n−1} obtained the vertex representation as follows\n\n1. For uk,l ∈ V (Amal (Fn, v, m)) and 1 ≤ l ≤ p − 1, d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk such that rm (uk,1\|S − Wk)≠rm (uk,2\|S − Wk). Since d (uk,1, w) = d (uk,2, w) where w ∈ Wk such that rm (uk,1\|Wk)≠rm (uk,2\|Wk). Thus, rm (uk,1\|S)≠rm (uk,2\|S).\n\n2. For uk, v ∈ V (Amal (Fn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n3. For uk, uk,l ∈ V ((Fn)k) where l≠p (mod4) and uk,l where l≠n − 2 for n − p ≡ 3(mod4). Since uk adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n4. For uk, i ∈ V ((Fn)k) and p + 1 ≤ i ≤ p + 3. Since d (uk, p+1, w)≠d (uk, p+2, w) where w ∈ S − Wk and d (uk, p+1, w)≠d (uk, p+2, w) where w ∈ Wk such that rm (uk, p+1\|S)≠rm (uk, p+2\|S). Since d (uk, p+2, w) = d (uk, p+3, w) where w ∈ S − Wk and d (uk, p+2, w)≠d (uk, p+3, w) where w ∈ Wk such that rm (uk, p+2\|S)≠rm (uk, p+3\|S).\n\n5. For uk, i ∈ V ((Fn)k) where p + 4l + 1 ≤ i ≤ p + 4l + 3 and 1≤l≤n4−1. Since d (uk, p+4l+1, w)≠d (uk, p+4l+2, w) where w ∈ S − Wk and d (uk, p+4l+1, w)≠d (uk, p+4l+2, w) where w ∈ Wk such that rm (uk, p+4l+1\|S)≠rm (uk, p+4l+2\|S). Since d (uk, p+4l+2, w) = d (uk, p+4l+3, w) where w ∈ S − Wk and d (uk, p+4l+2, w)≠d (uk, p+4l+3, w) where w ∈ Wk such that rm (uk, p+4l+2\|S)≠rm (uk, p+4l+3\|S).\n\n6. For uk, i ∈ V ((Fn)k) where i = n − 2, n. Since uk,n−2 is not adjacent to uk, n. It is clear.\n\nBased on the representation above that every two adjacent vertices has distinct representations such that S is local m-resolving set and mdlAmalFnvm≤m.p4+n−p4.\n\nFurthermore, we will show that mdlAmalFnvm≥m.p4+n−p4. Take any S ⊂ V (Amal (Fn, v, m)) with\|P\|<\|S\|. Suppose \|P\|=\|S\|−1=m.p4+n−p4−1. There are one copies of Fn, (Fn)k have m.p4+n−p4−1. There are three possibilities namely 1) uk,l ∉ P for 1 < l < n − 1 and 2) uk,n−1 ∉ P.\n\n1. Let uk,l ∉ P for 1 < l ≤ n − 1 or l ≡ p + 4s with 1≤s≤n−p4 and d (uk, p+4(s−1)+1, uk, p+4(s+1)−1) > 4, then rmuk,p+4s−1+2Wk=…=rmuk,p+4s+1−2Wk=2,2,2,…,2⏟n−p4. Since duk,p+4s−1+2w=…=duk,p+4s+1−2w for w ∈ P − Wk and rmuk,p+4s−1+2P=…=rmuk,p+4s+1−2P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n2. Let uk,n−1 ∉ P. Since rmuk,n−1Wk=rmuk,nWk=2,2,2,…,2⏟n−p4. Since d (uk,n−1, w) = d (uk, n, w) for w ∈ P − Wk and rm (uk,n−1\|P) = rm (uk, n\|P), then P is not local m-resolving set of Amal (Fn, v, m).\n\nBased on 1) and 2) that mdlAmalFnvm≥m.p4+n−p4. Thus, mdlAmalFnvm=m.p4+n−p4.\n\nFor 4≤p≤n4\n\nFor n − p ≡ 0, 1, 2(mod4)\n\nWe have some conditions for the set S as follows:\n\na for p ≡ 1(mod4), S = {uj, t;1 ≤ j ≤ m, t ≡ 1(mod4)} ∪ {uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p}.\n\nb for p ≡ 2(mod4), S = {uj, t;1 ≤ j ≤ m, t ≡ 2(mod4)} ∪ {uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p}.\n\nc for p ≡ 3(mod4), S = {uj, t;1 ≤ j ≤ m, t ≡ 3(mod4)} ∪ {uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p}.\n\nd for p ≡ 0(mod4), S = {uj, t;1 ≤ j ≤ m, t ≡ 0(mod4)} ∪ {uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p}.\n\nWe obtained the vertex representation as follows:\n\n1. For uk, i ∈ V ((Fn)k) where p − 3 ≤ i ≤ p − 1 and p ≡ 0, 1, 2, 3(mod4). Since d (uk, p−1, w)≠d (uk, p−2, w) where w ∈ S − Wk and d (uk, p−1, w)≠d (uk, p−2, w) where w ∈ Wk such that rm (uk, p−1\|S)≠rm (uk, p−2\|S). Since d (uk, p−2, w) = d (uk, p−3, w) where w ∈ S − Wk and d (uk, p−2, w)≠d (uk, p−3, w) where w ∈ Wk such that rm (uk, p−2\|S)≠rm (uk, p−3\|S).\n\n2. For uk, i ∈ V ((Fn)k) where p − 4l + 1 ≤ i ≤ p − 4l + 3, 2≤l≤n4−1, and ap ≡ 0, 1, 2, 3(mod4). Since d (uk, p−4l+1, w)≠d (uk, p−4l+2, w) where w ∈ S − Wk and d (uk, p−4l+1, w)≠d (uk, p−4l+2, w) where w ∈ Wk such that rm (uk, p−4l+1\|S)≠rm (uk, p−4l+2\|S). Since d (uk, p−4l+2, w) = d (uk, p−4l+3, w) where w ∈ S − Wk and d (uk, p−4l+2, w)≠d (uk, p−4l+3, w) where w ∈ Wk such that rm (uk, p−4l+2\|S)≠rm (uk, p−4l+3\|S).\n\n3. For uk,l ∈ V (Amal (Fn, v, m)) and 1 ≤ l ≤ p − 1, d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk such that rm (uk,1\|S − Wk)≠rm (uk,2\|S − Wk). Since d (uk,1, w) = d (uk,2, w) where w ∈ Wk such that rm (uk,1\|Wk)≠rm (uk,2\|Wk). Thus, rm (uk,1\|S)≠rm (uk,2\|S).\n\n4. For uk, v ∈ V (Amal (Fn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n5. For uk, uk,l ∈ V ((Fn)k) where l≠p (mod4) and uk,l where l≠n − 2 for n − p ≡ 2(mod4). Since uk adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n6. For uk, i ∈ V ((Fn)k) and p + 1 ≤ i ≤ p + 3. Since d (uk, p+1, w)≠d (uk, p+2, w) where w ∈ S − Wk and d (uk, p+1, w)≠d (uk, p+2, w) where w ∈ Wk such that rm (uk, p+1\|S)≠rm (uk, p+2\|S). Since d (uk, p+2, w) = d (uk, p+3, w) where w ∈ S − Wk and d (uk, p+2, w)≠d (uk, p+3, w) where w ∈ Wk such that rm (uk, p+2\|S)≠rm (uk, p+3\|S).\n\n7. For uk, i ∈ V ((Fn)k) where p + 4l + 1 ≤ i ≤ p + 4l + 3 and 1≤l≤n4−1. Since d (uk, p+4l+1, w)≠d (uk, p+4l+2, w) where w ∈ S − Wk and d (uk, p+4l+1, w)≠d (uk, p+4l+2, w) where w ∈ Wk such that rm (uk, p+4l+1\|S)≠rm (uk, p+4l+2\|S). Since d (uk, p+4l+2, w) = d (uk, p+4l+3, w) where w ∈ S − Wk and d (uk, p+4l+2, w)≠d (uk, p+4l+3, w) where w ∈ Wk such that rm (uk, p+4l+2\|S)≠rm (uk, p+4l+3\|S).\n\nBased on the representation above that every two adjacent vertices has distinct representations such that S is a local m-resolving set and mdlAmalFnvm≤m.p4+n−p4.\n\nFurthermore, we will show that mdlAmalFnvm≥m.p4+n−p4. Take any S ⊂ V (Amal (Fn, v, m)) with\|P\|<\|S\|. Suppose \|P\|=\|S\|−1=m.p4+n−p4−1. There are one copies of Fn, (Fn)k have m.p4+n−p4−1.\n\n1. Let uk,l ∉ P for p + 1 < l ≤ n − 1 or l ≡ p + 4s with 1≤s≤n−p4 and d (uk, p+4(s−1)+1, uk, p+4(s+1)−1) > 4, then rmuk,p+4s−1+2Wk=…=rmuk,p+4s+1−2Wk=2,2,2,…,2⏟n−p4−1. Since duk,p+4s−1+2w=…=duk,p+4s+1−2w for w ∈ P − Wk and rmuk,p+4s−1+2P=…=rmuk,p+4s+1−2P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n2. Let uk,l ∉ P for 1 < l ≤ p − 1 or l ≡ 1(mod4) and p ≡ 1(mod4), then rmuk,p−4s−2Wk=…=rmuk,p−4s+2Wk=2,2,2,…,2⏟n−p4−1. Since duk,p−4s−2w=…=duk,p−4s+2w for w ∈ P − Wk and rmuk,p−4s−2P=…=rmuk,p−4s+2P, then P is not local m-resolving set of Amal (Fn, v, m).\n\nThus, mdlAmalFnvm=m.p4+n−p4.\n\nFor n − p ≡ 3(mod4)\n\nWe have some conditions for the set S as follows\n\na for p ≡ 1(mod4), S = {uj, t;1 ≤ j ≤ m, t ≡ 1(mod4)}∪{uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p}∪{uj,n−1}.\n\nb for p ≡ 2(mod4), S = {uj, t;1 ≤ j ≤ m, t ≡ 2(mod4)}∪{uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p}∪{uj,n−1}.\n\nc for p ≡ 3(mod4), S = {uj, t;1 ≤ j ≤ m, t ≡ 3(mod4)}∪{uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p}∪{uj,n−1}.\n\nd for p ≡ 0(mod4), S = {uj, t;1 ≤ j ≤ m, t ≡ 0(mod4)}∪{uj,r;1 ≤ j ≤ m, r ≡ p (mod4), r > p}∪{uj,n−1}.\n\nWe obtained the vertex representation as follows:\n\n1. For uk, i ∈ V ((Fn)k) where p − 3 ≤ i ≤ p − 1 and p ≡ 0, 1, 2, 3(mod4). Since d (uk, p−1, w)≠d (uk, p−2, w) where w ∈ S − Wk and d (uk, p−1, w)≠d (uk, p−2, w) where w ∈ Wk such that rm (uk, p−1\|S)≠rm (uk, p−2\|S). Since d (uk, p−2, w) = d (uk, p−3, w) where w ∈ S − Wk and d (uk, p−2, w)≠d (uk, p−3, w) where w ∈ Wk such that rm (uk, p−2\|S)≠rm (uk, p−3\|S).\n\n2. For uk, i ∈ V ((Fn)k) where p − 4l + 1 ≤ i ≤ p − 4l + 3, 2≤l≤n4−1, and ap ≡ 0, 1, 2, 3(mod4). Since d (uk,p−4l+1, w)≠d (uk, p−4l+2, w) where w ∈ S − Wk and d (uk, p−4l+1, w)≠d (uk, p−4l+2, w) where w ∈ Wk such that rm (uk, p−4l+1\|S)≠rm (uk, p−4l+2\|S). Since d (uk, p−4l+2, w) = d (uk, p−4l+3, w) where w ∈ S − Wk and d (uk, p−4l+2,w)≠d (uk, p−4l+3, w) where w ∈ Wk such that rm (uk, p−4l+2\|S)≠rm (uk, p−4l+3\|S).\n\n3. For uk,l ∈ V (Amal (Fn, v, m)) and 1 ≤ l ≤ p − 1, d (uk,1, w)≠d (uk,2, w) where w ∈ S − Wk such that rm (uk,1\|S − Wk)≠rm (uk,2\|S − Wk). Since d (uk,1, w) = d (uk,2, w) where w ∈ Wk such that rm (uk,1\|Wk)≠rm (uk,2\|Wk). Thus, rm (uk,1\|S)≠rm (uk,2\|S).\n\n4. For uk, v ∈ V (Amal (Fn, v, m)), d(v, w)≠d (uk, w) where w ∈ S − Wk such that rm(v\|S − Wk)≠rm (uk\|S − Wk). Since d(v, w)≠d (uk, w) where w ∈ Wk such that rm(v\|Wk)≠rm (uk\|Wk). Thus, rm(v\|S)≠rm (uk\|S).\n\n5. For uk, uk,l ∈ V ((Fn)k) where l≠p (mod4) and uk,l where l≠n − 2 for n − p ≡ 3(mod4). Since uk adjacent to w where w ∈ Wk, such that rm (uk\|Wk)≠rm (uk,l\|Wk). Since d (uk, w)≠d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk)≠rm (uk,l\|S − Wk) with l≠1. Since d (uk, w) = d (uk,l, w) where w ∈ S − Wk such that rm (uk\|S − Wk) = rm (uk,l\|S − Wk) with l = 1. Thus, rm(v\|S)≠rm (uk\|S).\n\n6. For uk, i ∈ V ((Fn)k) and p + 1 ≤ i ≤ p + 3. Since d (uk, p+1, w)≠d (uk, p+2, w) where w ∈ S − Wk and d (uk, p+1, w)≠d (uk, p+2, w) where w ∈ Wk such that rm (uk, p+1\|S)≠rm (uk, p+2\|S). Since d (uk, p+2, w) = d (uk, p+3, w) where w ∈ S − Wk and d (uk, p+2, w)≠d (uk, p+3, w) where w ∈ Wk such that rm (uk, p+2\|S)≠rm (uk, p+3\|S).\n\n7. For uk, i ∈ V ((Fn)k) where p + 4l + 1 ≤ i ≤ p + 4l + 3 and 1≤l≤n4−1. Since d (uk, p+4l+1, w)≠d (uk, p+4l+2, w) where w ∈ S − Wk and d (uk, p+4l+1, w)≠d (uk, p+4l+2, w) where w ∈ Wk such that rm (uk, p+4l+1\|S)≠rm (uk, p+4l+2\|S). Since d (uk, p+4l+2, w) = d (uk, p+4l+3, w) where w ∈ S − Wk and d (uk, p+4l+2, w)≠d (uk, p+4l+3, w) where w ∈ Wk such that rm (uk, p+4l+2\|S)≠rm (uk, p+4l+3\|S).\n\n8. For uk, i ∈ V ((Fn)k) where i = n − 2, n. Since uk,n−2 does not adjacent to uk, n. It is clear.\n\nBased on the representation above that every two adjacent vertices have distinct representations such that S is a local m-resolving set and mdlAmalFnvm≤m.p4+n−p4.\n\nFurthermore, we will show that mdlAmalFnvm≥m.p4+n−p4. Take any S ⊂ V (Amal (Fn, v, m)) with\|P\|<\|S\|. Suppose \|P\|=\|S\|−1=m.p4+n−p4−1. There are one copies of Fn, (Fn)k have m.p4+n−p4−1. There are three possibilities namely 1) uk,l ∉ P for 1 < l < n − 1 and 2) uk,n−1 ∉ P.\n\n1. Let uk,l ∉ P for 1 < l ≤ n − 1 or l ≡ p + 4s with 1≤s≤n−p4 and d (uk, p+4(s−1)+1, uk, p+4(s+1)−1) > 4, then rmuk,p+4s−1+2Wk=…=rmuk,p+4s+1−2Wk=2,2,2,…,2⏟n−p4. Since duk,p+4s−1+2w=…=duk,p+4s+1−2w for w ∈ P − Wk and rmuk,p+4s−1+2P=…=rmuk,p+4s+1−2P, then P is not local m-resolving set of Amal (Fn, v, m).\n\n2. Let uk,n−1 ∉ P. Since rmuk,n−1Wk=rmuk,nWk=2,2,2,…,2⏟n−p4. Since d (uk,n−1, w) = d (uk, n, w) for w ∈ P − Wk and rm (uk,n−1\|P) = rm (uk, n\|P), then P is not local m-resolving set of Amal (Fn, v, m).\n\n3. Let uk,l ∉ P for 1 < l ≤ p − 1 or l ≡ 1(mod4) and p ≡ 1(mod4), then rmuk,p−4s−2Wk=…=rmuk,p−4s+2Wk=2,2,2,…,2⏟n−p4−1. Since duk,p−4s−2w=…=duk,p−4s+2w for w ∈ P − Wk and rmuk,p−4s−2P=…=rmuk,p−4s+2P, then P is not local m-resolving set of Amal (Fn, v, m).\n\nBased on 1) and 2) that mdlAmalFnvm≥m.p4+n−p4. Thus, mdlAmalFnvm=m.p4+n−p4. □\n\n\nConclusion\n\nWe have characterized the local multiset dimension of amalgamation graphs. We have found the upper bound of local multiset dimension and determined the exact value of local multiset dimension of path Pn, complete graph Kn, wheel graph Wn, and fan graph Fn. There are some graphs that attain the upper bound of local multiset dimension namely wheel graphs. On the otherhand, we found the following problem, as follows.\n\nOpen Problem 0.1 Determine the lower bound of local multiset dimension of amalgamation graphs.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nWe gratefully acknowledge the support from Universitas Airlangga and University of Jember of year 2022.\n\n\nReferences\n\nKhuller S, Raghavachari B, Rosenfeld A: Localization in Graphs. University of Maryland at College Park;1994. Technical Report CS-Tr-3326.\n\nReza M, Javaid M, Saleem N: Fractional metric dimension of metal-organic frameworks. Main Group Met. Chem. 2021; 44(1): 92–102. Publisher Full Text\n\nSaputro SW, Mardiana N, Purwasih IA: The metric. dimension of comb product graph. Mat. Vesn. 2017; 4: 248–258.\n\nOkamoto F, Phinezy B, Zhang P: The Local Metric Dimension of A Graph. Math. Bohem. 2010; 135(3): 239–255. Publisher Full Text\n\nSimanjuntak R, Siagian P, Vetrik T: The multiset dimension of graphs. arXiv preprint arXiv:1711.00225.2017.\n\nAlfarisi R, Lin Y, Ryan J, et al.: The Local Multiset Dimension of Graphs. IJET. 2019; 8(3): 890–901. Publisher Full Text\n\nAlfarisi R, Lin Y, Ryan J, et al.: A Note on Multiset Dimension and Local Multiset Dimension of Graphs. Stat. Optim. Inf. Comput. 2019; 8: 890–901. Accepted. Publisher Full Text\n\nAdawiyah R, Agustin IH, Prihandini RM, et al.: On the local multiset dimension of m-shadow graph. J. Phys. Conf. Ser. 2019; 1211(1): 012006. Publisher Full Text\n\nAdawiyah R, Prihandini RM, Albirri ER, et al.: The local multiset dimension of unicyclic graph. IOP Conf. Series: EES. 2019; 243(1): 012075.\n\nIswadi H, Baskoro ET, Salman ANM, et al.: The resolving graph of amalgamation of cycles Util. Math. 2010; 83: 121–132.\n\nDiestel R: Graph Theory, Graduate Texts in Mathematics. Springer;2016. 978-3-642-14278-91.\n\nAlfarisi R, SusilowatiDafik L: The Local Multiset Resolving of Graphs.2022. In Review." }	[ { "id": "161413", "date": "26 Jan 2023", "name": "Ismail Naci Cangul", "expertise": [ "Reviewer Expertise Graph theory", "number theory", "discrete group theory", "Molecular graphs" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSet dimension in graph theory is a very applicable area which collected a lot of attention by many people. Here, the authors continued their research with local multiset dimension as a variant and studied this number for amalgamation graphs. Amalgamation is one of the graph operations and this study can easily be carried to other graph operations. I also wondered that this ideas can be applied to algebra as amalgamation plays an important role in algebraic structures.\n\nThis manuscript is written very clearly as a new step in continuing theory and it will add value to the area.\n\nThe abstract seems to be uncompiled as there are \"$\" signs all around. Also Theorems, Propositions, Lemmas must be written in bold to get the attention of the reader.\nVery nice work on multiset theory.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9272", "date": "10 Mar 2023", "name": "Liliek Susilowati", "role": "Author Response", "response": "Dear Prof Ismail, For the abstract as there are \"$\" signs all around. The symbol \"$\", only editors can fix or remove the \"$\" sign. I've reported to the editor to remove the \"$\" sign. Best Regards Dr. Liliek Susilowati and Dr. Ridho Alfarisi" } ] }, { "id": "161414", "date": "31 Oct 2023", "name": "Muhammad Kamran Siddique", "expertise": [ "Reviewer Expertise Graph theory. Discrete Mathematics", "Chemical graph Theory", "Combinatorics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nLocal Multiset Dimension of Amalgamation Graphs\nI found that all the mathematical work is correct. Moreover paper is clearly written in a good way. It is new, as well as good contribution in the current area of research.\nCorrections:\nThe definitions of m-resolving set and local m-resolving set conveys the same meaning. The condition xy=E(G), should be removed from the definition of m-resolving set.\n\nOn page no. 4, local multiset dimension is denoted by μl(G). But mdl(G) is used in definition and other results.\n\nIn the illustration of local m-resolving set, W={v1} is the considered local m-resolving set, but the vertex representations are given with respect to Π.\n\nIn figure 2, the terminal vertex v0 is not labelled in the graphs.\n\nIn the line above Lemma 0.2, it is mentioned that upper bound for Amal(G,v,m) is given.\n\nIn the proof of Lemma 0.2, the terminal vertex v is not included in the vertex set of Amal(G,v,m). Instead, a vertex u is mentioned. The same mistake can be seen in Theorem 0.3 and Theorem 0.4.\n\nOn page no. 6, in the proof of Lemma 0.2, it is given that uk,r, uk,s∈V(G) are at equal distance from every w∈S-Wk and it is concluded that their representations differ with respect to W.\n\nIn the edge set of Amal(Pn,v,m) [Theorem 0.3] and Amal(Kn,v,m) [Theorem 0.4], an extra curly brace is placed.\n\nIn the proof of Theorem 0.4, two adjacent vertices x and y are mentioned to be equidistant from every w∈V(Amal(Kn,v,m)). Followed by that, it is given that they have different representation w.r.t W.\n\nIn the edge set of Amal(Wn,v,m), j=1mE(Wnj) is typed as j=1 j=mE(Wnj). Similarly, for Fn\n\nThe set P is not mentioned clearly in proof of Theorem 0.5, Theorem 0.7, Theorem 0.8 and Theorem 0.9.\n\nIn the proof of Theorem 0.7, (page no. 10, first line) ‘local m-resolvings of Fn’ should be changed as ‘local m-resolving set of Fn’.\n\nIt is mentioned in many places that there are three possibilities but followed by that only two cases are given.\n\nCite following recent paper about this topic1-6.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11177", "date": "13 Apr 2024", "name": "Liliek Susilowati", "role": "Author Response", "response": "Thank you for your suggestion. I will revise my paper accordingly to your comments and suggestions." } ] } ]	1	https://f1000research.com/articles/12-95
https://f1000research.com/articles/12-1077/v1	31 Aug 23	{ "type": "Research Article", "title": "Are circadian amplitudes and periods correlated? A new twist in the story", "authors": [ "Marta del Olmo", "Christoph Schmal", "Camillo Mizaikoff", "Saskia Grabe", "Christian Gabriel", "Achim Kramer", "Hanspeter Herzel", "Christoph Schmal", "Camillo Mizaikoff", "Saskia Grabe", "Christian Gabriel", "Achim Kramer", "Hanspeter Herzel" ], "abstract": "Three parameters are important to characterize a circadian and in general any biological clock: period, phase and amplitude. While circadian periods have been shown to correlate with entrainment phases, and clock amplitude influences the phase response of an oscillator to pulse-like zeitgeber signals, the co-modulations of amplitude and periods, which we term twist, have not been studied in detail. In this paper we define two concepts: parametric twist refers to amplitude-period correlations arising in ensembles of self-sustained clocks in the absence of external inputs, and phase space twist refers to the co-modulation of an individual clock's amplitude and period in response to external zeitgebers. Our findings show that twist influences the interaction of oscillators with the environment, facilitating entrainment, fastening recovery to pulse-like perturbations or modifying the response of an individual clock to coupling. This theoretical framework might be applied to understand the emerging properties of other oscillating systems.", "keywords": [ "circadian clocks", "mathematical modeling", "amplitudes", "periods", "twist", "heterogeneity", "entrainment", "coupling" ], "content": "Introduction\n\nOscillations are happening all around us, from the vibrating atoms constituting matter to the beating of the animal heart or to circadian clocks present in all kingdoms of life. Circadian clocks are autonomous clocks that tick in the absence of external timing cues with a period of about 24 h and regulate our behavior, physiology and metabolism. A fundamental property of circadian clocks is that their phase and periodicity can be adjusted to external timing signals (zeitgebers) in a process known as entrainment. It is believed that natural selection has acted on the phase relationship between biological rhythms and the environmental cycle, and thus, this phase of entrainment is of central importance for the fitness of the organism, allowing it to anticipate to changes in the external world. 1\n\nThree key properties of a circadian rhythm are its period, amplitude and phase. Chronobiological studies have usually focused on period because there are established tools that allow their direct measurement, including running wheels for mice or race tubes for fungi. Phase, which refers to the position of a point on the oscillation cycle relative to a reference point, can be measured similarly. Circadian rhythms can be entrained to various zeitgeber periods T as reviewed in, 2 but under the natural conditions of T=24 h, variations of intrinsic periods lead to different phases of entrainment that are the basis of chronotypes: faster running clocks (shorter endogenous periods) lead to early phases (‘morning larks’) and slower clocks (longer periods) correspond to later phases (‘night owls’). 3 – 7\n\nMeasuring amplitudes, however, is less straightforward. Some studies have considered activity recordings 8 , 9 or conidiation in race tubes, 10 but one might argue that these measures do not represent the clockwork’s amplitude, as they reflect outputs of the circadian system. Other studies have quantified gene expression profiles after careful normalization, 11 but from the ∼ 20 core clock genes that constitute the mammalian circadian oscillator, 12 it is not immediately evident which gene or protein is best representing the core clock amplitude. Actually, reporter signals monitoring expression of different clock genes and proteins have been used to quantify amplitudes. 4 , 13 , 14 Others have approached the amplitude challenge indirectly by measuring the response of an oscillator to zeitgeber pulses. 15 – 18 While small-amplitude clocks exhibit larger pulse-induced phase shifts and are easier to phase-reset, larger amplitude rhythms display smaller phase shifts, 17 – 22 with evident consequences in the size of the phase response curve 5 or in jet lag duration. 23 Amplitudes, together with periods, also govern entrainment 23 , 24 and seasonality. 22 , 23 , 25 There have been various theoretical and experimental studies showing, for example, how clocks with larger amplitudes display narrower ranges of entrainment than rhythms of lower amplitude, 20 and how the phase of entrainment is modulated by oscillator amplitude. 22 , 24\n\nTaken together, these observations indicate, firstly, that the phase of entrainment is correlated with the intrinsic period, and secondly, that both phase of entrainment and phase changes in response to perturbations also correlate with oscillator amplitude. This leads to the question of whether amplitudes and periods are also co-modulated and what insights these interdependencies provide about the underlying oscillator. These questions are the focus of this paper. Do faster-running clocks have larger or smaller amplitudes than slower clocks? What are the implications? Experimental observations have provided evidence for both: in a human osteosarcoma cell line in culture, clocks with longer periods display larger amplitudes; 26 but in cells from the choroid plexus, the major producer of cerebrospinal fluid of the central nervous system, clocks with shorter periods are associated with larger amplitudes 14 (scheme in Figure 1). This dependence between periods and amplitudes is what we here refer to as twist, also known as shear in the literature. 27 , 28 By convention, negative twist describes oscillators in which amplitude increases are accompanied by a decreasing period (also termed hard oscillators) and vice versa for positive twist (soft oscillators).\n\n(A) Positive correlations (i.e., positive twist) have been observed in U-2 OS cells kept in culture 26 ; (B) negative correlations have been observed in cells from the choroid plexus in the mouse brain. 14\n\nIn this paper we provide definitions for two important concepts: parametric twist and phase space twist. We show, firstly, that nonlinearities can introduce amplitude-period correlations in simple oscillator models. Moreover, clock models of different complexity can reproduce the experimentally-observed positive 26 and negative 14 twist effects, with the type of correlation depending on the model, on parameters, as well as on the variable being measured, illustrating the complexity in defining circadian amplitudes. Lastly, we show how twist effects can speed up or slow down zeitgeber-induced amplitude changes in a simple oscillator model. This helps the clock phase adapt and modulate entrainment of oscillators to a periodic signal or their response to coupling. Our results support the use of oscillator theory as a framework to understand emerging properties of circadian clocks with different twist. Moreover, they provide insights into how temporal or spatial phase patterning might arise in coupled networks, as well as how amplitude changes could help in stabilizing the circadian period in the face of temperature changes. Although we focus on circadian clocks, the presented theory can be applied to any other oscillatory system such as cardiac rhythms, flashing fireflies or voice production.\n\n\nMaterials and Methods\n\nIn classical mechanics, a mass-spring harmonic oscillator is a system of mass m that, when displaced from its equilibrium position, experiences a restoring force F proportional to the displacement x , namely F=−kx , where k is the spring constant. When F is the only restoring force, the system undergoes harmonic motion (sinusoidal oscillations) around its equilibrium point. In the absence of damping terms, the harmonic motion can be mathematically described by the following linear second order ordinary differential equation (ODE)\n\nThe solution to this differential equation is given by the function xt=Acos2πτ+ϕ , 29 , 30 where A represents the amplitude; ϕ , the phase; and τ represents the period of the motion, τ=2πmk . Thus the oscillatory period is determined only by the mass m and the spring constant k . The amplitude A , on the other hand, is determined solely by the starting conditions (by both initial displacement x and velocity v=ẋ ).\n\nIntroducing a non-linear term in the restoring force such that F=−kx−βx3 allows the conversion of the simple harmonic oscillator into a Duffing oscillator. 31 Depending on the sign of β , the coefficient that determines the strength of the non-linear term, the spring is termed hard or soft oscillator. The equation of the Duffing oscillator, in the absence of damping terms, reads\n\nDue to the non-linear term introduced in equation 2, it is helpful to write this system in a form that can be easily treated via numerical integration. Considering the following change of variable v=ẋ , the equation can be reformulated as a system of two first order ODEs:\n\nThe three-variable Goodwin model is a minimal model based on a single negative feedback loop that can describe the emergence of oscillations in simple biochemical systems. All synthesis and degradation terms are linear, with the exception of the repression that z exerts on x which is modeled with a sigmoidal Hill curve. The equations that describe the dynamics read\n\nThe Goodwin model, however, requires a very large Hill exponent ( n>8 ) to produce self-sustained oscillations, 32 which biologists and modelers have often considered unrealistic. Gonze 33 and others have shown that, by introducing additional nonlinearities in the system, the need for such high value of the Hill exponent can be reduced. In contrast to the linear degradation of variables of the original Goodwin model, the Gonze model 33 describes degradation processes with Michaelis-Menten kinetics as follows\n\nTo mimic clock heterogeneity and evaluate the amplitude-period correlations among ensembles of Gonze or Goodwin oscillators, degradation rates were varied around ±10% their default value (Table 1).\n\nTheir biological interpretation as well as the default values from publications are shown.\n\n* Parameters have been adapted to obtain limit cycle oscillations, since the default degradation parameters from 35 produced weakly damped rhythms.\n\nThe Almeida model 36 is a protein model of the mammalian clockwork that includes 7 core clock proteins along with the PER:CRY complex and the regulation (activatory or repressive) that these exert on DNA binding sites known as clock-controlled elements to regulate circadian gene expression. The regulation at these clock-controlled elements, namely E-boxes, D-boxes and RORE elements, is described by the following terms:\n\nThe system of ODEs that describes the dynamics of the clock proteins in the Almeida model reads\n\nAll parameter descriptions along with their default values are given in Table 2.\n\nTime units are given in hours and concentration units as arbitrary units. The default values are taken from. 36\n\nTo analyze the twist effects that arise from a population of heterogeneous clocks (i.e., parametric twist), all 18 model parameters were randomly varied around ±20% their default value (Table 2) one at a time. Since this model can lead to period-doubling effects upon changes of certain parameters, 37 those oscillations whose period change resulted in oscillations with period-doubling were removed from the analysis. Moreover, if changing the default parameter in the ensemble resulted in a range of ratio of amplitude variation relative to the default amplitude <0.1 , then we considered that ensemble to have no twist for that particular control parameter. Periods and amplitudes were determined from the peaks and troughs of oscillations using the continuation software XPP-AUTO.\n\nThe intrinsic dynamical properties from single oscillators and their interaction to external stimuli can be very conveniently described by means of a Poincaré model. 38 We here propose a modification of its generic formulation that explicitly takes into account twist effects through the phase space twist parameter ϵ . The modified Poincaré model with twist reads\n\nThe first equation describes the rate of change of the radial coordinate rt (i.e., the time-dependent distance from the origin), whereas the second equation determines the rate of change of the angular coordinate ϕt , where ω=2πτ . The parameters τ , A , λ and ϵ denote the free-running period (in units of time), amplitude (arbitrary units), amplitude relaxation rate (in units of time-1) and phase space twist of the oscillator (in units of time-1), respectively. In the absence of twist, namely ϵ=0 , the phase changes constantly along the limit cycle at a rate 2πτ , independently of the radius. In the case of ϵ≠0 , the phase changes at a constant rate only when r=A ; if any perturbation is to modify r such that r≠A , then the phase change will be accelerated or decelerated depending on the sign of ϵ and on whether r>A or r<A . The model parameters, unless otherwise specified in the figures or captions, are the following: A=1 a.u., λ=0.05h−1 , τ=24 h and ϵ values of 0 or ±0.1h−1 .\n\nTo study the effects of twist on the oscillator’s response to pulse-like perturbations pertt , periodic zeitgeber input Zt or mean-field coupling M , the individual Poincaré oscillators i were converted into Cartesian coordinates and the respective terms were added in the equations of the xi variable as follows:\n\nArthur T. Winfree introduced the concept of isochrones as any set of dynamical states which oscillate with the same phase when they reach the limit cycle at time t→∞ . 39 That asymptotic phase at t→∞ is what Winfree termed latent phase Φ . Since the dynamical flow of the Poincaré model has polar symmetry, the isochrones must also have polar symmetry such that\n\nBy definition, the latent phase velocity Φ̇ necessarily increases at units of the angular velocity ω=2πτ as the oscillator follows its kinetic equation:\n\nCombining the two previous equations and with the use of the chain rule, we can calculate the radius dependency of the latent phase Φ :\n\nThe terms dϕdt and drdt are defined in the Poincaré model (equation 7), so that the equation above can be rewritten as:\n\nSolving for dfrdr :\n\nNext, the solution for fr can be found through integration:\n\nIf A=1 (like in all our simulations), the last term can be neglected such that\n\nFinally, the solution of fr can be inserted in equation 9 to end up with the equation for isochrones as a function of the radius:\n\nIsochrones are thus loci of polar coordinates ϕr in phase space with the same latent phase Φ . Equation 11 shows how the shape of the isochrone for the Poincaré model in equation 7 depends on the ratio of twist ϵ to relaxation rate λ . Specifically, higher ϵ values (in modulus) and lower relaxation rates λ lead to more curved isochrones.\n\nTo plot the isochrones, we simply reorder equation 11 to plot ϕ as a function of r at isochrones with fixed values of latent phases Φ=0π4π23π4π−3π4−π2−π4 :\n\nAll numerical simulations were performed and analyzed in Python with the numpy, scipy, pandas and astropy libraries. The function odeint from scipy was used to numerically solve all ordinary differential equations. Bifurcation analyses were computed in XPP-AUTO 40 using the parameters Ntst=150,Nmax=20000,Dsmin=0.0001 and Dsmax=0.0002 .\n\nThroughout our analyses, periods were determined by (i) normalizing the solutions to their mean, (ii) centering them around 0 (by subtracting one unit from the normalized solution), and (iii) by then computing the zeroes of the normalized rhythms. The period was defined as the distance between two consecutive zeros with a negative slope. Amplitudes were determined as the average peak-to-trough distance of the last (normalized) oscillations after removing transients.\n\n\nResults\n\nThe simple harmonic oscillator (Figure 2A) is a classical model of a system that oscillates with a restoring force proportional to its displacement, namely F=−kx . 41 The ordinary differential equation that describes the motion of a mass attached on a spring is linear (equation 1 in Materials and Methods) and the solution can be found analytically. 29 , 30 The period is determined by the size of the mass m and the force constant k (see Materials and Methods), while the amplitude and phase are determined by the starting position and the velocity. Thus, an ensemble of harmonic oscillators with different initial conditions will produce results that differ in amplitudes but whose periods are the same (Figure 2B, C). When plotting amplitudes against periods, no correlation or twist is observed: the period of a simple harmonic oscillator is independent of its amplitude (Figure 2D).\n\nThe mass-spring harmonic oscillator (A) is a linear oscillator that, in the absence of friction, produces persistent undamped oscillations (B, in time series and C, in phase space). Different starting conditions produce oscillations that differ in amplitudes but whose period is independent of amplitude (D). The harmonic oscillator is converted to a Duffing oscillator (E, I) by introducing nonlinearities in the restoring force of the spring (the non-linear behavior is represented with deformations of the spring). The new restoring force results in slight changes in the initial conditions producing oscillations whose amplitude and period change (F, G, J, K) and become co-dependent (H, L) and where the correlations depend on the sign of the non-linear term. The terms soft and hard oscillators refer to, by convention, those with positive and negative twist, respectively. Period values in (F–H, J–L) are color-coded.\n\nThe simple harmonic oscillator can be converted into a Duffing oscillator 31 by including a cubic nonlinearity in its equation. In the Duffing oscillator (equations 2, 3 in Materials and Methods), the restoring force is no longer linear (see deformed springs in Figure 2) but instead described by F=−kx−βx3 , where β represents the coefficient of non-linear elasticity. These classical conservative oscillators instead are known to have an amplitude-dependent period. A network of Duffing clocks with different starting conditions will produce oscillations of different amplitudes as well as periods. Duffing oscillators with a negative cubic term have been termed soft oscillators and display periods that grow with amplitudes (Figure 2E–H), similar to Kepler’s Third Law of planetary motion, 42 where planets with larger distances to the Sun run at slower periods than those that are closer. On the other hand, Duffing oscillators with a positive β term are known as hard oscillators and show negative twist (amplitude-period correlations) (Figure 2I–L). 43 , 44\n\nIn short, nonlinearities in oscillator models can introduce twist effects among ensembles of oscillators with slight differences in their properties (initial conditions, parameters, etc.). Thus, models for the circadian clock, which are based on nonlinearities, are expected to show amplitude-period correlations.\n\nMost circadian clock models generate stable limit cycle oscillations. Limit cycles are isolated closed periodic orbits with a given amplitude and period, where neighboring trajectories (e.g. perturbations applied to the cycle) spiral either towards or out of the limit cycle. 38 , 45 Stable limit cycles are examples of attractors: they imply self-sustained oscillations. The closed trajectory describes the perfect periodic behavior of the system, and any small perturbation from this trajectory causes the system to return to it, to be attracted back to it.\n\nLimit cycles are inherently non-linear phenomena and they cannot occur in a linear system (i.e., a system in the form of x→̇=Ax→ , like the harmonic oscillator). From the previous section we have learned that non-linear terms can introduce amplitude-period co-dependencies. In this section we show that kinetic limit cycle models of the circadian clock also show twist effects. Instead of studying the amplitude-period correlation of an oscillator model with fixed parameters and changing initial conditions as in Figure 2 (as all initial conditions would be attracted to the same limit cycle), we study here the correlations that arise among different uncoupled oscillators due to oscillator heterogeneity (i.e., differences in biochemical parameters), as found experimentally. 14 , 26 We refer to amplitude-period correlations that arise due to oscillator heterogeneity as parametric twist.\n\nThe Goodwin model is a simple kinetic oscillator model 46 that is based on a delayed negative feedback loop, where the final product of a 3-step chain of reactions inhibits the production of the first component (equation 4 in Materials and Methods). In the context of circadian rhythms, 34 , 35 the model can be interpreted as a clock activator x that produces a clock protein y that, in turn, activates a transcriptional inhibitor z that represses x (Figure 3A). The Goodwin model has been extensively studied and fine-tuned by Gonze and others 33 to study fundamental properties of circadian clocks 47 – 50 or synchronization and entrainment. 33 , 51 , 52 The Gonze model 33 (equation 5) includes additional nonlinearities, where the degradation of all 3 variables is modeled with non-linear Michaelis Menten kinetics, to reduce the need of very large Hill exponents ( n>8 ), required in the original Goodwin model to generate self-sustained oscillations, 32 that have been questioned to be biologically meaningful. These Michaelian degradation processes can be interpreted as positive feedback loops which aid in the generation of oscillations 53 (Figure 3B).\n\nScheme of the Goodwin (A) and Gonze (B) oscillator models. Changes in degradation parameters result in twist effects when varied randomly around ± 10% their default parameter value, mimicking oscillator heterogeneity of the Goodwin (C) and Gonze (D) models. Simultaneous co-variation of degradation parameters results in parametric twist: changes of k2 and k4 produce significant positive amplitude-period correlations in both models (E, F); co-variations of k6 and k4 result in amplitude-period correlations that are not significant in the Goodwin model (G), but significant positive parametric twist in the Gonze model (H). Shown in all panels is Spearman’s R and the significance of the correlation (n. s.: not significant; ***: p value < 0.001). Default model parameters are summarized in Table 1. Relative amplitudes are computed as the peak-to-trough distance of the x variable. Oscillators from the ensemble whose amplitude was <0.1 have been removed from the plots; the total number of oscillators ( n ) is indicated in the plots.\n\nTo study whether twist effects are present in an ensemble of 100 uncoupled Goodwin and Gonze oscillators with different parameter values, we randomly varied the degradation parameters of x , y or z ( k2 , k4 and k6 , respectively) in each oscillator around ±10% their default parameter value (given in Table 1) and analyzed the resulting amplitude-period correlation. The resulting parametric twist depends on the model and on the parameter being changed: in the Goodwin model, variations in the degradation rate of the transcriptional activator ( k2 ) or of the clock protein ( k4 ) result in positive twist effects (i.e., soft twist-control), while changes in the transcriptional repressor’s degradation rate ( k6 ) result in a hard twist-control, i.e., negative amplitude-period correlation (Figure 3C). In the Gonze model, k2 , k4 and k6 are all soft twist-control parameters, as individual changes of any of them all produce positive parametric twist effects (Figure 3D).\n\nTo mimic cell-to-cell variability in a more realistic manner, we introduced heterogeneity by changing combinations of the degradation parameters simultaneously around ±10 % their default parameter value and analyzing the resulting periods and amplitudes. We observed that the overall twist behavior depends on the particular influence that each parameter has individually. Random co-variations of k2 and k4 produce significant positive parametric twist effects in ensembles of both Goodwin (Figure 3E) or Gonze clocks (Figure 3F), consistent with the positive correlations when either of the parameters is changed individually (Figure 3C, D). Nevertheless, when k6 , which has a negative twist effect in the Goodwin model, is changed at the same time as k4 (or k2 , data not shown) the correlation is not significant (Figure 3G). Random co-variation of k4 and k6 in an ensemble of Gonze clocks results in significant positive parametric twist effects (Figure 3H).\n\nChanges in parameter values can result in significant alterations to a system’s long-term behavior, which can include differences in the number of steady-states, limit cycles, or their stability properties. Such qualitative changes in non-linear dynamics are known as bifurcations, with the corresponding parameter values at which they occur being referred to as bifurcation points. In oscillatory systems, Hopf bifurcations are an important type of bifurcation point. They occur when a limit cycle arises from a stable steady-state that loses its stability. A 1-dimensional bifurcation diagram illustrates how changes in a mathematical model’s control parameter affect its final states, for example the period or amplitude of oscillations. The Hopf bubble refers to the region in parameter space where the limit cycle exists, and it is commonly represented with the peaks and troughs of a measured variable in the y axis, with the control parameter plotted on the x axis (Figure 4A). The term “bubble” is used because of the shape of the curve, that resembles a bubble that grows or shrinks as the parameter is changed. Such bifurcation analyses can be used to predict the type of twist that a system shows: the amplitude will increase with parameter changes if the default parameter value is close to the opening of the Hopf bifurcation, or will decrease if the value is near the closing of the bubble.\n\nBifurcation analysis of Gonze oscillators with changing k4 , simulating heterogeneous oscillators: (A) Hopf bubble representing the peaks (maxima) and troughs (minima) of variable x as a function of changes in the degradation rate of y ( k4 ); (B) monotonic period decrease for increasing k4 . Represented in (C) is the combination of (A) and (B), namely how the difference between the maxima and minima of x changes with the period: a non-monotonic behavior of parametric twist is observed, which depends on the values of k4 . Note that, since k4 results in a decrease in period length, the k4 dimension is included implicitly in (C) and k4 increases from the right to the left of the plot. Stars indicate the default parameter value, period or amplitude.\n\nWe observed that Gonze oscillators display self-sustained oscillations for values of k4 between 0.2 and 0.43 (Figure 4A) and that, for increasing k4 , periods decrease monotonically (Figure 4B). For oscillators with increasing k4 , the parametric twist effects from the ensemble are first negative (amplitudes increase and periods decrease); however, when Gonze clocks have k4 values that are part of the region of the bubble where amplitudes decrease, positive amplitude-period correlations appear in the ensemble (Figure 4C). In summary, the type of parametric twist depends on both the model and the parameter being studied but also on where the parameter is located within the Hopf bubble. Other more complex kinetic models of the mammalian circadian clockwork have shown that changes in some of the degradation parameters produce non-monotonic period changes, 54 and thus the twist picture is expected to become even more complex.\n\nThe Almeida model 36 is a more detailed model of the core clock network in mammals that includes seven core clock proteins that exert their regulation at E-boxes, D-boxes and ROR binding elements (RORE) through multiple positive and negative feedback loops (Figure 5A, equation 6 in Materials and Methods). To study parametric twist in an ensemble of uncoupled Almeida oscillators, we randomly changed all 18 parameters individually around ±20% their default value (Table 2 in Materials and Methods) and computed the amplitude-period correlations. In this case, we calculated the ratio of amplitude variation after the parameter change relative to the default amplitude.\n\n(A) Scheme of the Almeida model, 36 illustrating activation (green arrows) and inhibition (red arrows) of different clock-controlled elements (at E-boxes, D-boxes and ROR elements) by the respective core clock proteins. Parametric twist was studied by modeling a heterogeneous uncoupled ensemble where model parameters were randomly and individually varied around ±20% of their default value (shown in Table 2) and assessing the period-amplitude correlation of the ensemble. (B–D) Almeida oscillators ( n=40 ) with heterogeneous values in the activation rate of D-boxes ( VD ): the twist is negative from the perspective of BMAL1, positive from the perspective of PER:CRY, but the amplitude of PER is not greatly affected by changing VD . (E–G) Almeida oscillators ( n=40 ) with heterogeneous values in the degradation rate of PER ( γP ) show positive parametric twist effects for BMAL1, PER and PER:CRY. The twist in panels (B, E) is evaluated by comparing the relative amplitude of the respective protein/protein complex (computed as the average peak-to-trough distance) after parameter change to the default amplitude. Shown in (C, D, F, G) are representative oscillations with long and short periods: dashed lines represent rhythms of smallest amplitudes.\n\nWe found, interestingly, that the overall twist effects depend not only on the parameter being studied, but also on the variable which is measured. For example, changes in the rate of D-box activation parameter VD result in negative twist effects for BMAL1 (i.e., lower amplitude BMAL1 rhythms run slower than oscillators with higher amplitude BMAL1 rhythms), positive parametric twist for the PER:CRY complex but almost no parametric twist from the perspective of PER (Figure 5B–D). Changes in PER degradation γP produce positive parametric twist for BMAL1, PER and PER:CRY but of different magnitudes (Figure 5E–G). Supplementary Table S1 (in 57 ) summarizes the parametric twist effects for the additional parameters from the Almeida model, highlighting the complexity that arises with synergies of feedback loops and bringing us again to the question of defining what the relevant amplitude of a complex oscillator is.\n\nUp until now, our results have focused on studying amplitude-correlations among ensembles of self-sustained oscillators with differences in their intrinsic properties (e.g. biochemical parameters) in the absence of external cues. However, when a clock is exposed to external stimuli, its amplitude and period undergo adaptation. We refer to these amplitude-period correlations in individual clocks as they return to their steady-state oscillation after a stimulus as phase space twist. In contrast to parametric twist, which emerged as a result of a heterogenous population of oscillators, here we focus on individual clocks.\n\nTo further explore the correlation and interdependence between the frequency of an oscillator and its amplitude upon an external stimulus, more generalized models can be of use. The Poincaré oscillator model (equation 7 in Materials and Methods) is a simple conceptual oscillator model with only two variables, amplitude and phase, that has been widely used in chronobiology research. 20 , 22 , 24 , 38 , 39 , 55 This amplitude-phase model, regardless of molecular details, can capture the dynamics of an oscillating system and what happens when perturbations push the system away from the limit cycle. When a pulse is applied and an oscillating system is ‘kicked out’ from the limit cycle, the perturbed trajectory is attracted back to it at a rate λ . Within the limit cycle, the dynamics are strictly periodic: if one takes a point in phase space and observes where the system returns to after exactly one period, the answer is trivial: to exactly the same spot (Figure 6, red dots). Nevertheless, outside the limit cycle, during the transient relaxation time (i.e., time between the perturbation and the moment that the trajectory reaches the limit cycle), the time between two consecutive peaks might be shorter or longer than the period of the limit cycle orbit. We will come back to this point in the next section.\n\nTo understand the concept of isochrones, a simple experiment is performed: if one considers a point in phase space (shown in red) within a limit cycle (black) and observes where the system returns to after exactly one period, the answer is trivial: to the same spot. If, however, now a perturbation is applied (red arrow) such that the system starts in a section of the state space which is outside of the stable periodic orbit, and one maps the points that the system ‘leaves as a footprint’ after exactly one period as it relaxes back to the limit cycle (blue trajectories), these points (shown in yellow) will outline an isochrone (grey line). The twist parameter ϵ affects the curvature of the isochrone, with implications in the response of the oscillating system to the perturbation. The oscillator with positive twist (B) arrives at a later phase than that with no twist (A), resulting in a phase delay with respect the clock with no twist, whereas the clock with negative twist (C) arrives to the limit cycle at an earlier phase (i.e., advanced with respect to the clock with no twist).\n\nArthur T. Winfree introduced a practical term, isochrones, to conceptualize timing relations in oscillators perturbed off their attracting cycles, 39 which becomes important in physiological applications because often, biological oscillators are not on their attracting limit cycles. To understand what isochrones are, Winfree proposes in 39 a simple experiment where a pulse-like perturbation applied in a system produces a ‘bump’ in the limit cycle. As the perturbation relaxes and spirals towards the attracting limit cycle, one records the position of the oscillator in time steps which equal the period of the unperturbed limit cycle. The sequence of points left as a footprint will converge to a fixed point on the cycle and will outline an isochrone (Figure 6). Isochrones are related to oscillator twist, and whereas in a Poincaré oscillator with no twist, the isochrones are straight and radial (Figure 6A), when twist is present, the isochrones become bent or skewed (Figure 6B, C).\n\nIn an individual oscillator with positive twist, a perturbation that increases the oscillator’s instantaneous amplitude will relax back and intersect the isochrone at an angle <360∘ (Figure 6B) than an oscillator with no twist in the time of one period, whereas an oscillator with negative twist will cover an angle >360∘ in the time of one period (Figure 6C). Thus, isochrones and consequently twist illustrate how a perturbation away from the limit cycle is decelerated or accelerated during the course of relaxation.\n\nMathematically, the ‘skewness’ of isochrones in an amplitude-phase oscillator is directly related to the twist parameter ϵ, that adds a radius dependency on the phase dynamics. The phase changes at a constant rate ω=2πτ in the limit cycle, but in conditions outside the limit cycle, the phase is made to be modulated by the radius through the twist parameter ϵ until r=A (equation 7 in Materials and Methods). This phase space twist parameter ϵ now represents the amplitude-period correlations (acceleration/deceleration) as an individual oscillator returns to its steady-state oscillation.\n\nWe have seen how, in an individual oscillator, the twist parameter ϵ acts to slow down (in case of positive twist) or to speed up (in case of negative twist) trajectories further away from the limit cycle compared to those closer to it. As a result, ϵ has a direct consequence on how the individual oscillator responds to pulse-like perturbations or periodic zeitgebers coming from the environment.\n\nTo analyze how phase space twist affects the response of an oscillator to a zeitgeber pulse, we applied a pulse-like perturbation to individual Poincaré oscillators with different phase space twist values ϵ . The pulse was applied at CT3 and was made to increase the instantaneous amplitude (such that r>A ). If the oscillator has no twist ( ϵ=0 , Figure 7A), the isochrones are straight and radial, but for a soft or a hard oscillator with positive or negative ϵ values, respectively, isochrones get skewed (Figure 7B, C, also Figure 6). In the case of a soft oscillator with positive ϵ (Figure 7B), the pulse at CT3 gets decelerated during the course of its relaxation, and as a consequence, the oscillator arrives back to the limit cycle at an later phase than the oscillator with ϵ=0 (Figure 7D, E). The same can also be inferred mathematically: for this particular perturbation where r>A , A−r<0 holds and hence the phase velocity outside the limit cycle is smaller ( ϕ̇<ω ) than at the limit cycle for the oscillator with positive twist, since ϕ̇=ω+ϵA−r (equation 7). The opposite holds for the oscillator with negative twist: this clock arrives at an earlier phase to the limit cycle (Figure 7C, F).\n\nThe positive and negative amplitude-period correlations characteristic of twist effects are evident in how, upon the pulse-like perturbation, the peak-to-peak distance changes (compared to the limit cycle period) as the perturbation returns to the periodic orbit. For a clock with ϵ=0 , the peak-to-peak distance outside the limit cycle after a perturbation coincides with the 24 h peak-to-peak distance within the periodic orbit (Figure 7G). In the case of the Poincaré oscillator with positive twist, the peak-to-peak distance of the oscillator after the perturbation that increases the instantaneous amplitude is longer than the period of the steady-state rhythm (24 h), since ϕ̇<ω . As the perturbed amplitude decreases and is attracted back to the stable cycle, the peak-to-peak distance approaches 24 hours (Figure 7H, consistent with the formulation ‘positive’ twist, which implies positive amplitude-period correlations). Conversely, the clock with negative twist exhibits a shorter peak-to-peak distance than the 24 h rhythm during the relaxation time ϕ̇>ω , which subsequently increases as the system returns to the stable periodic orbit (Figure 7I). When considering the findings from the last two paragraphs as a whole, it becomes clear how the extent of the phase shift between a perturbed and an unperturbed oscillator (red and black dashed lines in Figure 7D–F, respectively) depends on ϵ and thus the shape of the phase response curve (PRC) and magnitude of the phase shift depend on this twist parameter (Figure 7J–L).\n\nWe then evaluated how twist affects the response of an individual oscillator to a periodic zeitgeber input. We observed how the range of entrainment becomes larger with larger values of absolute value ϵ , as seen by the wider Arnold tongues in Figure 7M–O. It is widely known that, when the frequency of an applied periodic force is equal or close to the natural frequency of the system on which it acts, the amplitude of the oscillator on which the driving force (zeitgeber) acts on increases due to resonance effects. Interestingly, also the resonance curve was affected by twist: for the oscillator with no twist, the maximum amplitude occurred as expected for a zeitgeber period of 24 h, matching the intrinsic oscillator’s frequency (Figure 7P). In oscillators with positive or negative twist, however, the maximum amplitude after zeitgeber forcing increases and decreases with zeitgeber period, respectively (Figure 7Q, R), resulting in skewed resonance curves. 56 Interestingly, we observed that twist also affects the entrainment of an individual clock, and oscillators with high absolute values of twist cannot entrain to a periodic signal (Supplementary Figure S1 in 57 ), a phenomenon that has previously been described as shear-induced chaos 27 , 58 , 59 and that arises because the isochrones become so skewed, that the trajectory of the relaxation gets stretched and folded.\n\n(A–C) Poincaré oscillator models for different twist values ϵ , shown in phase space. The limit cycle is shown in black; perturbed trajectories are shown in red; isochrones are depicted in grey. (D–F) Time series corresponding to panels (A–C): the unperturbed limit cycle oscillations are shown with a dashed black line; perturbed trajectories are shown in red. (G–I) Peak-to-trough distance as a function of the peak-to-peak distance from the perturbed time series from (D–F) relaxing back to the limit cycle (the implicit time dimension is indicated in the panels). (J–L) Phase response curves: the shape of the PRC and the extent of the phase shifts (in hours) depends on the twist ϵ . (M–O) Arnold tongues illustrating entrainment ranges of an individual oscillator with different phase space twist values to a periodic sinusoidal zeitgeber input of different periods T . The amplitude of the entrained clock is color-coded, with yellow colors corresponding to larger amplitudes. (P–R) The amplitude of an individual oscillator driven by a sinusoidal zeitgeber also depends on the twist of the individual oscillator. Shown are the resonance curves as a response to a zeitgeber input of strength F=0.05 and varying periods T . Amplitudes are defined as the average peak-to-trough distances of the entrained signal.\n\nNot only the twist parameter ϵ , but also the amplitude relaxation rate λ affects the response of oscillators to perturbations and consequently the entrainment range. We have seen how, in the Poincaré model (equation 7), the twist parameter ϵ dictates how much trajectories are ‘slowed down’ or ‘sped up’ dependent on their distance from the limit cycle. The amplitude relaxation rate λ describes the rate of attraction back to the limit cycle, which is independent of ϵ . Together, these parameters both dictate how ‘skewed’ the isochrones are in phase space (see analytical expression in Materials and Methods, equation 11). For Poincaré oscillators with twist, the isochrones become more radial and straight as the amplitude relaxation rate increases (Figure 8A–C), with the implications that this has on PRCs and entrainment that have been mentioned before. A more ‘plastic’ clock (with a lower λ value) responds to an external pulse with larger phase shifts than a more rigid clock (with higher λ ), resulting in phase response curves of larger amplitude (Figure 8D–F). This is also intuitive, as it is clear that for larger values of λ , the twist has shorter effective time to act upon perturbed trajectories because the perturbation spends less time outside the limit cycle.\n\n(A–C) Poincaré oscillator models with different amplitude relaxation values λ , but otherwise identical (free running period τ=24 h, amplitude A=1 and twist ϵ=0.05h−1 ), shown in phase space. The limit cycle is shown in black; perturbed trajectories are shown in red; isochrones are depicted in grey. (D–F) Phase response curves: the shape of the PRC and the extent of the phase shifts depends on the relaxation rate λ . See Materials and Methods for details on the analytical derivation of the equation of isochrones and roles of λ and ϵ .\n\nBiological oscillators are rarely alone and uncoupled. Coupled oscillators, instead, are at the heart of a wide spectrum of living things: pacemaker cells in the heart, 38 insulin- and glucagon-secreting cells in the pancreas 60 or neural networks in the brain and spinal cord that control rhythmic behavior as breathing, running and chewing. 61 A number of studies have shown that networks of coupled oscillators behave in a fundamentally different way than ‘plain’ uncoupled oscillators. 33 , 62 , 63 This suggests that single oscillator twist might also affect how coupling synchronizes a network of oscillators.\n\nTo analyze the effect of twist on coupled oscillators, we study systems of Poincaré oscillators coupled through a mean-field (equation 8). We start by coupling two identical oscillators and analyzing the effect that different twist values have on the behavior of the coupled network. The numerical simulations show that increasing coupling strengths affect the period of the coupled system: oscillators with positive twist show longer periods as the coupling strength increases, whereas oscillators with negative twist show period-shortening (Figure 9A and Supplementary Figure S2A–C in 57 ). Coupling results in an increase in amplitude but, for our default relaxation rate value ( λ=0.05h−1 ), no significant differences across oscillators with different twist values were found (Supplementary Figure S2 in 57 ). Increasing relaxation rates (oscillators that are attracted faster back to the limit cycle upon a perturbation) nevertheless resulted in less coupling-induced period or amplitude changes (Supplementary Figure S3 in 57 ).\n\n(A) Mean-field coupling of two identical Poincaré oscillators (sharing the same value of twist ϵ) and the effect on the period of the coupled system: whereas coupling among oscillators with positive twist results in longer periods of the coupled network, mean-field coupling among oscillators with negative twist results in the network running at a faster pace (period shortening). (B) Mean-field coupling can synchronize a network of oscillators with different twist values. Shown are three oscillators that only differ in their twist parameters (but else identical: amplitude, amplitude relaxation rate and period are the same for the three oscillators). All oscillations overlap during the first part of the time series, since twist has no effect within the limit cycle. At a certain point (indicated by the red arrow), mean-field coupling is turned on and it is observed how the oscillators respond differently to that mean-field coupling, ending up with different individual amplitudes as well as relative phases to the mean-field (depicted in dashed black line).\n\nWe then analyzed what happens when oscillators with different phase space twist values are coupled through their mean-field. For this purpose, we took a system of 3 oscillators (with twist values ϵ=0 , ϵ<0 and ϵ>0 ) and turned on mean-field coupling after a certain time. We observed that all three oscillators synchronize to the mean-field for low values of the absolute value of twist (Figure 9B) although, due to the coupling-induced period differences, the relative phases of the individual oscillators to the mean-field depend on the specific twist values of the individual clocks: those with negative twist oscillate ‘ahead’ of the mean-field (with a phase advance) but clocks with positive twist cycle with a phase delay (Figure 9B). Very large absolute values of twist, interestingly, produce again complex chaotic dynamics (Supplementary Figure S4 in 57 ). The oscillator with a large value of ϵ does not synchronize to the mean-field and, as a result of the inter-oscillator coupling, this desynchronized oscillator ‘pulls’ to desynchronization the other two oscillators which otherwise would have remained in sync.\n\n\nDiscussion\n\nThis study aimed at characterizing period-amplitude correlations across circadian clock models of different complexity. Body clocks have to cope with cellular heterogeneity, what results in cellular clocks being variable across networks and tissues. We addressed whether the amplitude-period correlations that have been observed experimentally can be explained through heterogeneity in the cellular clocks, and what design principles are needed to produce such twist effects that we term parametric twist. Moreover, clocks live in constantly changing environments, that requires them to get adapted in the face of external changes. With the concept of phase space twist we study how this parameter, included explicitly in models, tunes the oscillator’s response to coupling, entrainment and pulse-like perturbations. We also retrieve the ‘old’ terminology of hard versus soft oscillators to refer to oscillations with negative and positive amplitude-period correlations, respectively.\n\nIt is important to note that a limit cycle oscillates with a characteristic period and amplitude regardless of the initial conditions. In contrast, conservative oscillations, like the Duffing oscillator (Figure 2), have a period and amplitude defined by the initial conditions. For this reason we have not termed twist, in the context of conservative oscillations, parametric or phase space. We refer to parametric twist as that type of amplitude-period correlations that appears when studying an ensemble of limit cycle oscillators with differences in their intrinsic properties (i.e., biochemical parameters) and phase space twist, as that type of transient amplitude-period correlation that an individual oscillator experiences when encountering an external stimulus that results in an adaptation of its period and amplitude.\n\nParametric twist effects appear when analyzing populations of cells and require nonlinearities in oscillator models. The feedback loops needed to generate oscillations, which are commonly modeled with non-linear terms, 33 , 36 , 47 , 54 result in variations of parameters producing oscillations of different but correlated amplitudes and periods. We found that the type of parametric twist (positive or negative) depends on a number of factors: (i) on the biochemical parameter being affected, since different model parameters control the oscillation properties (amplitude and period) differently (Figures 3 and 5); (ii) on the region within the Hopf bubble where the clock’s parameter set is at (Figure 4); (iii) on the type of model and variable being measured: simple models with single negative feedback loops show the same parametric twist effects for all variables because the parameter of interest has the same effect on the amplitude of all variables. In complex models with synergies of loops, a change in one parameter might increase the amplitude of one variable but decrease the amplitude of a second variable (Figure 5 and Supplementary Table S1 in 57 ). This highlights the challenge of defining circadian amplitude (and twist effects) to find a metric for the whole oscillating system. Our findings explain why some experimental studies have found positive twist, 26 others negative, 14 whereas some other works found very little correlations. 64\n\nWe also addressed the concept of phase space twist, a parameter that we (and others 14 , 38 , 39 ) introduced in a generic Poincaré oscillator. This twist parameter ϵ refers to period-amplitude correlations within a single oscillator, and it is a measure of the modulation of both instantaneous amplitude and period of the clock as the perturbed clock returns to the steady-state rhythm (i.e., limit cycle). Zeitgeber pulses, recurring zeitgeber inputs or coupling can all be regarded as ‘perturbations’, as any of these inputs modifies the natural clock’s limit cycle in phase space. Given this, it is not surprising that phase space twist, which characterizes the adaptation to a perturbation, has significant implications for phase response curves (PRCs), entrainment and coupling.\n\nWe start by discussing the role of twist in PRCs. The twist parameter affects the extent of the phase shift after a zeitgeber pulse (Figure 7D–F): increasing the twist parameter in absolute value results in alterations in the phase response curves and consequently in the resetting properties of oscillators. In particular, increasing \|ϵ\| increases the amplitude of the PRC (Figure 7J–L) until the PRC is converted from a type 1 PRC to a type 0 PRC. 19 , 65 Consistently, amplitudes 17 , 18 , 20 , 21 , 66 and periods 18 of oscillators have also been shown to modulate their resetting properties. In these examples, clocks with short periods 18 and small amplitudes (in mathematical models 17 , 18 , 20 or in experiments with reduced coupling 20 , 21 or mutations 66 that disrupt the normal rhythmicity) are easier to reset.\n\nOne can easily extrapolate these findings to responses to jet lag. If twist modulates the extent of a phase shift in response to a perturbation, it will also be critical in the adaptation to jet lag. This has indeed been found by Ananthasubramaniam et al. 23 Interestingly, the authors found that the instantaneous amplitude effects induced by jet lag are also modulated by twist. In particular, positive twist aided recovery to jet lag in simple Goodwin-like models: reduced amplitudes were accompanied by faster clocks (i.e., shorter periods) upon a phase advance (e.g. when traveling eastwards), but larger amplitudes coincided with longer periods when the phase had to be delayed (e.g. when traveling westwards). Consistent with these theoretical observations are experiments performed in mice, where compromising coupling in the SCN (and thus decreasing amplitudes) reduce jet lag drastically, since resetting signals are much more efficient. 21\n\nTransient amplitude-period correlations also affect the entrainment properties of an oscillator. Twist increases the range of zeitgeber periods to which the Poincaré oscillator can entrain (resulting in larger entrainment ranges, i.e., wider Arnold tongues, Figure 7M–O) and skews the resonance curves (Figure 7P–R). Some studies have even found coexisting limit cycles for driven oscillators with twist. 31 , 67 Of note, however, is that the period of the Poincaré oscillator in all our phase space twist simulations was set to 24 h. Other theoretical studies have shown that clocks with different intrinsic periods show different amplitude responses to entrainment, 23 , 68 thus combining phase space and parametric twist effects.\n\nSingle cells harbor self-sustained clocks, but they are coupled (see 69 for a review on coupling) to produce a coherent rhythm at the level of tissues and organisms. Coupled networks show different rhythmic properties than clocks in isolation: phases synchronize and ensemble amplitudes increase for over-critical values of coupling strengths. 62 Our simulations provide an additional level of regulation, by showing that twist influences period length of individual clocks due to coupling. Positive twist results in periods lengthening upon mean-field coupling (Figure 9). The presence of coupling-induced changes in the oscillation period or amplitude can provide insights into the underlying oscillator type and the presence of twist. For instance, the longer period that has been observed in dispersed (and presumably uncoupled) U-2 OS cells compared to high-density cultures, 70 but not in dispersed SCN neurons in culture, 71 , 72 could be explained by different implicit oscillator twist and amplitude relaxation rate values in different tissues.\n\nIn addition, the twist-induced modulation of period also affects the phase relation with which the clock oscillates respect to the mean-field: clocks with positive twist that tend to period-lengthen in response to coupling show later phases than those with negative twist, which tend to run quicker, consistent with chronotypes. It should be noted, however, that different phase relationships to the mean-field can also be obtained without twist, in networks of coupled oscillators with different intrinsic periods. 62 But here again, the slower running clocks will tend to be phase-delayed in comparison to the faster-running clocks which will be phase-advanced. This suggests that twist is critical in how synchronization arises in network of coupled oscillators.\n\nOur simulations assume that the coupling strength is constant across all oscillators. This assumption however might be questioned, since oscillators might ‘talk’ with different strengths to each other, especially because individual clocks are spatially organized within tissues, and have been shown to produce waves of oscillations for example in the SCN. 73 – 75 Thus, a more plausible scenario may involve local coupling, where clocks couple to neighbor clocks with a strength proportional to the oscillator distance. In fact, spatial gradient in nearest neighbor coupling can lead to a robust phase patterning. 62 Thus twist might not only be critical in how temporal synchronization but also spatial patterning arises in coupled ensembles.\n\nThe focus of this paper has been predominantly on twist, but it is important to remark that also the relaxation rate λ (i.e., how rigid/plastic an oscillator is) affects the response of oscillators to perturbations, consistent with previous computational work. 20 , 55 It is in fact the ratio of ϵ to λ what determines the skewing of isochrones (see the analytical derivation in Materials and Methods) and the oscillator’s response to zeitgebers. Larger values of λ (more ‘rigid’ oscillators) imply that any perturbation is attracted back to the limit cycle at a higher rate and thus, perturbations ‘spend less time’ outside the limit cycle. Consequently, the twist parameter ϵ has a shorter effective time to act on the perturbed trajectory, and the isochrones become more straight and radial. Relaxation rate also has implications on coupling and entrainment. Rigid oscillators with ϵ≠0 display less coupling-induced amplitude expansions (Supplementary Figure S3B in, 57 also 20 ) and less period variations (Supplementary Figure S3A in 57 ) in response to coupling than more ‘plastic’ oscillators with lower λ values. Moreover, rigid oscillators have smaller ranges of entrainment and narrower Arnold tongues. 20 Again, our results imply that any observation of resonant behavior and/or period changes might provide information on whether the underlying oscillator is a rigid versus plastic and hard versus soft clock.\n\nWe finish with an open question. Throughout our work we have claimed that period-amplitude correlations are widespread in both in vivo and in in silico clocks, and how they are critical to define how oscillators function in their environment. But, how does one integrate the circadian clock’s property of temperature compensation within this framework? The circadian clockwork is temperature-compensated, 18 , 49 , 76 – 78 which means that increasing temperatures do not speed up significantly the clock, which still runs at approximately 24 h. A proposed hypothesis for temperature compensation suggests that temperature-sensitivity of oscillation amplitude could stabilize the period. 18 , 78 In support of this supposition is evidence from Neurospora 18 and Gonyaulax 79 suggesting that amplitude increases in response to temperature, but decreases in Drosophila. 80 What are the twist effects behind this adaptation? Twist might play a role in how fast that temperature variation is sensed in the clockwork and modulate the adaptation to find the new steady-state rhythm of larger or smaller amplitude at the new temperature.\n\n\nConclusions\n\nDespite the complexities in quantifying amplitude, our models stress the important role of circadian amplitudes and their correlation with oscillator period. Although amplitudes are known to be regulated by a number of internal and external cellular factors, including cellular biochemical rates, light conditions, 81 coupling, 62 genetic and epigenetic factors 82 or ageing, 83 our findings stress that twist effects (i.e., co-modulations of amplitudes and periods) also ‘feed back’ and affect the interaction of oscillators with the environment, facilitating entrainment, fastening response to pulse-like perturbations or modifying the response of a system to coupling. The theory of our conceptual models can also be applied to other oscillating system such as cardiac rhythms, somite formation, central pattern generators or voice production.", "appendix": "Data and code availability\n\nGitHub: Simulated (numerical) data generated for the manuscript. https://github.com/olmom/twist\n\nGitHub: Supplementary Material. https://github.com/olmom/twist\n\nGitHub: Source code to generate and analyze the data and to reproduce all figures. https://github.com/olmom/twist\n\nData and codes are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors thank Gianmarco Ducci, Bharath Ananthasubramaniam and Adrián Granada for stimulating and helpful comments as well as constructive criticism. The authors would also like to acknowledge the work done by the Bachelor and Master students Pia Rose, Julia K. Schlichting, Barbara Zita Peters Couto and Rebekka Trenkle.\n\n\nReferences\n\nAschoff J: Exogenous and endogenous components in circadian rhythms. Cold Spring Harb Symp Quant Biol. Cold Spring Harbor Laboratory Press; 1960; vol. 25. : 11–28.\n\nAschoff J, Pohl H: Phase relations between a circadian rhythm and its zeitgeber within the range of entrainment. Naturwissenschaften. 1978; 65: 80–84. PubMed Abstract \| Publisher Full Text\n\nDuffy JF, Wright KP Jr: Entrainment of the human circadian system by light. J. Biol. Rhythm. 2005; 20: 326–338. Publisher Full Text\n\nBrown SA, et al.: Molecular insights into human daily behavior. Proc. Natl. Acad. Sci. U. S. A. 2008; 105: 1602–1607. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGranada AE, Bordyugov G, Kramer A, et al.: Human chronotypes from a theoretical perspective. PLoS One. 2013; 8: e59464. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoffmann K: Zum Einfluss der Zeitgeberstärke auf die Phasenlage der synchronisierten circadianen Periodik. J. Comp. Physiol. 1969; 62: 93–110.\n\nVanselow K, et al.: Differential effects of PER2 phosphorylation: molecular basis for the human familial advanced sleep phase syndrome (FASPS). Genes Dev. 2006; 20: 2660–2672. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBode B, Shahmoradi A, Rossner MJ, et al.: Genetic interaction of Per1 and Dec1/2 in the regulation of circadian locomotor activity. J. Biol. Rhythm. 2011; 26: 530–540. PubMed Abstract \| Publisher Full Text\n\nErzberger A, Hampp G, Granada A, et al.: Genetic redundancy strengthens the circadian clock leading to a narrow entrainment range. J. R. Soc. Interface. 2013; 10: 20130221. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMerrow M, Brunner M, Roenneberg T: Assignment of circadian function for the Neurospora clock gene frequency. Nature. 1999; 399: 584–586. PubMed Abstract \| Publisher Full Text\n\nKorenčič A, et al.: The interplay of cis-regulatory elements rules circadian rhythms in mouse liver. PLoS One. 2012; 7: e46835. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUeda HR, et al.: System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat. Genet. 2005; 37: 187–192. PubMed Abstract \| Publisher Full Text\n\nLeise TL, Wang CW, Gitis PJ, et al.: Persistent cell-autonomous circadian oscillations in fibroblasts revealed by six-week single-cell imaging of PER2::LUC bioluminescence. PLoS One. 2012; 7: e33334. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMyung J, et al.: The choroid plexus is an important circadian clock component. Nat. Commun. 2018; 9: 1062. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPittendrigh CS, Kyner WT, Takamura T: The amplitude of circadian oscillations: temperature dependence, latitudinal clines, and the photoperiodic time measurement. J. Biol. Rhythm. 1991; 6: 299–313. PubMed Abstract \| Publisher Full Text\n\nBarrett RK, Takahashi JS: Lability of circadian pacemaker amplitude in chick pineal cells: a temperature-dependent process. J. Biol. Rhythm. 1997; 12: 309–318. PubMed Abstract \| Publisher Full Text\n\nShaw J, Brody S: Circadian rhythms in Neurospora: a new measurement, the reset zone. J. Biol. Rhythm. 2000; 15: 225–240. PubMed Abstract \| Publisher Full Text\n\nLakin-Thomas PL, Brody S, Coté GG: Amplitude model for the effects of mutations and temperature on period and phase resetting of the Neurospora circadian oscillator. J. Biol. Rhythm. 1991; 6: 281–297. PubMed Abstract \| Publisher Full Text\n\nGranada A, Hennig R, Ronacher B, et al.: Phase response curves: elucidating the dynamics of coupled oscillators. Methods Enzymol. 2009; 454: 1–27. PubMed Abstract \| Publisher Full Text\n\nAbraham U, et al.: Coupling governs entrainment range of circadian clocks. Mol. Syst. Biol. 2010; 6: 438. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYamaguchi Y, et al.: Mice genetically deficient in vasopressin V1a and V1b receptors are resistant to jet lag. Science. 2013; 342: 85–90. PubMed Abstract \| Publisher Full Text\n\nTokuda IT, Schmal C, Ananthasubramaniam B, et al.: Conceptual models of entrainment, jet lag, and seasonality. Front. Physiol. 2020; 11: 334. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnanthasubramaniam B, Schmal C, Herzel H: Amplitude effects allow short jet lags and large seasonal phase shifts in minimal clock models. J. Mol. Biol. 2020; 432: 3722–3737. PubMed Abstract \| Publisher Full Text\n\nBordyugov G, et al.: Tuning the phase of circadian entrainment. J. R. Soc. Interface. 2015; 12: 20150282. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmal C, Myung J, Herzel H, et al.: A theoretical study on seasonality. Front. Neurol. 2015; 6: 94.\n\nGabriel CH, et al.: Live-cell imaging of circadian clock protein dynamics in CRISPR-generated knock-in cells. Nat. Commun. 2021; 12: 3796. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAshwin P, Coombes S, Nicks R: Mathematical frameworks for oscillatory network dynamics in neuroscience. J. Math. Neurosci. 2016; 6: 1–92. Publisher Full Text\n\nHolmes P: A nonlinear oscillator with a strange attractor. Philos Trans Royal Soc A. 1979; 292: 419–448.\n\nBerge P, Pomeau Y, Vidal C: Order within Chaos, translated by L. Tuckerman.1984.\n\nKaplan D, Glass L: Understanding nonlinear dynamics. Springer Science & Business Media; 1997.\n\nDuffing G: Erzwungene Schwingungen bei veränderlicher Eigenfrequenz und ihre technische Bedeutung. Vieweg; 1918; 41–42.\n\nGriffith JS: Mathematics of cellular control processes I. negative feedback to one gene. J. Theor. Biol. 1968; 20: 202–208. Publisher Full Text\n\nGonze D, Bernard S, Waltermann C, et al.: Spontaneous synchronization of coupled circadian oscillators. Biophys. J. 2005; 89: 120–129. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRuoff P, Rensing L: The temperature-compensated Goodwin model simulates many circadian clock properties. J. Theor. Biol. 1996; 179: 275–285. Publisher Full Text\n\nRuoff P, Vinsjevik M, Monnerjahn C, et al.: The Goodwin oscillator: on the importance of degradation reactions in the circadian clock. J. Biol. Rhythm. 1999; 14: 469–479. Publisher Full Text\n\nAlmeida S, Chaves M, Delaunay F: Transcription-based circadian mechanism controls the duration of molecular clock states in response to signaling inputs. J. Theor. Biol. 2020; 484: 110015. PubMed Abstract \| Publisher Full Text\n\nVan Soest I, Del Olmo M, Schmal C, et al.: Nonlinear phenomena in models of the circadian clock. J. R. Soc. Interface. 2020; 17: 20200556. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGlass L, Mackey MC: From clocks to chaos: The rhythms of life. Princeton University Press; 1988.\n\nWinfree AT: The geometry of biological time. Springer; 1980; vol. 2. .\n\nSchmal C, Leloup J-C, Gonze D: Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO. Plant Circadian Networks: Methods and Protocols. Springer; 2014; 337–358.\n\nHooke R: De potentia restitutiva, or of spring explaining the power of springing bodies. London, UK: John Martyn; 1678; vol. 23. .\n\nKepler J: The harmony of the world, vol. 209 (American Philosophical Society, 1997). Translated into English with an introduction and notes. Aiton EJ, Duncan AM, Field JV, editors.\n\nThompson JMT, Stewart HB: Nonlinear dynamics and chaos. John Wiley & Sons; 2002.\n\nKovacic I, Brennan MJ: The Duffing equation: nonlinear oscillators and their behaviour. John Wiley & Sons; 2011.\n\nStrogatz SH: Nonlinear dynamics and chaos with student solutions manual: With applications to physics, biology, chemistry, and engineering. CRC press; 2018.\n\nGoodwin BC: Oscillatory behavior in enzymatic control processes. Adv. Enzym. Regul. 1965; 3: 425–437. PubMed Abstract \| Publisher Full Text\n\nGonze D, Ruoff P: The Goodwin oscillator and its legacy. Acta Biotheor. 2021; 69: 857–874. Publisher Full Text\n\nWoller A, Gonze D, Erneux T: The Goodwin model revisited: Hopf bifurcation, limit-cycle, and periodic entrainment. Phys. Biol. 2014; 11: 045002. PubMed Abstract \| Publisher Full Text\n\nRuoff P, Loros JJ, Dunlap JC: The relationship between FRQ-protein stability and temperature compensation in the Neurospora circadian clock. Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 17681–17686. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRuoff P, Vinsjevik M, Monnerjahn C, et al.: The Goodwin model: simulating the effect of light pulses on the circadian sporulation rhythm of Neurospora crassa. J. Theor. Biol. 2001; 209: 29–42. PubMed Abstract \| Publisher Full Text\n\nLocke JC, Westermark PO, Kramer A, et al.: Global parameter search reveals design principles of the mammalian circadian clock. BMC Syst. Biol. 2008; 2: 1–9. Publisher Full Text\n\nKomin N, Murza AC, Hernández-García E, et al.: Synchronization and entrainment of coupled circadian oscillators. Interface Focus. 2011; 1: 167–176. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnanthasubramaniam B, Herzel H: Positive feedback promotes oscillations in negative feedback loops. PLoS One. 2014; 9: e104761. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRelógio A, et al.: Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Comput. Biol. 2011; 7: e1002309. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGranada AE, Herzel H: How to achieve fast entrainment? The timescale to synchronization. PLoS One. 2009; 4: e7057. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrabe S, Mahammadov E, Olmo MD, et al.: Synergies of multiple zeitgebers tune entrainment. Front Netw Physiol. 2022; 1: 803011. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDel Olmo M: Supplementary Material for the manuscript ‘Are circadian amplitudes and periods correlated? A new twist in the story’.2023. Reference Source\n\nOtt W, Stenlund M: From limit cycles to strange attractors. Commun. Math. Phys. 2010; 296: 215–249. Publisher Full Text\n\nWedgwood KC, Lin KK, Thul R, et al.: Phase-amplitude descriptions of neural oscillator models. J. Math. Neurosci. 2013; 3: 2–22. Publisher Full Text\n\nPetrenko V, et al.: Pancreatic α -and β -cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression. Genes Dev. 2017; 31: 383–398. PubMed Abstract \| Publisher Full Text\n\nMarder E, Bucher D: Central pattern generators and the control of rhythmic movements. Curr. Biol. 2001; 11: R986–R996. Publisher Full Text\n\nSchmal C, Herzog ED, Herzel H: Measuring relative coupling strength in circadian systems. J. Biol. Rhythm. 2018; 33: 84–98. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrogatz SH, Stewart I: Coupled oscillators and biological synchronization. Sci. Am. 1993; 269: 102–109. Publisher Full Text\n\nLi Y, et al.: Noise-driven cellular heterogeneity in circadian periodicity. Proc. Natl. Acad. Sci. U. S. A. 2020; 117: 10350–10356. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJohnson CH: Forty years of prcs-what have we learned?. Chronobiol. Int. 1999; 16: 711–743. PubMed Abstract \| Publisher Full Text\n\nVitaterna MH, et al.: The mouse Clock mutation reduces circadian pacemaker amplitude and enhances efficacy of resetting stimuli and phase–response curve amplitude. Proc. Natl. Acad. Sci. U. S. A. 2006; 103: 9327–9332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nParlitz U, Lauterborn W: Superstructure in the bifurcation set of the duffing equation x¨+ dx˙+ x3= f cos ( ω t). Phys. Lett. A. 1985; 107: 351–355.\n\nKurosawa G, Goldbeter A: Amplitude of circadian oscillations entrained by 24-h light–dark cycles. J. Theor. Biol. 2006; 242: 478–488. PubMed Abstract \| Publisher Full Text\n\nPilorz V, Astiz M, Heinen KO, et al.: The concept of coupling in the mammalian circadian clock network. J. Mol. Biol. 2020; 432: 3618–3638. PubMed Abstract \| Publisher Full Text\n\nFinger A-M, et al.: Intercellular coupling between peripheral circadian oscillators by TGF- β signaling. Sci. Adv. 2021; 7: eabg5174.\n\nAton SJ, Colwell CS, Harmar AJ, et al.: Vasoactive intestinal polypeptide mediates circadian rhythmicity and synchrony in mammalian clock neurons. Nat. Neurosci. 2005; 8: 476–483. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOno D, Honma S, Honma K-i: Cryptochromes are critical for the development of coherent circadian rhythms in the mouse suprachiasmatic nucleus. Nat. Commun. 2013; 4: 1666. PubMed Abstract \| Publisher Full Text\n\nTaylor SR, Wang TJ, Granados-Fuentes D, et al.: Resynchronization dynamics reveal that the ventral entrains the dorsal suprachiasmatic nucleus. J. Biol. Rhythm. 2017; 32: 35–47. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHerzog ED, Hermanstyne T, Smyllie NJ, et al.: Regulating the suprachiasmatic nucleus (SCN) circadian clockwork: interplay between cell-autonomous and circuit-level mechanisms. Cold Spring Harb. Perspect. Biol. 2017; 9: a027706. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEvans JA, Leise TL, Castanon-Cervantes O, et al.: Dynamic interactions mediated by nonredundant signaling mechanisms couple circadian clock neurons. Neuron. 2013; 80: 973–983. Publisher Full Text\n\nTerauchi K, et al.: ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteria. Proc. Natl. Acad. Sci. U. S. A. 2007; 104: 16377–16381. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRuoff P: Introducing temperature-compensation in any reaction kinetic oscillator model. J Interdiscipl Cycle Res. 1992; 23: 92–99. Publisher Full Text\n\nKurosawa G, Fujioka A, Koinuma S, et al.: Temperature–amplitude coupling for stable biological rhythms at different temperatures. PLoS Comput. Biol. 2017; 13: e1005501. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHastings JW, Sweeney BM: On the mechanism of temperature independence in a biological clock. Proc. Natl. Acad. Sci. U. S. A. 1957; 43: 804–811. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPittendrigh CS, Takamura T: Latitudinal clines in the properties of a circadian pacemaker. J. Biol. Rhythm. 1989; 4: 105–123. Publisher Full Text\n\nBano-Otalora B, et al.: Bright daytime light enhances circadian amplitude in a diurnal mammal. Proc. Natl. Acad. Sci. U. S. A. 2021; 118: e2100094118. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEmmett MJ, Lazar MA: Integrative regulation of physiology by histone deacetylase 3. Nat. Rev. Mol. Cell Biol. 2019; 20: 102–115. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTalamanca L, Gobet C, Naef F: Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans. Science. 2023; 379: 478–483. PubMed Abstract \| Publisher Full Text" }	[ { "id": "202732", "date": "18 Sep 2023", "name": "Jihwan Myung", "expertise": [ "Reviewer Expertise Circadian rhythms", "computational modeling of circadian clocks", "suprachiasmatic nucleus (SCN)", "bioluminescence reporter imaging" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript, the authors make a comprehensive exploration of the \"twist\" (amplitude-period correlation) in nonlinear oscillators, especially in the context of circadian rhythms. The Introduction insightfully summarizes the background and offers a clear explanation of the topic. While some sections exhibit a degree of coarseness in their explanations, the central theme remains consistently and clearly highlighted. Overall, this manuscript is a noteworthy addition to the field, and I recommend its acceptance for indexing with minor revisions.\nMinor comments:\n1. Abstract: I suggest changing \"..., fastening recovery...\" to either \"speeding up recovery\" or \"accelerating recovery\".\n2. p.4, subsection \"Goodwin-like models\": I recommend changing \"sigmoidal Hill curve\" to \"Hill curve\", as \"sigmoidal\" often refers to forms involving exponential functions.\n3. p.4, subsection \"Goodwin-like models\": Add biological interpretations of the variables x, y, and z (mRNA, ...).\n4. p.5. ll.4-5: While the Gonze model[33] describes degradation processes with Michaelis-Menten dynamics, it may not provide sufficient historical context. I recommend citing Kurosawa & Iwasa (2002)1 for a more comprehensive historical perspective.\n5. p.6, Table 2: The reference [36] should be spelled out in \"The default values are taken from [36].\n6. p.11. Figure 4: It is unclear if the graphs are figurative cartoons or based on actual numerical data from Gonze oscillators.\n7. pp.11-12: The justification for the use of the Almeida model can be described. For example, why not use the detailed Gonze model or Becker-Weimann model?\n8. p.13, ll.1-2: It is challenging to assert that the \"parametric twist\" emerges solely due to a heterogeneous population. While it describes the average oscillator behavior in a population (often assumed to be normally distributed), it essentially characterizes the behavior of a single representative oscillator.\n9. p.14, \"... 24 h, matching the intrinsic oscillator's frequency (Figure 7P).\": I suggest to rephrase it to \"... 24 h, matching the oscillator's intrinsic period (Figure 7P).\" The change from \"frequency\" to \"intrinsic period\" would provide more specificity and clarity.\n10. p.18 \"the longer period that has been observed in dispersed... , but not in dispersed SCN neurons in culture\": In light of the findings in Figure 5, it's noteworthy that when Bmal1 oscillation is observed (as opposed to Per2), the SCN period lengthens under pharmacological decoupling or physical sub-sectioning of the SCN (Myung et al., 20122),.\n11. p.18 \"Thus, a more plausible scenario may involve local coupling...\": Especially in the SCN, there are papers that highlight the role of specific coupling among subregions, which can reproduce the wave-like spatial patterns and seasonal encoding of circadian time. These can be discussed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11468", "date": "20 Jun 2024", "name": "Marta del Olmo", "role": "Author Response", "response": "Reviewer 3: Jihwan Myung, Graduate Institute of Mind, Brain and Consciousness (GIMBC), Taipei Medical University, Taipei, Taiwan In this manuscript, the authors make a comprehensive exploration of the \"twist\" (amplitude-period correlation) in nonlinear oscillators, especially in the context of circadian rhythms. The Introduction insightfully summarizes the background and offers a clear explanation of the topic. While some sections exhibit a degree of coarseness in their explanations, the central theme remains consistently and clearly highlighted. Overall, this manuscript is a noteworthy addition to the field, and I recommend its acceptance for indexing with minor revisions. Minor comments: 1. Abstract: I suggest changing \"..., fastening recovery...\" to either \"speeding up recovery\" or \"accelerating recovery\". 2. p.4, subsection \"Goodwin-like models\": I recommend changing \"sigmoidal Hill curve\" to \"Hill curve\", as \"sigmoidal\" often refers to forms involving exponential functions. 3. p.4, subsection \"Goodwin-like models\": Add biological interpretations of the variables x, y, and z (mRNA, ...). 4. p.5. ll.4-5: While the Gonze model[33] describes degradation processes with Michaelis-Menten dynamics, it may not provide sufficient historical context. I recommend citing Kurosawa & Iwasa (2002) for a more comprehensive historical perspective. 5. p.6, Table 2: The reference [36] should be spelled out in \"The default values are taken from [36]. 6. p.11. Figure 4: It is unclear if the graphs are figurative cartoons or based on actual numerical data from Gonze oscillators. 7. pp.11-12: The justification for the use of the Almeida model can be described. For example, why not use the detailed Gonze model or Becker-Weimann model? 8. p.13, ll.1-2: It is challenging to assert that the \"parametric twist\" emerges solely due to a heterogeneous population. While it describes the average oscillator behavior in a population (often assumed to be normally distributed), it essentially characterizes the behavior of a single representative oscillator. 9. p.14, \"... 24 h, matching the intrinsic oscillator's frequency (Figure 7P).\": I suggest rephrasing it to \"... 24 h, matching the oscillator's intrinsic period (Figure 7P).\" The change from \"frequency\" to \"intrinsic period\" would provide more specificity and clarity. 10. p.18 \"the longer period that has been observed in dispersed... , but not in dispersed SCN neurons in culture\": In light of the findings in Figure 5, it's noteworthy that when Bmal1 oscillation is observed (as opposed to Per2), the SCN period lengthens under pharmacological decoupling or physical sub-sectioning of the SCN (Myung et al., 2012). 11. p.18 \"Thus, a more plausible scenario may involve local coupling...\": Especially in the SCN, there are papers that highlight the role of specific coupling among subregions, which can reproduce the wave-like spatial patterns and seasonal encoding of circadian time. These can be discussed. We thank all three reviewers for their constructive comments and literature suggestions, which have helped improve our manuscript greatly. Below we summarize the changes that we have implemented in response to the reviewer’s suggestions: We have revised the manuscript and rephrased points 1, 2, 5 and 9. We have included the biological interpretation of the 3 variables in the Goodwin model in the Methods section. We have added the more historical reference on saturation kinetics for the degradation processes (Kurosawa and Iwasa, [1]). We have clarified in the caption of Figure 4, that the results are based on actual numerical data from Gonze oscillators. We have justified the use of the Almeida model. It is a simple enough model in the sense that it does not take into account post-translational modifications of the core clock proteins, nor nuclear import/export processes (which other more complex models of the mammalian clockwork do consider [2]), and complex enough in the sense that it contains synergies of feedback loops (the Per–Cry–Bmal1 loop, the Bmal1–Rev-Erb loop or Bmal1–Ror loop, which other older models do not take into account [3]). We have revised the text to clarify that while the term ‘parametric twist’ characterizes the average behavior of a population, it also provides a means to describe the behavior of a representative oscillator within that population. We have revised the Discussion to comment on the findings of Myung et al. [4], namely that Bmal1 rhythms in the SCN, in contrast to Per2 oscillations, exhibit longer periods when the SCN is pharmacologically decoupled or physically subdivided. In the discussion, we have further elaborated on coupling within the SCN and how it has been shown to regulate complex phenomena like wave-like spatial patterns and even encode seasonality. References Kurosawa, G., & Iwasa, Y. (2002). Saturation of enzyme kinetics in circadian clock models. Journal of Biological Rhythms, 17(6), 568-577. Relógio, A., Westermark, P. O., Wallach, T., Schellenberg, K., Kramer, A., & Herzel, H. (2011). Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Computational Biology, 7(12), e1002309. Becker-Weimann, S., Wolf, J., Herzel, H., & Kramer, A. (2004). Modeling feedback loops of the mammalian circadian oscillator. Biophysical Journal, 87(5), 3023-3034. Myung, J., Hong, S., Hatanaka, F., Nakajima, Y., De Schutter, E., & Takumi, T. (2012). Period coding of Bmal1 oscillators in the suprachiasmatic nucleus. Journal of Neuroscience, 32(26), 8900-8918." } ] }, { "id": "202731", "date": "18 Sep 2023", "name": "Stephanie Taylor", "expertise": [ "Reviewer Expertise I study the response of limit cycle oscillators to signals and sensitivity analysis involving isochrons." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article, the authors describe the phenomenon of twist (period-amplitude inter-dependence) using a range of differential equation oscillator models, ultimately with a view to understanding circadian clocks. The simplest models (harmonic and Duffing) are used to demonstrate the non-linearity introduces a relationship between amplitude and period. The authors then switch to limit-cycle oscillators, because limit-cycle oscillators are more appropriate for studying circadian clocks. They use two approaches to studying twist. The first, referred to as \"parametric twist\", computes the periods and amplitudes of oscillators with varied parameter values, creating graphs that relates period to amplitude (and thus demonstrate twist - if the correlation is positive, there is positive twist, and negative correlation indicates negative twist). This parametric twist analysis is performed using two limit cycle models, one with one feedback loop and one with more (synergistic) loops. The second, referred to as \"phase space twist\", examines the response of a single oscillator to a temporary change in one parameter, mimicking signaling. A separate limit-cycle model (a Poincare oscillator) is used for this analysis. Important to the discussion of phase space twist is the concept of isochrons, which are useful for understanding the effects of perturbations on the phase and speed of the clock (does it speed up or slow down the clock?) and it is easy to see how amplitude and phase response are related, when we look at how curved the isochrons are. The authors relate these analyses to phase response curves, recovery from jetlag, the range of entrainment, and temperature compensation and conclude, that although measuring amplitude and understanding relationship between amplitude and period are highly complicated, it is nonetheless important to be mindful of the role of amplitude and its correlation to period when studying clocks.\nOn the one hand, I really appreciated that the authors chose models that best illustrated the points and that the paper is organized to go from simple ideas to more complex ideas. It was helpful to have the initial explanation of twist use duffing oscillator (which has non-linearity) as a contrast to a harmonic oscillator (which doesn't). It provided a nice introduction to the cause of twist and helped me to develop an intuition. Then, it made sense to use a very simple (3-ODE Goodwin oscillator) as the first example of a limit cycle oscillator. Since it has so few parameters, it was possible to perturb them one at a time and in pairs to illustrate a good portion of the possibilities for how one might observe heterogeneity in the system. Then, moving to Almeida's oscillator demonstrated how quickly the analysis can become very complex. All of this provides a nice progression of complexity. Then, we pivot a bit to the Poincare oscillator, to study twist in a more dynamical way - instead of permanently choosing different parameters, the authors model light signaling (at least, initially) and study the effects of the model returning to its limit cycle after the perturbation is over. This model is particularly appropriate for studying the dynamics of recovery because it is a 2-ode model (so we can examine it in \"phase space\", which is helpful for visualizing the clock) and because there is a parameter that controls how related period and amplitude are. It is also straight-forward to adjust how curved the isochrons are, which makes illustrating twist very clear. Then, after studying the response of a single oscillator to light, they use the same model to study the effects of intercellular signaling and the effects of different twist on the properties of the ensemble oscillation (e.g. how long the ensemble period is in contrast to that of individual oscillators).\nOn the other hand, I would have appreciated a more explicit connection between the discussion of \"parametric twist\" and \"phase space twist\". They are both due to changes in parameter values causing changes in period and amplitude. In the one case, we measure the period and amplitude of oscillators with different (constant) parameter values. In the second case, we measure instantaneous changes in period and amplitude due to a temporary changes in parameter values (I am referring to Z(t) as a parameter here). In both cases, the shape of the isochrons in the unperturbed condition should help us to predict what will happen in the perturbed condition. There are two challenges with making that point clear with the Goodwin and Almeida models - 1) the isochrons aren't lines, they are multi-dimensional manifolds, and 2) the isochrons in the unperturbed and perturbed systems are different. So I am asking for too much to relate the two discussions by using images of isochrons, but a more explicit comparison would help the reader understand how the analyses are related to each other.\nIn the analysis of the modified Poincare oscillator, the term \"twist\" is used differently than it is in the \"parametric twist\" analysis. In the parametric analysis, the twist captures the full effects of the perturbations (we plot the measured periods and amplitudes across the heterogeneous set of oscillators). In the phase space analysis, \"twist\" refers to a particular parameter \\epsilon that, when non-zero, introduces a dependence of the speed and amplitude on each other. However, that twist parameter (\\epsilon) is not the only parameter that affects the skewness of the isochrons. The relaxation rate \\lambda also affects the skewness of the isochrons. And the skewness of the isochrons affects the changes in speed and amplitude when the oscillator is signaled (i.e. a parameter is temporarily perturbed). So, if we were to measure the effects on period and amplitude (as is done with figures 7G, H, and I), that reflects that values of both \\lambda and \\epsilon. When I was thinking about how to relate the \"parametric twist\" and \"phase twist\" analysis, I was looking for aspects of figures 3 (Gonze model), 5 (Almeida model), and 7 (poincare model) to relate and it seemed to me that that the subfigures that related the amplitude of the oscillator to its period (3C, 3D, 3E, 3F, 3G, 3H, 5B, 5B, 5E, 7G, 7H, 7I) should be the figures that I can connect. They are labeled as twist in figures 3 and 5. In Figure 7, they show an approximation of instantaneous amplitude and period (rather than steady-state amplitude and period), so it isn't a perfect 1-1 mapping, but it is still the closest that makes sense to me. And in all of these cases, the output could be labeled twist if \\epsilon didn't get to claim that label. I think it would make the concept of twist clearer to the reader if it were consistent across both analyses that twist is the \"effect\" we can measure. My reading of the text as it is currently written is that twist is a phenomenon we can measure in \"parametric twist\" analyses and that twist is a parameter that causes one change in the isochrons (but not all of the changes that can happen) that ultimately leads to something we can measure. Also, labeling the parameter as twist in the Poincare oscillator makes it seem like we need to use the Poincare oscillator to perform a \"phase space twist\" analysis. But we aren't limited to the Poincare oscillator for such analyses.\nSpecific Points\nIt would be helpful to have a little more framing text that indicates the different models are used to make different points.\n\nI think of the \"phase space twist\" analysis as analysis of recovery from temporary changes to parameters and \"parametric twist\" as analysis of permanent differences in parameters. If that is the way you intend readers to think about it, then I would suggest changing the names to reflect those ideas more directly. Right now, the term \"phase space twist\" stands out as a highly specific analysis - the model most be 2D so you can draw the isochrons. But I think that is limiting. I totally embrace idea that there is both heterogeneity among oscillators and temporary changes due to intercellular signaling, so I would love to see it characterized that way more explicitly. What about \"twist due to heterogeneity\" and \"twist due to signaling\"? They aren't quite zippy enough and rely on my characterization of twist as a measurable phenomenon, so I don't push those terms exactly.\n\nOn page 8, when you are introducing isochrons, it would be helpful to have a figure to refer to. The most natural figure is Figure 7, but that would force you to make an unnatural re-ordering of the figures. So maybe introduce a new figure?\n\nOn Page 11, (analyses shown in Figure 3), how did you choose which parameters to pair together?\n\nOn Page 11, there is a discussion of the Hopf bifurcation that is interesting (and highlights how sensitivity twist is to our choice of parameters). It occurs to me that this has implications for modeling SCN oscillators as they recover from TTX treatment. The individual oscillator amplitude crashes and the oscillators lose synchrony during TTX and both recover after TTX is washed out. Is there anything you could add to the discussion about this?\n\nOn Page 12, in the paragraph about how overall twist effects depend not only on the parameter being studies, but also on the variable that is measured, I was reminded of early modeling studies that showed not-immediately intuitive results. In his 1995 fly model paper (A model of circadian oscillations in the Drosophila period protein, Proc. R. Soc. Lond. B, 1995), Goldbeter showed that the rate of (doubly-phosphorylated) PER degradation affected both period and amplitude and that increasing this rate led to PER amplitude increasing (rather than decreasing, as one might expect). This can be reasoned through, but it is another illustration of the complexity of the non-linear feedback and the relationship between period and amplitude. Is this worth bringing up here or on the discussion?\n\nFigure 6. Why are there no yellow dots on the limit cycle for A and B? Also, maybe make the dot color on the limit cycle different from yellow (e.g. to blue), so that you can describe what is happening over time with even more clarity (i.e. that the simulation eventually reaches the \"blue\" dot after enough cycles).\n\nFigure 8 and text referring to it. I appreciate that you relate twist to entrainment and PRCs. I think this is interesting and shows why twist is important to understand.\n\nPage 16 first paragraph. \"This suggests that single oscillator twist might also affect how coupling synchronizes a network of oscillators\" is too weak. Given that coupling (M) and the perturbation used in Figure 7 (Z(t)) both affect the model the same way (they both are added to the rate equation for the x variable), Figure 7 shows that the PRCs are affected by twist. Not only are they affected, they are affected dramatically - Figures 7K and 7L look like they are opposite each other (i.e. flipped sign). This means we are guaranteed that the oscillators will respond differently to intercellular signaling and that that the ensemble oscillation will be different.\n\nPage 16, in the discussion of the ensemble period, we see that for this model that positive twist leads to longer periods (and negative twist to shorter). What is missing from this discussion is that the relative phase of the signal and of the PRC of the receiver determine the period of the ensemble. Positive twist leads to longer periods because the mean field is determined by the value of the x variable. If it were determined by a variable with the opposite phase, then we would have the opposite effect. This affects the related paragraph in the Discussion as well.\n\nPage 17. The meaning of \"For this reason we have not termed twist, in the context of conservative oscillations, parametric or phase space\" wasn't clear to me. I think you mean you can't study twist in non-limit-cycle oscillators in the same way you can for limit cycle oscillators. Is that correct?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11470", "date": "20 Jun 2024", "name": "Marta del Olmo", "role": "Author Response", "response": "Reviewer 2: Stephanie Taylor, Department of Computer Science, Colby College, Waterville, Maine, USA We thank all three reviewers for their constructive comments and literature suggestions, which have helped improve our manuscript greatly. Below we give a detailed response to the individual comments. In this article, the authors describe the phenomenon of twist (period-amplitude inter-dependence) using a range of differential equation oscillator models, ultimately with a view to understanding circadian clocks. The simplest models (harmonic and Duffing) are used to demonstrate that nonlinearity introduces a relationship between amplitude and period. The authors then switch to limit-cycle oscillators, because limit-cycle oscillators are more appropriate for studying circadian clocks. They use two approaches to studying twist. The first, referred to as \"parametric twist\", computes the periods and amplitudes of oscillators with varied parameter values, creating graphs that relates period to amplitude (and thus demonstrate twist - if the correlation is positive, there is positive twist, and negative correlation indicates negative twist). This parametric twist analysis is performed using two limit cycle models, one with one feedback loop and one with more (synergistic) loops. The second, referred to as \"phase space twist\", examines the response of a single oscillator to a temporary change in one parameter, mimicking signaling. A separate limit-cycle model (a Poincare oscillator) is used for this analysis. Important to the discussion of phase space twist is the concept of isochrons, which are useful for understanding the effects of perturbations on the phase and speed of the clock (does it speed up or slow down the clock?) and it is easy to see how amplitude and phase response are related, when we look at how curved the isochrons are. The authors relate these analyses to phase response curves, recovery from jetlag, the range of entrainment, and temperature compensation and conclude, that although measuring amplitude and understanding relationship between amplitude and period are highly complicated, it is nonetheless important to be mindful of the role of amplitude and its correlation to period when studying clocks. On the one hand, I really appreciated that the authors chose models that best illustrated the points and that the paper is organized to go from simple ideas to more complex ideas. It was helpful to have the initial explanation of twist using a duffing oscillator (which has non-linearity) as a contrast to a harmonic oscillator (which doesn't). It provided a nice introduction to the cause of twist and helped me to develop an intuition. Then, it made sense to use a very simple (3-ODE Goodwin oscillator) as the first example of a limit cycle oscillator. Since it has so few parameters, it was possible to perturb them one at a time and in pairs to illustrate a good portion of the possibilities for how one might observe heterogeneity in the system. Then, moving to Almeida's oscillator demonstrated how quickly the analysis can become very complex. All of this provides a nice progression of complexity. Then, we pivot a bit to the Poincare oscillator, to study twist in a more dynamical way - instead of permanently choosing different parameters, the authors model light signaling (at least, initially) and study the effects of the model returning to its limit cycle after the perturbation is over. This model is particularly appropriate for studying the dynamics of recovery because it is a 2-ode model (so we can examine it in \"phase space\", which is helpful for visualizing the clock) and because there is a parameter that controls how related period and amplitude are. It is also straight-forward to adjust how curved the isochrons are, which makes illustrating twist very clear. Then, after studying the response of a single oscillator to light, they use the same model to study the effects of intercellular signaling and the effects of different twist on the properties of the ensemble oscillation (e.g. how long the ensemble period is in contrast to that of individual oscillators). On the other hand, I would have appreciated a more explicit connection between the discussion of \"parametric twist\" and \"phase space twist\". They are both due to changes in parameter values causing changes in period and amplitude. In the one case, we measure the period and amplitude of oscillators with different (constant) parameter values. In the second case, we measure instantaneous changes in period and amplitude due to temporary changes in parameter values (I am referring to Z(t) as a parameter here). In both cases, the shape of the isochrons in the unperturbed condition should help us to predict what will happen in the perturbed condition. There are two challenges with making that point clear with the Goodwin and Almeida models - 1) the isochrons aren't lines, they are multi-dimensional manifolds, and 2) the isochrons in the unperturbed and perturbed systems are different. So I am asking for too much to relate the two discussions by using images of isochrons, but a more explicit comparison would help the reader understand how the analyses are related to each other. We thank the reviewer for this insightful observation that we have also spent a lot of time thinking about, and for which we lack a clear answer. However, we aim to shed light on some thoughts that may help clarify the distinctions (and similarities) between parametric and phase space twist. The concept “twist” was historically coined on conservative, non-limit cycle oscillations. It was first described in the Duffing oscillator [1] –an adaptation of the harmonic oscillator with an additional nonlinear term. This nonlinear term introduces unique properties to the system, as depicted in our Figure 1 from the manuscript: whereas harmonic, linear oscillators have no amplitude-period co-dependencies, the introduction of nonlinearities in the harmonic oscillator result in amplitude-period correlations, i.e. twist. Unlike limit cycle oscillators, non-limit cycle oscillators are conservative and do not dissipate energy. In more practical terms, this means that the initial conditions persist indefinitely, as no energy is dissipated, and thus the oscillator’s amplitude is defined by initial conditions (or by the energy of the system). Most biological oscillations, however, are of limit cycle type. Limit cycles are dissipative, and different initial conditions relax (i.e., lose energy) and converge to the stable cycle, characterized by a given period and amplitude. In limit cycle oscillations, twist has to be studied in a different way than it is studied for non-limit cycle oscillators. Because different initial conditions do not produce different cycles, if we want to study how amplitudes and periods correlate in different cycles, one has to study this by altering parameters in the model. This is what we have termed parametric twist: the amplitude-period correlations arising from changes in model parameters, thus altering the original limit cycle slightly. Another form of amplitude-period correlations can occur within an oscillator’s time series: what we term phase space twist. In a perfect stable limit cycle, period and amplitude do not change from cycle to cycle. But upon its interaction with the environment, the oscillator encounters perturbations that modify its amplitude and period transiently. The transient correlations between period and amplitude that appear as the oscillator relaxes and “adapts” to the perturbation is what we have termed “phase space twist” throughout our analyses. This is related to Winfree’s “invention” of isochrones in phase space [2]. Such “transient” correlations (i.e., phase space twist), have implications for PRCs, entrainment and coupling, as shown in Figure 7 and Figure 9. In the realm of conservative systems, one does not need the distinction between phase space twist and parametric twist, as isochrones lack the relevance that they hold in limit cycles. It is for this reason that we have exclusively introduced these terms in the “limit cycle world”. While in phase space twist, isochrones are well defined manifolds, in the “world of parametric twist”, each new limit cycle has its own properties and isochrone manifolds, which makes the manifolds of parametric twist very difficult to visualize graphically. In the analysis of the modified Poincare oscillator, the term \"twist\" is used differently than it is in the \"parametric twist\" analysis. In the parametric analysis, the twist captures the full effects of the perturbations (we plot the measured periods and amplitudes across the heterogeneous set of oscillators). In the phase space analysis, \"twist\" refers to a particular parameter \\epsilon that, when non-zero, introduces a dependence of the speed and amplitude on each other. However, that twist parameter (\\epsilon) is not the only parameter that affects the skewness of the isochrons. The relaxation rate \\lambda also affects the skewness of the isochrons. And the skewness of the isochrons affects the changes in speed and amplitude when the oscillator is signaled (i.e. a parameter is temporarily perturbed). So, if we were to measure the effects on period and amplitude (as is done with figures 7G, H, and I), that reflects that values of both \\lambda and \\epsilon. When I was thinking about how to relate the \"parametric twist\" and \"phase twist\" analysis, I was looking for aspects of figures 3 (Gonze model), 5 (Almeida model), and 7 (poincare model) to relate and it seemed to me that that the subfigures that related the amplitude of the oscillator to its period (3C, 3D, 3E, 3F, 3G, 3H, 5B, 5B, 5E, 7G, 7H, 7I) should be the figures that I can connect. They are labeled as twist in figures 3 and 5. In Figure 7, they show an approximation of instantaneous amplitude and period (rather than steady-state amplitude and period), so it isn't a perfect 1-1 mapping, but it is still the closest that makes sense to me. And in all of these cases, the output could be labeled twist if \\epsilon didn't get to claim that label. I think it would make the concept of twist clearer to the reader if it were consistent across both analyses that twist is the \"effect\" we can measure. My reading of the text as it is currently written is that twist is a phenomenon we can measure in \"parametric twist\" analyses and that twist is a parameter that causes one change in the isochrons (but not all of the changes that can happen) that ultimately leads to something we can measure. Also, labeling the parameter as twist in the Poincare oscillator makes it seem like we need to use the Poincare oscillator to perform a \"phase space twist\" analysis. But we aren't limited to the Poincare oscillator for such analyses. We acknowledge the reviewer's valid point regarding the unclear distinction between the \\epsilon parameter and phase space twist effects, which sometimes led to confusion. To address this, we now explicitly define phase space twist as the observable amplitude-period correlations in an oscillator's response to a perturbation—the measurable 'phenotype'. The reviewer is right that in the Poincaré oscillator, phase space twist effects are a consequence of the \\epsilon parameter. However, other models might also display such correlations without the explicit \\epsilon parameter. We have clarified this in the Methods and in the Discussion. Moreover, as the reviewer correctly points out, \\epsilon is not the only parameter influencing the skewness of isochrones, also \\lambda plays a role. Thus, both \\epsilon and \\lambda modulate the extent of phase space twist effects that become apparent in an oscillator as it encounters and responds to a perturbation. We have revised Figure 8 in the manuscript and added panels to show the phase space twist effects for oscillators with the same \\epsilon but changing \\lambda values. We now show how the correlation between both variables decreases for oscillators with higher amplitude relaxation rates \\lambda. We have revised the manuscript to consistently refer to the \\epsilon parameter as the \"twist parameter \\epsilon\" (like in prior studies [3]), clarifying that phase space twist denotes the amplitude-period correlations emerging from varying \\epsilon and \\lambda values. Specific Points: It would be helpful to have a little more framing text that indicates the different models are used to make different points. We have justified the use of the different models. I think of the \"phase space twist\" analysis as analysis of recovery from temporary changes to parameters and \"parametric twist\" as analysis of permanent differences in parameters. If that is the way you intend readers to think about it, then I would suggest changing the names to reflect those ideas more directly. Right now, the term \"phase space twist\" stands out as a highly specific analysis - the model must be 2D so you can draw the isochrons. But I think that is limiting. I totally embrace the idea that there is both heterogeneity among oscillators and temporary changes due to intercellular signaling, so I would love to see it characterized that way more explicitly. What about \"twist due to heterogeneity\" and \"twist due to signaling\"? They aren't quite zippy enough and rely on my characterization of twist as a measurable phenomenon, so I don't push those terms exactly. In response to the reviewer’s on-point comment, we have clarified what are the “practical” implications of parametric and phase space twist throughout the revised text, but without changing the terminology. We wish to highlight here again, that whereas phase space twist refers to the transient amplitude-period changes that a limit cycle oscillator suffers when it encounters a perturbation (with consequences for coupling and entrainment), the concept of parametric twist “lives” in the domain of oscillator heterogeneity. Although parametric twist might be an intrinsic property of an oscillator (i.e. cells of the choroid plexus show negative twist; whereas U-2 OS cells are positive twist oscillators), it only becomes evident in heterogeneous systems, when different parameter schemes (i.e. oscillator heterogeneity) come into play. On page 8, when you are introducing isochrons, it would be helpful to have a figure to refer to. The most natural figure is Figure 7, but that would force you to make an unnatural re-ordering of the figures. So maybe introduce a new figure? We refer to the section from the Results already in the Materials and Methods, when we introduce the definition of isochrones. We opted against adding a new figure in the Methods section because, in our eyes, it would be redundant with the current Figure 7. We believe that this figure is more needed in the Results section, where we emphasize in the text how isochrones and the parameters \\epsilon and \\lambda can affect the acceleration at which a perturbation relaxes back to the limit cycle. On Page 11, (analyses shown in Figure 3), how did you choose which parameters to pair together? We paired all degradation parameters with each other, namely k2 with k4, k4 with k6 and k6 with k2, but we only show two representative pairs. We have clarified that in the revised text and in the caption of Figure 3. On Page 11, there is a discussion of the Hopf bifurcation that is interesting (and highlights how sensitivity twist is to our choice of parameters). It occurs to me that this has implications for modeling SCN oscillators as they recover from TTX treatment. The individual oscillator amplitude crashes and the oscillators lose synchrony during TTX and both recover after TTX is washed out. Is there anything you could add to the discussion about this? We thank the reviewer for this observation. One of the messages of Figure 4 is indeed that parametric twist in an ensemble of oscillators is sensitive to the default parameter set of an individual oscillator. However, it is important to highlight that the analysis in that figure refers to uncoupled oscillators. The results shown in the Figure could be regarded as a population of oscillators with heterogeneous k4 values. Depending on how ‘spreaded’ such heterogeneity is, the expected parametric twist will be different. While a population of oscillators with small deviations around the default value k4=0.35, let’s say ±5%, would likely result in a population where one would almost have no (or partly positive) parametric twist (see Figure 4C, the variation in k4 would result in very minor differences in periods and peak-trough distances), a population of oscillators with larger heterogeneity in their k4 values would span a larger region of the bubble, resulting in complex parametric twist effects (both positive and negative, see Figure 4C). Coupling in the SCN (or in any other oscillatory network) is expected to reduce the phenotypic differences in their periods and amplitude distributions, reducing the period heterogeneity (at least to some extent) and increasing amplitude due to resonance effects [4]. For this reason, we would expect that, upon overcritical coupling, the population of uncoupled oscillators with heterogeneous k4 values oscillates at a common period and amplitude. In other words, coupling would reduce, at least to some extent, the degree of parametric twist in a population of heterogeneous oscillators. Upon disruption of inter-oscillator coupling, such as TTX treatment in the SCN, one would expect the oscillators to return to their ‘original’ degree of parametric twist. We have added a short paragraph on the Discussion on how coupling is expected to affect parametric twist. On Page 12, in the paragraph about how overall twist effects depend not only on the parameter being studied, but also on the variable that is measured, I was reminded of early modeling studies that showed not-immediately intuitive results. In his 1995 fly model paper (A model of circadian oscillations in the Drosophila period protein, Proc. R. Soc. Lond. B, 1995), Goldbeter showed that the rate of (doubly-phosphorylated) PER degradation affected both period and amplitude and that increasing this rate led to PER amplitude increasing (rather than decreasing, as one might expect). This can be reasoned through, but it is another illustration of the complexity of the non-linear feedback and the relationship between period and amplitude. Is this worth bringing up here or on the discussion? We have discussed this point (and added the respective reference [5]) in the discussion and highlighted that different oscillator models (which have different nonlinear dependencies) result in different parametric twist effects. For this reason, it is important to know what is the type of twist in a population of oscillators (experimentally), to be able to devise a model that captures such properties. Figure 6. Why are there no yellow dots on the limit cycle for A and B? Also, maybe make the dot color on the limit cycle different from yellow (e.g. to blue), so that you can describe what is happening over time with even more clarity (i.e. that the simulation eventually reaches the \"blue\" dot after enough cycles). We have added yellow dots on the limit cycles for A and B. We have revised the text to more clearly describe what happens over time. Figure 8 and text referring to it. I appreciate that you relate the twist to entrainment and PRCs. I think this is interesting and shows why twist is important to understand. We would like to thank the reviewer for the positive comment. Page 16 first paragraph. \"This suggests that single oscillator twist might also affect how coupling synchronizes a network of oscillators\" is too weak. Given that coupling (M) and the perturbation used in Figure 7 (Z(t)) both affect the model the same way (they both are added to the rate equation for the x variable), Figure 7 shows that the PRCs are affected by twist. Not only are they affected, they are affected dramatically - Figures 7K and 7L look like they are opposite each other (i.e. flipped sign). This means we are guaranteed that the oscillators will respond differently to intercellular signaling and that the ensemble oscillation will be different. We thank the reviewer for the suggestion. We have now strengthened that point in the revised manuscript. Page 16, in the discussion of the ensemble period, we see that for this model that positive twist leads to longer periods (and negative twist to shorter). What is missing from this discussion is that the relative phase of the signal and of the PRC of the receiver determine the period of the ensemble. Positive twist leads to longer periods because the mean field is determined by the value of the x variable. If it were determined by a variable with the opposite phase, then we would have the opposite effect. This affects the related paragraph in the Discussion as well. We appreciate the reviewer's clarification regarding the dependence of phase on the direction of pulse-like perturbations, and we agree with the observation that pulses of opposite directions induce different phase shifts. However, in Figure 9 we present analyses that offer a comparable scenario to the dynamics observed in chronotypes, albeit without an external zeitgeber. Instead, we focus on examining the long-term effects on the rhythmic properties of coupled oscillators. First, we show that mean-field coupling between two identical oscillators leads to amplitude expansions (Supplementary Figure S2) and period alterations dependent on the twist parameter \\epsilon (Figure 9A). Subsequently, we couple three Poincaré oscillators, which differ only in their \\epsilon values, via their mean field (the arrow in Figure 9B indicates when mean-field coupling is ‘turned on’). We observe an increase in the amplitude of individual oscillators (consistent with Supplementary Figure S2). Although the periods of all three oscillators (as well as that of the mean-field) synchronize due to coupling, their phases relative to the mean field rhythm align with our predictions from Figure 9A and the theory from chronotypes: the oscillator with negative \\epsilon exhibits an advanced rhythm compared to the mean field, while the oscillator with positive \\epsilon displays a delayed rhythm relative to the mean field. These results remain consistent regardless of whether mean-field coupling is introduced in the x or y coordinate of the Poincaré oscillator. The observation from Figure 9B is consistent with our findings in Figure 9A, where the phase delay of the oscillator with positive \\epsilon aligns with this clock displaying longer periods upon coupling. This phenomenon resonates with chronotypes, where individuals with longer free-running periods have later phases of entrainment. Page 17. The meaning of \"For this reason we have not termed twist, in the context of conservative oscillations, parametric or phase space\" wasn't clear to me. I think you mean you can't study twist in non-limit-cycle oscillators in the same way you can for limit cycle oscillators. Is that correct? That is correct (also related to the first point of the report). We have clarified it throughout the revised manuscript. References Duffing, G. (1918). Erzwungene Schwingungen bei veränderlicher Eigenfrequenz und ihre technische Bedeutung (No. 41-42). Vieweg. Winfree, A. T. (1980). The geometry of biological time (Vol. 2). New York: Springer. Myung, J., Schmal, C., Hong, S., Tsukizawa, Y., Rose, P., Zhang, Y., ... & Takumi, T. (2018). The choroid plexus is an important circadian clock component. Nature Communications, 9(1), 1062. Schmal, C., Herzog, E. D., & Herzel, H. (2018). Measuring relative coupling strength in circadian systems. Journal of Biological Rhythms, 33(1), 84-98. Goldbeter, A. (1995). A model for circadian oscillations in the Drosophila period protein (PER). Proceedings of the Royal Society of London. Series B: Biological Sciences, 261(1362), 319-324." } ] }, { "id": "202730", "date": "29 Sep 2023", "name": "Jae Kim", "expertise": [ "Reviewer Expertise Circadian rhythms", "mathematical modeling" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have conducted a study on the relationship between amplitude and period in various circadian clock models. However, it is crucial to address the novelty and distinctions of this study compared to prior work, specifically the study by Bokka et al. in 2018 (https://doi.org/10.1049/iet-syb.2018.0015). Additionally, while the models in this manuscript are based on Hill-type repression (such as the Goodwin and Gonze models), it is important to acknowledge recent research findings that reveal different repression mechanisms in the Drosophila (https://doi.org/10.1073/pnas.2113403119) and mammalian circadian clocks (https://doi.org/10.1098/rsfs.2021.0084). These studies demonstrate that the use of multiple repression mechanisms, including protein sequestration, can substantially alter the oscillator dynamics (https://doi.org/10.1049/iet-syb.2015.0090). Given these discoveries, it would be valuable to explore or discuss how different repression mechanisms impact the relationship between period and amplitude, as demonstrated by Bokka et al. in 2018.\n\nIn the Conclusions section on page 19, please provide a reference for 'cellular biochemical rates' as a factor influencing circadian amplitudes. For instance, it was demonstrated that faster production and degradation rates of proteins can generate circadian rhythms with higher amplitudes in the Drosophila circadian clock (https://doi.org/10.1073/pnas.2113403119).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11469", "date": "20 Jun 2024", "name": "Marta del Olmo", "role": "Author Response", "response": "Reviewer 1: Jae Kim, Department of Mathematical Sciences, KAIST, Daejeon, South Korea The authors have conducted a study on the relationship between amplitude and period in various circadian clock models. However, it is crucial to address the novelty and distinctions of this study compared to prior work, specifically the study by Bokka et al. in 2018 (https://doi.org/10.1049/iet-syb.2018.0015). Additionally, while the models in this manuscript are based on Hill-type repression (such as the Goodwin and Gonze models), it is important to acknowledge recent research findings that reveal different repression mechanisms in the Drosophila (https://doi.org/10.1073/pnas.2113403119) and mammalian circadian clocks (https://doi.org/10.1098/rsfs.2021.0084). These studies demonstrate that the use of multiple repression mechanisms, including protein sequestration, can substantially alter the oscillator dynamics (https://doi.org/10.1049/iet-syb.2015.0090). Given these discoveries, it would be valuable to explore or discuss how different repression mechanisms impact the relationship between period and amplitude, as demonstrated by Bokka et al. in 2018. We thank all three reviewers for their constructive comments and literature suggestions, which have helped improve our manuscript greatly. We have included a paragraph in the Discussion addressing how our manuscript supports and builds upon the findings from Bokka et al. [1]. The authors conduct a comprehensive analysis of parametric twist in different ODE-based models that have been used to model biological oscillatory processes but do not study phase space twist. They classify the models depending on how amplitudes and periods co-vary, where their type 1 corresponds to positive amplitude-period co-variation (what we have termed positive parametric twist in our manuscript) and type 2, to negative amplitude-period correlations (negative twist). The authors consider additional correlations, e.g. constant amplitude but changing period, constant period but changing amplitude (both of which we consider no twist) or more complex co-variations of combinations of positive and negative twist effects. Among these models, the authors study the Goodwin model. Their analysis of the Goodwin model shows that, for changes in k2, amplitude increases but period remains constant (i.e. no twist). For changes in k4, amplitude increases and period decreases (negative twist). Lastly, for changes in k6, both amplitude and period decrease (positive twist). This is in contrast to our bifurcation analyses, which revealed positive correlations of amplitude and period upon changes in k2 or k4, but a negative correlation upon changes of k6. The differences in our and their results might stem from 3 sources: A possible explanation might come from the fact that the authors define amplitude as an absolute value of the difference between peak and trough of oscillations, whereas we define amplitude as a relative measure (difference between peak and trough of the oscillation but normalized to the mean). While we have used the x variable from the Goodwin system to define amplitude, it is unclear from the main text in [1] which variable is used from the whole ODE system to define amplitude. Period is expected to change equally for all the variables upon change of one parameter; amplitude, however, might change differently for the different model variables (as shown in our Figure 5B, Figure 5E). This highlights again the difficulty in defining amplitude in circadian studies. Bokka et al. [1] partly circumvent this issue by defining amplitude as the geometric mean of all biomolecular species in the model. This metric, nevertheless, is difficult to measure in or translate to an experimental setup, as (i) the circadian network does not yet agree on what are the core elements of the clock network for a particular species, and (ii) even if we all agreed on the same core clock elements, it is often not possible to measure all the species at the same time within one experiment. Moreover, additional differences may stem from the fact that we have used a different parameter set than the one in the original Goodwin model [2] to generate circadian oscillations (taken and adapted from [3] as indicated in Table 1 in the main text), and thus our default parameter set might be at a different region of the Hopf bubble. Interestingly, the authors describe the presence of a ‘forbidden region’, where oscillations with large amplitude but small periods (or fast frequencies) might be difficult. This is consistent with oscillations emerging from Hopf bifurcations. It would be interesting to study the amplitude-period correlations on oscillations that arise after other types of bifurcation points, including a saddle-node-on-invariant cycle (SNIC), but such analyses are out of the scope of this manuscript. Tsai and colleagues showed in [4] how systems with positive feedback loops can present high amplitude and high frequency rhythms and thus the ‘forbidden region’ might differ. In a more theoretical study by Bose [5], it is also shown how the onset of oscillations through a Hopf bifurcation does not allow for high frequency rhythms, whereas when oscillations emerge through a SNIC bifurcation, periods increase more gradually. We would also like to acknowledge the reviewer’s on-point comment on the existence of different repression mechanisms in different species, which we also have discussed in the manuscript. For example, in Drosophila and in mammals, inhibition of transcriptional activity is achieved through the formation of a 1:1 stoichiometric complex between activators and inhibitors [6-10]. In this type of repression mechanism, frequently termed protein sequestration-based repression [11, 12], repressors tightly bind to activators to form an inactive 1:1 stoichiometric complex, thus ‘sequestering’ the activator. Such protein sequestration processes can be described with terms that differ from the Hill function [11, 12]. In other species, like Neurospora, the stoichiometry between activators and repressors in nuclei is much less than 1:1 [13]. In this fungus, a large number of phosphorylation sites in the activator is required for self-sustained oscillations. As the number of mutated phosphorylation sites increases, the circadian rhythms become weaker and finally arrhythmic [13]. Such multistep cooperative reactions can be described with Hill curves [14, 15]. It is important to note that there is also evidence supporting an additional mode of repression in the mammalian TTFL mediated by CRY1 alone. After inhibition of the CLOCK:BMAL1 activator complex by the macromolecular repressive complex containing PER and CRY proteins, delayed expression of CRY1 can still independently repress transcription from E-boxes [16-19]. This mode of repression cannot be explained according to a protein sequestration repression, and occurs through direct blocking of the activators [18-20]. Such a blocking-type of inhibition might be accurately modeled with a Hill function, especially provided the observations that CRY1 is gradually phosphorylated until it becomes the late monomeric repressive CRY1 [21]. Such multistep phosphorylations, as mentioned earlier, can be described with the use of Hill functions. Depending on whether the design of a TTFL contains a Hill-type or a protein sequestration-based repression mechanism, the conditions to achieve self-sustained limit cycle oscillations are different [11]. Models that are based on a Hill-type repression need a large Hill exponent in order to generate self-sustained oscillations, whereas models based on a sequestration repression need a 1:1 stoichiometry between repressor and activator for a successful onset of oscillations. Our manuscript only addresses models that use Hill functions to model transcriptional repression and we have partly extended the discussion to account for additional modes of repression. However, given our and others’ [1] observations that all kinds of parametric twist effects are possible upon changing one parameter in a certain model, we expect that protein sequestration-based models might also result in complex parametric twist effects upon changes of one parameter that likely depend on the default parameter set of the model (and where this is located at within the Hopf bubble) as well as on the variable whose amplitude is being measured. In the Conclusions section on page 19, please provide a reference for 'cellular biochemical rates' as a factor influencing circadian amplitudes. For instance, it was demonstrated that faster production and degradation rates of proteins can generate circadian rhythms with higher amplitudes in the Drosophila circadian clock (https://doi.org/10.1073/pnas.2113403119). We have now added the reference [22] to our conclusions. References Bokka, V., Dey, A., & Sen, S. (2018). Period–amplitude co‐variation in biomolecular oscillators. IET Systems Biology, 12(4), 190-198. Goodwin, B. C. (1965). Oscillatory behavior in enzymatic control processes. Advances in Enzyme Regulation, 3, 425-437. Ruoff, P., Vinsjevik, M., Monnerjahn, C., & Rensing, L. (1999). The Goodwin oscillator: on the importance of degradation reactions in the circadian clock. Journal of Biological Rhythms, 14(6), 469-479. Tsai, T. Y. C., Choi, Y. S., Ma, W., Pomerening, J. R., Tang, C., & Ferrell Jr, J. E. (2008). Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science, 321(5885), 126-129. Bose, A. (2014). Bifurcations Dynamics of Single Neurons and Small Networks. In: Jaeger, D., Jung, R. (eds) Encyclopedia of Computational Neuroscience. Springer, New York, NY. Nangle, S. N., Rosensweig, C., Koike, N., Tei, H., Takahashi, J. S., Green, C. B., & Zheng, N. (2014). Molecular assembly of the period-cryptochrome circadian transcriptional repressor complex. Elife, 3, e03674. Aryal, R. P., Kwak, P. B., Tamayo, A. G., Gebert, M., Chiu, P. L., Walz, T., & Weitz, C. J. (2017). Macromolecular assemblies of the mammalian circadian clock. Molecular Cell, 67(5), 770-782. Schmalen, I., Reischl, S., Wallach, T., Klemz, R., Grudziecki, A., Prabu, J. R., ... & Wolf, E. (2014). Interaction of circadian clock proteins CRY1 and PER2 is modulated by zinc binding and disulfide bond formation. Cell, 157(5), 1203-1215. Ye, R., Selby, C. P., Chiou, Y. Y., Ozkan-Dagliyan, I., Gaddameedhi, S., & Sancar, A. (2014). Dual modes of CLOCK: BMAL1 inhibition mediated by Cryptochrome and Period proteins in the mammalian circadian clock. Genes & Development, 28(18), 1989-1998. Menet, J. S., Abruzzi, K. C., Desrochers, J., Rodriguez, J., & Rosbash, M. (2010). Dynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNA. Genes & Development, 24(4), 358-367. Kim, J. K. (2016). Protein sequestration versus Hill‐type repression in circadian clock models. IET Systems Biology, 10(4), 125-135. Kim, J. K., & Forger, D. B. (2012). A mechanism for robust circadian timekeeping via stoichiometric balance. Molecular Systems Biology, 8(1), 630. Schafmeier, T., Haase, A., Káldi, K., Scholz, J., Fuchs, M., & Brunner, M. (2005). Transcriptional feedback of Neurospora circadian clock gene by phosphorylation-dependent inactivation of its transcription factor. Cell, 122(2), 235-246. Ferrell, J. E., & Ha, S. H. (2014). Ultrasensitivity part II: multisite phosphorylation, stoichiometric inhibitors, and positive feedback. Trends in Biochemical Sciences, 39(11), 556-569. Gonze, D., & Abou-Jaoudé, W. (2013). The Goodwin model: behind the Hill function. PloS One, 8(8), e69573. Koike, N., Yoo, S. H., Huang, H. C., Kumar, V., Lee, C., Kim, T. K., & Takahashi, J. S. (2012). Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science, 338(6105), 349-354. Ukai-Tadenuma, M., Yamada, R. G., Xu, H., Ripperger, J. A., Liu, A. C., & Ueda, H. R. (2011). Delay in feedback repression by cryptochrome 1 is required for circadian clock function. Cell, 144(2), 268-281. Cao, X., Yang, Y., Selby, C. P., Liu, Z., & Sancar, A. (2021). Molecular mechanism of the repressive phase of the mammalian circadian clock. Proceedings of the National Academy of Sciences, 118(2), e2021174118. Cao, X., Wang, L., Selby, C. P., Lindsey-Boltz, L. A., & Sancar, A. (2023). Analysis of mammalian circadian clock protein complexes over a circadian cycle. Journal of Biological Chemistry, 299(3). Jeong, E. M., Song, Y. M., & Kim, J. K. (2022). Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations. Interface Focus, 12(3), 20210084. Liu, N., & Zhang, E. E. (2016). Phosphorylation regulating the ratio of intracellular CRY1 protein determines the circadian period. Frontiers in Neurology, 7, 159. Jeong, E. M., Kwon, M., Cho, E., Lee, S. H., Kim, H., Kim, E. Y., & Kim, J. K. (2022). Systematic modeling-driven experiments identify distinct molecular clockworks underlying hierarchically organized pacemaker neurons. Proceedings of the National Academy of Sciences, 119(8), e2113403119." } ] } ]	1	https://f1000research.com/articles/12-1077
https://f1000research.com/articles/12-1075/v1	31 Aug 23	{ "type": "Research Article", "title": "Traditional medicine in Incahuasi: An ethnobotanical study", "authors": [ "Jorge Guillermo Morales Ramos", "Darwin A. León-Figueroa", "María Susana Picón Pérez", "Marco Agustín Arbulú Ballesteros", "Enrique Guillermo Llontop Ynga", "Luis A. Coaguila Cusicanqui", "Sofía Mariagracia Morales Ramírez", "Carlos Alberto Chirinos Ríos", "Darwin A. León-Figueroa", "María Susana Picón Pérez", "Marco Agustín Arbulú Ballesteros", "Enrique Guillermo Llontop Ynga", "Luis A. Coaguila Cusicanqui", "Sofía Mariagracia Morales Ramírez", "Carlos Alberto Chirinos Ríos" ], "abstract": "Introduction: Understanding the use of medicinal plants as herbal medicines is considered essential for the survival and continuity of humanity. Since ancient times, the origin and development of natural and traditional medicine have been intrinsically linked to humanity struggle for survival. Nowadays, ethnobotanical studies are employed as a tool for the preservation and conservation not only of taxonomic biodiversity but also of cultural biodiversity. Methodology: A descriptive research with a quantitative, non-experimental cross-sectional design was carried out. The study was conducted in six Quechua-speaking communities in the district of Incahuasi (3,000 meters above sea level), selected for convenience considering factors such as altitude, accessibility, and proximity to the city. A questionnaire was administered to 32 residents from the communities, who shared their knowledge about medicinal plants, providing relevant information about them. The gender of the participants was considered because men and women use traditional medicine and the knowledge of them is transmitted from parents to children. Results: During the study, a total of 46 medicinal species were recorded, belonging to 42 genera and 22 botanical families. The most representative medicinal families used by the informants of the communities were Asteraceae (30.4%) and Lamiaceae (15.2%). It is also worth mentioning the genera Salvia and Baccharis, with 3 and 2 species respectively, which are commonly used to treat various ailments and diseases. Conclusions: Ethnobotanical information was collected on the medicinal plants used by the community members of the selected communities in Incahuasi, and the corresponding data were recorded. A total of 46 plants were collected, with the majority belonging to the Asteraceae and Lamiaceae families.", "keywords": [ "Traditional medicine", "ethnobotany", "systematic botany", "medicinal plants" ], "content": "Introduction\n\nThe knowledge of using medicinal plants as herbal remedies is considered an important factor for the survival and continuity of the human population, especially in the case of populations that, for various reasons,1 find it difficult to access official healthcare services and therefore rely on medicinal plants.2\n\nSince the appearance of human beings on Earth, all cultures existing in a specific space-time dimension have always met their needs, such as food, healing common ailments in each place, clothing, food processing, shelter, among others. As a result, cultural evolution, and the evolution of knowledge about the natural environment have progressed hand in hand.3\n\nFrom an anthropological perspective, human life is intimately related to plant biodiversity and depends on it in various ways in which they are used, which is determined by cultural evolution in general. Therefore, regarding medicinal plants, the diversity in their utility and multiple applications can be studied transculturally, inferring changes in their use over time.4\n\nThe origin of natural and traditional medicine is closely linked to that of humanity and mankind's struggle for survival. Traditional medicine, also known as unconventional medicine or complementary medicine, is a central component in healthcare systems worldwide.5 The World Health Organization (WHO) defines traditional medicine as the sum of skills, knowledge, and practices used to maintain health, diagnose, prevent, improve, and treat physical and mental illnesses, based on beliefs, theories, and experiences specific to different cultures.6\n\nOver 80,000 out of the 250,000 species of flowering plants are used by human civilizations for medicinal purposes.7 The use of Traditional Chinese Medicine (TCM), which dates back 3,000 years, has become popular worldwide, especially in China. However, Traditional Japanese Medicine, with a history of 1,500 years and including Kampo-yaku (herbal medicine), has also been incorporated. Nearly 148 different Kampo formulations can be prescribed within the Japanese national health insurance system.8\n\nEthnobotany is a discipline that studies the interaction between humans and their plant environment, taking into account three dimensions: (1) cultural perception and taxonomy, (2) the biological and cultural dimension of plant use and management, and (3) cultural foundations and conservation of natural resources.9 Ethnobotanical studies are used as a tool for conservation, not only of biological diversity but also of cultural heritage.10 The ethnobotanical approach is one of the most specific and successful methods as it provides important clues for the discovery of new drugs or information about the pharmacological effects and biological impact of plants. This knowledge is rooted in accumulated practical knowledge and experiences over time by many ancient civilizations.11,12\n\nIn general, ethnobotanical studies are one of the main steps in the identification and development of drugs from medicinal plants.13\n\nA clear example in the field of the influence of ethnobotany and the study of the medicinal properties of plants is the cure for malaria through the use of artemisinin, an active ingredient extracted from a Chinese plant called Artemisia annua, known as “qinghao” and “sweet wormwood”. This discovery earned Youyou Tu from the Republic of China the Nobel Prize in Medicine in 2015.14,15\n\nVarious ethnobotanical studies have been conducted in the Amazon, where a diverse range of ethnic and cultural groups of indigenous and non-indigenous peoples depend on natural resources for their subsistence. One of these studies established an inventory with the objective of assessing the ethnobotanical knowledge of the inhabitants of three communities residing in the Marajó-Pará Coastal Island Marine Extractive Reserve, located at the mouth of the Amazon. The study was carried out using semi-structured interviews and participatory observation methods. Additionally, a non-probabilistic sampling through rational selection was employed. The study utilized indices such as total species diversity (SDtot) and informant diversity (IDs), consensus of use value (UDs), and use diversity value (UDs). The results allowed for the identification of a list of 215 ethnobotanical species, with 79 of them being cited by the interviewed inhabitants of the three communities. The most frequently cited category was medicinal plants.16\n\nAnother research, conducted in 5 Shuar communities residing in the province of Zamora Chinchipe, in the Amazon region of Ecuador, collected information on the use of medicinal plants from 60 inhabitants over the age of 18. This study allowed for the determination of the significant use level (NUS), the use value index (IVU), and the ethnomedicinal knowledge index (ICE). The ICE revealed that it is concentrated among housewives, farmers, shamans or healers, and elderly individuals. The same study documented 69 species from 34 botanical families with medicinal uses.17\n\nIn the Peruvian Amazon, an ethnomedicinal inventory was also conducted, analyzing its importance in 4 communities located on the outskirts of the San Antonio Private Conservation Area, in the province of Chachapoyas, Amazonas region. In the same study, the most frequently cited medical disorders among the residents (FCI), the most important medicinal plants in terms of relative importance (IR), and the level of cultural knowledge in each studied community (H index) were determined. A total of 124 medicinal species belonging to 104 genera and 47 taxonomic families were listed, with Lamiaceae and Asteraceae being the most representative families.18\n\nA systematic review of various ethnographic studies was carried out in Mexico, focusing only on species from the Verbenaceae family that were used as herbal resources. A total of 41 taxa corresponding to 12 genera and 37 species were recognized, with Lantana camara, Verbena carolina, Phyla scaberrima, and Lippia graveolens being the most cited ones. Furthermore, 92% of the species were used to treat digestive system disorders.19\n\nAnother article highlights a systematic review on the ethnobotany, phytochemistry, and pharmacology of Senecio tephrosioides Turz, a plant from the Asteraceae family, which is a traditional medicinal plant used in ancient medicine systems in Peru and holds significant ethnopharmacological value. The plant contains various active compounds, such as terpenes (1-isopropyl-4-methyl bicyclo[3.1.0] hexane and terpinene), phenolic compounds (5,7-dihydroxy-4',6',8-trimethoxyflavanonone; 3',5-dihydroxy-4-methoxy-7-O-rhannoglucoside), flavonoids (quercetin-3-rutinoside), pyrrolizidine alkaloids (neoplatifiline, senecionine, seneciphylline, seneciphylline N-oxide, and senkirkine), and lactones (sylflavanonone and 5,4-dihydroxychalcone).20\n\nThis research will be of great interest for further exploration of the beneficial effects of medicinal plants, and their inventory would help establish common characteristics among different cultures related to their use in treating diseases. Additionally, it is observed that if a plant species is common in a specific geographic area, its use is often specific to a particular community, symbolizing valuable knowledge that is being sought to protect and preserve. Such preliminary investigations, from a public health perspective, emphasize the relevance of traditional medicine, which should be understood as a community that formulates, interprets, participates, and addresses the health problems of its community. Moreover, it aims to contribute to a therapeutic option of natural origin based on traditional knowledge.\n\nThe objectives of this study are to document the ethnobotanical data of medicinal plants in Incahuasi and to understand the native medicinal flora present in the area.\n\n\nMethods\n\nThe study was conducted in the Peruvian district of Incahuasi, a Quechua word meaning “house of the Inca,” named after an ancient indigenous city located at an altitude of 3,100 meters above sea level (m.a.s.l.). It is one of the six districts of the Ferreñafe province, located in the Lambayeque region, Peru. Incahuasi is situated in the high Andean zone and consists of 127 populated centers (cps), ranging in elevation from 203 to 3,447 meters above sea level. The study focused on Quechua-speaking inhabitants who are users of traditional medicine, consumers, and herbalists from various populated centers in the district of Incahuasi. The cps were selected for convenience, taking into account factors such as altitude, accessibility, and proximity to the city.\n\nThe gender of the participants was considered, because men and women use traditional medicine and the knowledge of them is transmitted from parents to children. The selected cps were: Incahuasi, Sinchihual, Huasicaj, Tungula, Uyurpampa, and Huar-huar. All the collected plants originated from the Jalca (3,200 meters above sea level), were taxonomically identified. They were then organized systematically based on their medicinal use.\n\nThe study population consisted of informants from 6 populated centers in the district of Incahuasi, with an approximate total population of 3,200 residents. To determine the sample, 32 participants were selected, including 28 users of traditional medicine and 4 herbal healers, one of whom was a midwife.\n\nA non-probability convenience sampling method was used to select the participants.\n\nFor data collection, the following activities were carried out: 1) Data collection began in January 2022 and concluded in December 2022, taking advantage of favorable weather conditions with lower precipitation. For the initial outing, a truck was hired to transport the project staff. This truck was used to survey the populated centers and conduct a pilot survey with some residents. 2) Transportation from the city of Chiclayo to Incahuasi (operations center) and vice versa was done using public transportation, with an approximate duration of 8 hours. Data collection and identification of medicinal plants were scheduled every 15 days, from Friday to Sunday. 3) The project leader, one of the co-authors, a botanist hired for on-site plant identification and systematization, and a Quechua-speaking translator were present on all outings. 4) The researchers traveled on foot to the selected populated centers to administer questionnaires to residents who met the inclusion criteria. They also visited healers and midwives living in rural areas. 5) When necessary, a Quechua-speaking translator was available to ask questions and translate the responses. A recorder was used as an additional tool for data collection, and the answers were recorded on the questionnaires. 6) The identification of medicinal plants was conducted on-site in the Jalca, located at an altitude of 3,200 meters above sea level, by the botanist who took photographs of the plants for taxonomy purposes (https://zenodo.org/record/8231817). This process took place over the course of a year, considering the plants development and flowering stages. Finally, they were systematically organized based on their medicinal use. 7) It is important to mention that data collection was delayed during periods of high precipitation. While it was possible to reach the city, traveling to the populated centers during those times was not possible. The corresponding permits for the identification of the medicinal plants were processed through the competent Peruvian agency “Servicio Nacional Forestal y de Fauna Silvestre” (SERFOR).\n\nAfter conducting the interviews, the data was transcribed using Microsoft Excel 2019 software. This allowed for the recording of responses provided by each participant in the study, with each record identified by a code to ensure the anonymity of each response. Additionally, the collection of medicinal plants included recording their order, family, species, and common name. The collected data was used to generate frequency tables and summary tables. To ensure data integrity, validation functions in Excel were employed to verify that all data accurately corresponded to each of the previously recorded medicinal plant names. After conducting the interviews, the data was transcribed using Microsoft Excel 2019 software. This allowed for the recording of responses provided by each participant in the study, with each record identified by a code to ensure the anonymity of each response. Additionally, the collection of medicinal plants included recording their order, family, species, and common name. The collected data was used to generate frequency tables and summary tables. To ensure data integrity, validation functions were employed in Excel to verify that all data precisely corresponded to each of the previously recorded medicinal plant names.\n\nA questionnaire used was validated in a study carried out in 2016 by Gallegos et al.21 called “Design and validation of the U-PlanMed questionnaire to identify the use of medicinal plants in Babahoyo, Ecuador” (https://zenodo.org/record/8231817). The questionnaire was built with 6 domains, expressed in questions closed and multiple choice that were directed to identify the plants and parts used, therapeutic applications, purpose, forms of preparation, routes of administration, doses and duration of treatment. Cronbach's α values and even-odd reliability coefficient of the measuring instrument on the use of medicinal plants in rural communities was 0.82.\n\nThe questionnaire45 consisted of 3 items related to sociodemographic aspects and 16 items on the use of medicinal plants, the parts of the plant, its preparation, the diseases that are treated with them, the doses, the form of administration and the duration of treatment.\n\nTo obtain the results, the statistical software SPSS v. 27 and Excel 2019 were used to analyze the data. Simple frequency tables and bivariate tables were generated as tools for analysis.\n\nInclusion criteria\n\n• Residents of both genders\n\n• Quechua-speaking residents\n\n• Residents older than 20 years\n\n• Residents users of traditional medicine\n\nExclusion criteria\n\n• Foreign residents settled in Incahuasi\n\n• Users of conventional medicine\n\nThe research complies with the ethical principles established in the Declaration of Helsinki, where autonomy and informed consent are fundamental elements of the scientific process. All research participants were informed in advance of the purpose of the study and freely agreed to participate by signing an informed consent letter that established the limits of their participation. The research was approved by the Ethics Committee of the Universidad de San Martín de Porres, Filial Norte, Chiclayo - Peru, through letter No. 139-2021 - CIEI-FMH-USMP, dated February 22, 2021.\n\n\nResults\n\nTable 1 presents the classification of sociodemographic variables. It can be observed that the majority of the interviewed individuals are residents of the populated center of Incahuasi. Regarding the gender of the surveyed residents, there is no significant difference between both genders. Lastly, the age group with the highest frequency is the 50-59 age group, representing approximately 47% of the surveyed population.\n\nTable 2 displays the taxonomic classification of the identified medicinal plants, organized by class, order, family, species, and common name. A total of 46 species of medicinal plants were collected, belonging to 42 genera and 22 botanical families. The most representative botanical families, with a high percentage of species, were Asteraceae (30.4%) and Lamiaceae (15.2%). The genera Salvia (3 species) and Baccharis (2 species) also stand out.\n\nTable 3 presents a list of medicinal plants and their traditional uses, including the plant part used and the method of preparation. It can be observed that some plants, such as “Cutiquero,” are used to treat up to 11 different types of diseases or symptoms. Furthermore, from the data, it can be inferred that leaves are the most commonly used plant part by the residents, followed by stems, flowers, and roots, in that order. The most common method of preparation is infusion, followed by decoction, ointment, extract, and cooking. Regarding the combination of plants to treat specific illnesses, “asolanjea,” “perlilla,” and “chompe ojsha” are used for the treatment of muscle strains and injuries.\n\nTable 4 provides a detailed description of diseases and the plants used to treat them. It also gives an overview of the number of plants used to treat a single disease or multiple diseases. For example, 24 plant species are used to treat acute respiratory infections, while 14 species are employed for treating gastroenterocolitis. Overall, the information extracted from the table is valuable for understanding the use of medicinal plants in various treatments.\n\nTable 5 highlights the most commonly treated diseases using medicinal plants, with viral infections being the highest at 25.4%. Additionally, certain symptoms are also addressed, such as stomach pain at 16.6%, placenta expulsion and reduction of bleeding at 5.8%, “mal de aire” (a condition related to cold or sudden temperature changes) at 5.7%, altitude sickness (soroche) at 4.0%, headaches at 2.9%, muscle strains at 2.9%, and inflammation at 2.9%.\n\n\nDiscussion\n\nThe results presented in Table 1, considering sociodemographic factors, indicate that both genders significantly utilize and practice traditional medicine, knowledge that has been passed down from ancestors to their children.22 The vast majority of residents (98%) first consult herbal healers and then seek medical assistance at health centers. Accordingly, highland populated centers embrace traditional medicine, biomedicine, self-treatment, and other options based on their own worldview.23 The study suggests that there is no significant difference between both sexes, and the age range with the highest frequency is between 50 to 59 years, representing approximately 47% of the surveyed population. This finding aligns with the data showing that the ethnomedicinal knowledge is concentrated among elderly individuals, healers, or shamans.24\n\nThe results extracted from Table 2 indicate that the most representative families are Asteraceae and Lamiaceae, with the leaf being the most commonly used part (Table 3), which coincides with published works.25‐27 Asteraceae is the most diverse group of flowering plants on the planet, with records of ethnobotanical uses dating back to ancient times. A study published in 2021 established that Asteraceae species found in Quinua (Ayacucho) and Lircay (Huancavelica) were used for digestive and genitourinary ailments (22.8% and 13.1% respectively).28 80.0% of the Asteraceae collected in the populated centers of Incahuasi are used for the treatment of infections (earache, stomachache, bronchitis, cold). The most representative collected Asteraceae species are: Ambrosia arborescens Mill. “Marco,” and two species from the genus Baccharis: Baccharis tricuneata (L.f.) Pers. (pichana) and Baccharis latifolia (Ruiz & Pav.) Pers.\n\nAmbrosia arborescens Mill. 'Marco' is used in traditional Incahuasi medicine for the treatment of muscular contracture, cold, and chucaque. A phytochemical study identified 113 compounds, including β-acoradiene (15.3%) and chrysanthenone (11.3%), as the main constituents of the essential oil with antioxidant capacity.29 It also exhibits anti-inflammatory activity, with metabolites such as tannins and flavonoids being identified. A systematic review refers to the use of 'Marco' for treating the common cold.30\n\nBaccharis tricuneata (L.f.) Pers. (pichana) and Baccharis latifolia (Ruiz & Pav.) Pers. (chilca): both species are used by the interviewees for the treatment of the common cold. However, a study published in 2023 states that both species are indicated as antibacterial and antidiabetic agents.31,32 In general, the genus is used as an anti-inflammatory due to the presence of ethyl acetate and hexane fractions.33\n\nAmong the most representative species of the Lamiaceae family, we find Salvia revoluta Ruiz & Pav. “Cutiquero,” which is used by the residents of Incahuasi for the treatment of bad air, influenza, common cold, diarrhea, headache, stomach pain, knee pain, and bleeding during childbirth; and Minthostachys mollis (Benth) Grieseb “muña.” The largest genus within the Lamiaceae family is Salvia, which encompasses 1,010 species, several of which are globally used in traditional medicine for the treatment of conditions such as angiogenesis, viral and bacterial infections, inflammation, and oxidative stress.34\n\nSalvia revoluta Ruiz & Pav. “Cutiquero.” Central and South America host the highest number of Salvia species worldwide, with 510 species.35 A study reveals the antibacterial power of the genus in 11 species in Iran, where the main components detected were β-caryophyllene, 1,8-cineole, and α and β-pinene. The most susceptible organisms were Salmonella typhi and Bacillus subtilis.36\n\nMinthostachys mollis (Benth) Grieseb., known as “muña,” is commonly used in traditional South American medicine.37 In the Incahuasi community, it is used as an infusion to treat various health disorders such as stomach cramps, flu, and colds (Tables 3, 4, 5). Peruvian muña produces compounds of medicinal interest, and one of the most abundant compounds in muña oil is the monoterpene Pulegone. Pulegone possesses anti-inflammatory activity as it inhibits the expression of lipopolysaccharides and regulates inflammation in vitro by modulating the inducible nitric oxide synthase (iNOS) isoform and cyclooxygenase-2 (COX-2) expression. It participates in the inhibition of NF-κB (nuclear factor kappa B) and MAPKs (nitrogen-activated protein kinases) signaling pathways, while strengthening the Nrf-2/HO-1 (nuclear factor E2-related factor 2/heme oxygenase 1) pathways. In vivo, it suppresses NLRP3 inflammasome and reduces cytokine production. Additionally, it exhibits psychoactive activity and acts as an analgesic, antibacterial, antifungal, and insecticidal agent.38 Nrf-2 plays a fundamental role in redox homeostasis.39 Moreover, a cytoprotective effect has been demonstrated in gastric lesions induced in rats.40\n\nThe majority of medicinal plant species in the Quero district are used for specific traumas, particularly for injuries and wounds.41 In Chachapoyas, Peru, they are used as medical indications for digestive diseases.41,43,44 However, this study shows that there is a higher number of plant species used for acute respiratory diseases and gastroenterocolitis (Tables 4 and 5), which frequently include viral infections and the characteristic symptom of stomach pain. The research findings are consistent with the study conducted by Mostacero et al.45\n\n\nConclusion\n\nDuring the study, ethnobotanical data on medicinal plants used in the selected communities of Incahuasi were recorded. Various aspects were collected, including the common names of the collected plants, their mode of use, the characteristics of the environment where they were found, whether they were used fresh or dried, the parts utilized, the preparation method of home remedies, as well as the form and frequency of administration. Additionally, the transmission of ancestral knowledge related to these medicinal plants was taken into account.\n\nDuring the study, 46 medicinal plants were collected, with the majority of them belonging to the Asteraceae and Lamiaceae families, which were considered the most representative. Among the plants belonging to the Asteraceae family, Ambrosia arborescens Mill., known as “Marco,” Baccharis tricuneata (L.f.) Pers., called “pichana,” and Baccharis latifolia (Ruiz & Pav.) Pers. were found. On the other hand, among the plants belonging to the Lamiaceae family, Salvia revoluta Ruiz & Pav., known as “Cutiquero,” and Minthostachys mollis (Benth) Grieseb., known as “muña,” stood out.\n\nThe research results were obtained throughout the different seasons of the year. It should be noted that the climate posed a limitation for sample collection during the rainy season, while the altitude and rugged nature of the areas also presented a challenge. It is important to highlight that these results may vary over time and with the inclusion of a greater number of communities in the study. Additionally, since the interviewed population speaks Quechua, the presence of a translator was often required to facilitate communication.", "appendix": "Data availability\n\nZenodo: Traditional medicine in Incahuasi: ethnobotanical study. https://zenodo.org/record/8231817. 46\n\nThe project contains the following underlying data:\n\n• Base de datos agrupada - General.xlsx\n\nZenodo: Traditional medicine in Incahuasi: ethnobotanical study. https://zenodo.org/record/8231817. 46\n\nThis project contains the following extended data:\n\n• Questionnaire\n\nThe data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe research team expresses special gratitude to the University De San Martín de Porres Filial Norte - Peru for their commitment to scientific research and continuous support provided to the research team throughout the study until its completion.\n\n\nReferences\n\nGuadalupe LAS: Conocimiento ancestral de plantas medicinales en la comunidad de Sahuangal, parroquia Pacto, Pichincha, Ecuador. VIVE Revista de Investigación en Salud. 2021; 4(10): 72–85. Publisher Full Text\n\nTainá Teixeira Rocha ACCT-M&. FCAL: Traditional populations in environmentally protected areas: an ethnobotanical study in the Soure Marine Extractive Reserve of Brazil. Boletín Latinoamericano y del Caribe de Plantas Medicinales y Aromáticas (Blacpma). 2017; 16(4): 410–427. Reference Source\n\nTowle M: The ethnobotany of Pre-columbian Peru. New York, NY, Estados Unidos de América: Routledge Member of the Taylor and Francis Group; 2017. Publisher Full Text\n\nTeixidor-Toneu I, Jordan FM, Hawkins JA: Comparative phylogenetic methods and the cultural evolution of medicinal plant use. Nature Plants. 2018; 4: 754–761. PubMed Abstract \| Publisher Full Text\n\nBetancourt CA, García M, Fernández M, et al.: Fitoterapia y apiterapia en la obra de José Martí. Revista Información Científica. 2015; 92(4): 945–955. Reference Source\n\nOrganización Mundial de la Salud: Estrategia de la OMS sobre medicina tradicional 2014-2023. Ginebra: Ediciones de la OMS; 2013. Reference Source\n\nVallisuta O, Olimat S: Drug Discovery and Development - From Molecules to Medicine. InTech; 2015. Publisher Full Text\n\nRemya S, Kenichi W, Somasundaram A: Chapter 1 - Introduction to Japanese Kampo Medicines.Academic Press, editor. Japanese Kampo Medicines for the Treatment of Common Diseases: Focus on Inflammation. Paseo de la Castellana 163, 3a planta. 28046 Madrid: Elsevier; 2017; p. 1–11. Publisher Full Text\n\nRíos A, Alanís G, Favela S: Etnobotánica de los recursos vegetales, sus formas de uso y manejo, en Bustamante, Nuevo León. Revista mexicana de ciencias fo. 2017; 8(44). Publisher Full Text Reference Source\n\nSieber SS, da Silva TC , Campos LZdO, et al.: Participatory Methods in Ethnobiological and Ethnoecological Research.Albuquerque U, Cruz da Cunha L, de Lucena R , et al., editors. Methods and Techniques in Ethnobiology and Ethnoecology. Springer Protocols Handbooks. New York, NY: Humana Press; 2014. Publisher Full Text\n\nBrinckmann JA: Owning up to Owning Traditional Knowledge of Medicinal Plants.A CriticalGuide to Intellectual PropertyCallahan M, Rogers J, editors. London, UK: Zed Books Limited; 2017. 9781786991133. Reference Source\n\nJantan I, Bukhari SNA, Mohamed MAS, et al.: The Evolving Role of Natural Products from the Tropical Rainforests as a Replenishable Source of New Drug Leads. Drug Discovery and Development - From Molecules to Medicine. InTech; 2015. Publisher Full Text\n\nAbubakar US, Yusuf KM, Abdu GT, et al.: Ethnopharmacological survey of medicinal plants used for the management of pediatric ailments in Kano State, Nigeria. Res. J. Pharmacogn. 2017; 4(3): 29–39. Reference Source\n\nLegua-Leiva P: Qinghaosu, el antimalárico de la materia médica china. spmi. 12 de julio de 2019 [date of citation: July 1st 2023]; 30(2): 109–112. Reference Source\n\nPerdomo-Delgado J, González-Pla E: Medicina Tradicional China y el Premio Nobel 2015. Revista Cubana de Plantas Medicinales. 2015 [date of citation: December 19th 2022]; 20(4). Reference Source\n\nTeixeira Rocha T, Caldeira Tavares - Martins AC, Araújo Lucas FC: Traditional populations in environmentally protected areas: an ethnobotanical study in the Soure Marine Extractive Reserve of Brazil. Boletín Latinoamericano y del Caribe de Plantas Medicinales y Aromáticas. 2017; 16(4): 410–427. Reference Source\n\nAguirre Z, Arévalo D, Cajilima J, et al.: Etnobotánica en cinco comunidades amazónicas y prendimiento de las especies de mayor importancia en el Jardín Botánico El Padmi, Zamora Chinchipe, Ecuador. Ciencia Latina. 2022; 6(3): 76–93. Publisher Full Text Reference Source\n\nChilquillo EA, Albán J, Muñoz A: Estudio etnobotánico de plantas medicinales utilizadas en comunidades adyacentes al Área de Conservación Privada San Antonio, Chachapoyas, Amazonas. Perú. ciencias naturales e ing. 2018; 1(1): 65. Publisher Full Text Reference Source\n\nLópez MA, Aguilar A, Aguilar S, et al.: Las Verbenaceae empleadas como recurso herbolario en México: Una revisión etnobotánica-médica. polibotánic. 2017; 44: 195–216. Reference Source\n\nBlanco C, Olascuaga AK, Rubio S, et al.: Senecio tephrosioides Turcz. (Asteraceae): Una revisión de etnobotánica, fitoquímica y farmacología. ethnobotany. 2020; 19(14): 1–14. Publisher Full Text Reference Source\n\nMaritza G-Z, Betty M, Luzmila T: Diseño y validación del cuestionario U-PlanMed para identificación del uso de plantas medicinales en Babahoyo, Ecuador. An. Fac. med. 2016 Jul [date of citation: March 20th]; 77(3): 207–212. Publisher Full Text Reference Source\n\nJiménez PA: Los saberes en medicina tradicional y su contribución al desarrollo rural: estudio de caso Región Totonaca, Veracruz. Revista mexicana de cien. 2015; 6(8): 1791–1805. Publisher Full Text Reference Source\n\nOchoa WW, Rodríguez M: Fitoterapia altoandina como potencial ante la COVID-19. Revista cubana de investi. 2020; 39(4). Reference Source\n\nGomides NA, Guarim G, Pereira M, et al.: Ethnobotanical and ethnopharmacological survey of medicinal species utilized in the Coqueiros Community, Brazil. Boletín latinoamericano de. 2022; 21(6): 671–715. Publisher Full Text Reference Source\n\nMendoza AH, Niño MA, Chaloupková P, et al.: Estudio etnobotánico del uso de las plantas medicinales en la comunidad indígena Pijao en Natagaima, Colombia. boletín latinoame. 2021; 20(5): 482–495. Publisher Full Text Reference Source\n\nFernández E, Espinel V, Gordillo S, et al.: Estudio etnobotánico de plantas medicinales utilizadas en tres cantones de la provincia Imbabura, Ecuador. Agrociencia. 2019; 53(5): 797–810. Reference Source\n\nTello G, Flores M, Gómez V: Uso de las plantas medicinales del distrito de Quero, Jauja, Región Junín, Perú. Ecología apli. 2019; 18(1): 11. Publisher Full Text Reference Source\n\nHurtado-Huarcaya J, Castañeda R, Albán-Castillo J: Asteráceas medicinales en dos comunidades andinas del sur del Perú: Quinua (Ayacucho) y Lircay (Huancavelica). Bol Latinoam Caribe Plant Med Aromat. 2021; 20(4): 351–366. Publisher Full Text\n\nQuispe L, Pino JA, Marín-Villa JZ, et al.: Chemical composition and antioxidant activity of Ambrosia arborescens Miller leaf essential oil from Peruvian Andes. J. Essent. Oil Res. 2022; 34(5): 439–445. Publisher Full Text\n\nIsabel RRM, Duvia DA, Angel MLJ: Actividad antiinflamatoria de plantas medicinales. Bol Latinoam Caribe Plant Med Aromat. 2020; 16(1): 2–14. Reference Source\n\nRuíz Santillán María Pilar FRMC: Artículo de revisión: Plantas utilizadas en medicina tradicional para afecciones respiratorias virales. Revista de Investigación Científica REBIOL. 2020; 40: 109–130. Publisher Full Text\n\nLoja B, Alvarado A, Salazar A, et al.: Cribado fitoquímico del Baccharis latifolia (R&P.) Pers. (chilca). Revista cubana de plantas. 2017; 22(1). Reference Source\n\nCarrillo L, Mora C, Álvarez R, et al.: Chemical composition and antibacterial activity against Enterobacter cloacae of essential oils from Asteraceae species growing in the Páramos of Colombia. Ind. Crop. Prod. 2015; 77(23): 108–115. Publisher Full Text Reference Source\n\nBurgos C, Alvarenga N, Sotelo PH, et al.: Anti-inflammatory activity of Baccharis notosergila against lipopolysaccharide (LPS)-induced inflammation and identification of active fractions and their chemical constituents. European journal of integrati. 2023; 57: 102208. Publisher Full Text Reference Source\n\nRattray RD, Mokwena L, Stander MA, et al.: Essential Oil Composition and Traditional Uses of Salvia dentata, a Poorly Known Medicinal Plant from Namaqualand, South Africa. Molecules. 2022; 27(19). PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nWei Y, Wang Q, Huang Y: Species diversity and distribution of Salvia (Lamiaceae). Biodivers. Sci. 2015; 23(1): 3–10. Publisher Full Text\n\nAsadollahi M, Firuzi O, Heidary F, et al.: Ethnopharmacological studies, chemical composition, antibacterial and cytotoxic activities of essential oils of eleven Salvia in Iran. Journal of herbal. 2019; 17-18: 100218–100250. Publisher Full Text Reference Source\n\nFaraone I, Russo D, Chiummiento L, et al.: Phytochemicals of Minthostachys diffusa Epling and Their Health-Promoting Bioactivities. Foods. 2020; 9(2). Publisher Full Text Reference Source\n\nLinares V: Considerations for the use and study of the Peruvian “muña” Minthostachys mollis (Benth.) Griseb and Minthostachys setosa (Briq.) Epling. Ethnobotany. 2020; 19: 19. Publisher Full Text Reference Source\n\nFurfaro AL, Traverso N, Domenicotti C, et al.: The Nrf2/HO-1 Axis in Cancer Cell Growth and Chemoresistance. Oxidative medi. 2015; 2016: 1–14. Publisher Full Text Reference Source\n\nGonzáles LF, Chico J, Chotón MR: Efecto citoprotector del extracto mixto de Sollanum tuberosum L. “papa”; Minthostachys mollis L. “muña” y Uncaria tormentosa L. “uña de gato” en las lesiones ulcerosas de ratas inducidas por etanol. Revista de investigación científica REBIOL. 2020; 40(2): 177–187. Publisher Full Text Reference Source\n\nGladys T-C, Mercedes FP, Vilma GG: Uso de las plantas medicinales del distrito de Quero, Jauja, Región Junín, Perú. Ecol. apl. January 2019 [date of citation: September 4th 2022]; 18(1): 11–20. Publisher Full Text Reference Source\n\nCoroto F, Rascón J, Barboza E, et al.: Plantas medicinales para ricos versus plantas medicinales para pobres: un estudio de caso de los Andes peruanos. Plantas. August 9th 2021; 10(8): 1634. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJoaquina A-C, Chilquillo TE, Briggitthe M-C, et al.: Categorización de usos de plantas utilizadas por los pobladores de zonas urbanas y rurales del Perú. Arnaldoa. January 2021 [date of citation: September 4th 2022]; 28(1): 85–108. Publisher Full Text Reference Source\n\nMostacero-León J, García-Izquierdo LG, López-Medina SE, et al.: Valor de uso medicinal de la flora empleada por la Comunidad Andina de Jesús, Cajamarca. PerúBol Latinoam Caribe Plant Med Aromat. 2022; 21(5): 561–576. Publisher Full Text\n\nGuillermo MRJ, León-Figueroa Darwin A, Susana PPM, et al.: Traditional medicine in Inkahuasi: ethnobotanical study. [dataset]. 2023. Reference Source" }	[ { "id": "224505", "date": "10 Jan 2024", "name": "Adriana Beatriz Sánchez-Urdaneta", "expertise": [ "Reviewer Expertise My areas of expertise are plant morphoanatomy", "plant physiology", "crop production and management", "some aspects of plant systematics." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nBased on a detailed reading of the article, here is my analysis: The article has a logical and coherent structure. The introduction adequately presents the topic and its relevance. The methodology clearly describes the research design, study population, instruments used to collect data, and the analysis performed. The results are presented in an organized manner in tables that facilitate understanding. The discussion appropriately analyzes the findings, comparing them with previous studies cited in the references. Finally, the conclusions summarize the main findings of the study. There is an argumentative line that connects the different sections of the article. The objectives set out in the introduction are addressed throughout the document. The article includes an adequate number of quality bibliographic references that support the statements made. The references mostly follow the Vancouver style standards. Some details to improve: the volume number is missing in some journals, sometimes the page range of the cited articles is not included. Most references are current, after 2015, although some older relevant sources are also cited.\nThe writing is generally clear and understandable, with good language quality. Tables and figures are mentioned in the text and add value by presenting results. The article complies with the ethical principles of research in human beings. However, there are some recommendations that I would like to make, with the aim of improving the manuscript. The names of families, orders and types of plants do not have to be written in italics. Numbers greater than 10 should be written in letters and not in numbers, unless they are preceded by a unit of measurement recognized by the international system. With respect to scientific names, once the genus is named, the following times it appears, the initial of the genus is used, unless a paragraph begins with a scientific name. For example: Baccharis tricuneata (L.f.) Pers. (pichana) and Baccharis latifolia (Ruiz & Pav.) Pers. (chilca), should be changed to Baccharis tricuneata (L.f.) Pers. (pichana) and B. latifolia (Ruiz & Pav.) Pers. (chilca), among other examples.\nIn conclusion, the article has a very good quality in terms of structure, internal coherence, bibliographic support and writing. With some minor adjustments in the reference format, the document could be ready to be indexed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11303", "date": "23 Apr 2024", "name": "Jorge Guillermo Morales Ramos", "role": "Author Response", "response": "Reviewer 1: Adriana Beatriz Sánchez-Urdaneta Thank you very much, dear doctor, for reviewing our article. Your comments and recommendations have been beneficial for improving the quality of the article. The comments raised are listed below. The reviewer says: Based on a detailed reading of the article, here is my analysis: The article has a logical and coherent structure. The introduction adequately presents the topic and its relevance. The methodology clearly describes the research design, study population, instruments used to collect data, and the analysis performed. The results are presented in an organized manner in tables that facilitate understanding. The discussion appropriately analyzes the findings, comparing them with previous studies cited in the references. Finally, the conclusions summarize the main findings of the study. There is an argumentative line that connects the different sections of the article. The objectives set out in the introduction are addressed throughout the document. The article includes an adequate number of quality bibliographic references that support the statements made. Our answer: Thank you for your appreciation of the structure and wording of our article. The reviewer says: The references mostly follow the Vancouver style standards. Some details to improve: the volume number is missing in some journals, sometimes the page range of the cited articles is not included. Most references are current, after 2015, although some older relevant sources are also cited. Our answer: We have sequentially adapted the indicated references. The author instruction guide proposed by the journal was checked to adapt it to the requested format. The reviewer says: The writing is generally clear and understandable, with good language quality. Tables and figures are mentioned in the text and add value by presenting results. The article complies with the ethical principles of research in human beings. However, there are some recommendations that I would like to make, with the aim of improving the manuscript. The names of families, orders and types of plants do not have to be written in italics. Our answer: Observations raised regarding italic writing in plant types, orders, and families. The reviewer says: Numbers greater than 10 should be written in letters and not in numbers, unless they are preceded by a unit of measurement recognized by the international system. Our answer: The reviewer says: With respect to scientific names, once the genus is named, the following times it appears, the initial of the genus is used, unless a paragraph begins with a scientific name. For example: Baccharis tricuneata (L.f.) Pers. (pichana) and Baccharis latifolia (Ruiz & Pav.) Pers. (chilca), should be changed to Baccharis tricuneata (L.f.) Pers. (pichana) and B. latifolia (Ruiz & Pav.) Pers. (chilca), among other examples. Our answer: The observation on scientific names was lifted. The reviewer says: In conclusion, the article has a very good quality in terms of structure, internal coherence, bibliographic support, and writing. With some minor adjustments in the reference format, the document could be ready to be indexed. Our answer: Thank you for your final comments." } ] }, { "id": "224508", "date": "18 Mar 2024", "name": "César Grandez Ríos", "expertise": [ "Reviewer Expertise Taxonomist", "Ethnobotanist", "economic botanic" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI have reviewed the article proposed by Morales Ramos JG, et al. I have detailed each section in order for the authors to carefully consider the observations and comments that need to be addressed and resolved. This division will facilitate a more effective review and allow for an appropriate response to each point made, thus contributing to the overall improvement of the content. Introduction: A thorough review has been carried out, incorporating references relevant to the proposed topic. As a result, the quality of both the writing and the information is considered adequate and compliant with established standards. Methodology: The methodology described fits consistently with the proposed research design, providing a detailed approach. It is notable that the study includes a data validation sheet, highlighting the rigor in data collection and analysis. Additionally, I suggest including mention of the herbarium, where the processing of the plants for identification and taxonomic classification was carried out. This additional information will not only enrich the transparency of the study but will also allow readers to better understand the source and context of the botanical data analyzed. Results The wording of the tables demonstrates an adequate level of accuracy. However, I propose to avoid repeating the full scientific names of the plants in order to follow appropriate standards. Discussion This section was written in detail. A comparison of the results with other relevant publications in the field was made. Furthermore, it has been ensured that references are up to date and relevant, thus contributing to the robustness and relevance of the information presented. Conclusions The conclusions are in line with the research objectives. References They comply with the Vancouver standards established in the journal.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11304", "date": "23 Apr 2024", "name": "Jorge Guillermo Morales Ramos", "role": "Author Response", "response": "Reviewer 2: César Grandez Ríos The reviewer says: I have reviewed the article proposed by Morales Ramos JG, et al. I have detailed each section in order for the authors to carefully consider the observations and comments that need to be addressed and resolved. This division will facilitate a more effective review and allow for an appropriate response to each point made, thus contributing to the overall improvement of the content. Our answer: Dear Doctor, we are deeply grateful for the review you have done, which enhances our work. The reviewer says: Introduction: A thorough review has been carried out, incorporating references relevant to the proposed topic. As a result, the quality of both the writing and the information is considered adequate and compliant with established standards. Our answer: Thank you for your comment. The reviewer says: Methodology: The methodology described fits consistently with the proposed research design, providing a detailed approach. It is notable that the study includes a data validation sheet, highlighting the rigor in data collection and analysis. Our answer: We agree with your assessment. The reviewer says: Additionally, I suggest including mention of the herbarium, where the processing of the plants for identification and taxonomic classification was carried out. This additional information will not only enrich the transparency of the study but will also allow readers to better understand the source and context of the botanical data analyzed. Our answer: We have included the name of the herbarium. The reviewer says: Results: The wording of the tables demonstrates an adequate level of accuracy. However, I propose to avoid repeating the full scientific names of the plants in order to follow appropriate standards. Our answer: Your recommendation was taken into account. The reviewer says: Discussion: This section was written in detail. A comparison of the results with other relevant publications in the field was made. Furthermore, it has been ensured that references are up to date and relevant, thus contributing to the robustness and relevance of the information presented. Our answer: Thank you very much for your comments. The reviewer says: Conclusions: The conclusions are in line with the research objectives. Our answer: Thank you very much for your comments. The reviewer says: References: They comply with the Vancouver standards established in the journal. Our answer: Thank you very much for your comments." } ] }, { "id": "224511", "date": "03 Apr 2024", "name": "José Mostacero León", "expertise": [ "Reviewer Expertise cultural anthropology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study highlights the importance of knowing medicinal plants in populations with difficult access to conventional health services. It presents an Anthropological and cultural approach by connecting knowledge of the natural environment with human survival in the relationship between human life and plant biodiversity. Provides clarity and institutional support when defining traditional medicine; geographically expands the concept by mentioning examples in other latitudes, contributing to the cultural diversity of the investigation. Thus, it highlights the importance of ethnobotany in the conservation of biological biodiversity and cultural heritage. Methodologically, the study is well structured, it also considers ethical aspects and points out limitations, strengthening the integrity of the research approach. The results provide a comprehensive look at the use of medicinal plants in Incahuasi, highlighting their diversity, common uses and their role in the treatment of dissimilar diseases and symptoms; They accentuate the richness of traditional medicine in Incahuasi, the value of certain families and species in treating various conditions, highlighting their potential in local medical care.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11420", "date": "21 Jun 2024", "name": "Jorge Guillermo Morales Ramos", "role": "Author Response", "response": "Thank you for your comment." } ] }, { "id": "203201", "date": "09 Apr 2024", "name": "José Yovera Saldarriaga", "expertise": [ "Reviewer Expertise My research area is cultural anthropology." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study highlights the importance of knowing medicinal plants in populations with difficult access to conventional health services. It presents an Anthropological and cultural approach by connecting knowledge of the natural environment with human survival in the relationship between human life and plant biodiversity.\nIt provides clarity and institutional support when defining traditional medicine; geographically expands the concept by mentioning examples in other latitudes, contributing to the cultural diversity of the investigation. Thus, it highlights the importance of ethnobotany in the conservation of biological biodiversity and cultural heritage.\nMethodologically, the study is well structured, it also considers ethical aspects and points out limitations, strengthening the integrity of the research approach.\nThe results provide a comprehensive look at the use of medicinal plants in Incahuasi, highlighting their diversity, common uses and their role in the treatment of dissimilar diseases and symptoms; They accentuate the richness of traditional medicine in Incahuasi, the value of certain families and species in treating various conditions, highlighting their potential in local medical care.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11421", "date": "20 Jun 2024", "name": "Jorge Guillermo Morales Ramos", "role": "Author Response", "response": "Thank you for your comment." } ] } ]	1	https://f1000research.com/articles/12-1075
https://f1000research.com/articles/13-310/v1	22 Apr 24	{ "type": "Research Article", "title": "Impact of CYP3A4 rs2242480 polymorphisms on Imatinib HPLC determined trough concentration and response in Chronic Myeloid Leukaemia in Pakistani patients", "authors": [ "Dr. Asma Khan", "Dr. Zunera Hakim", "Dr. Akbar Waheed", "Dr. Naila Abrar", "Dr. Zunera Hakim", "Dr. Akbar Waheed", "Dr. Naila Abrar" ], "abstract": "Objective To ascertain the impact of CYP3A4 polymorphism on the therapeutic outcome of imatinib and its trough concentration\n\nStudy design Descriptive analytical study\n\nPlace and duration of the study This study was conducted in the Department of Pharmacology & Therapeutics, Islamic International Medical College, between December 2020 and February 2022, in collaboration with the Institute of Biomedical Genetic Engineering, KRL Hospital Islamabad.\n\nMethods Patients with Chronic Myeloid Leukaemia age range–18-70 years were included in this study. One group comprised responders and the other group comprised non-responders. Imatinib trough levels in both groups were determined using High-performance Liquid Chromatography and compared, and the association was determined with therapeutic outcomes. DNA was extracted, and the PCR restriction fragment length polymorphism technique was used to identify the alleles. The results were analyzed using Statistical Package for Social Sciences (SPSS) version 22.0.\n\nResults The imatinib concentration in patients with the homozygous wild allele CC of rs2242480 was higher(1298ng/ml) as compared with the mutant homozygous TT allele (489ng/ml) or heterozygous allele CT(873ng/ml)\n\nConclusion There was a significant association between imatinib trough levels and CYP3A4 polymorphism, and trough concentration was found to be lower in patients with the TT or CT variant of rs2242480 than in patients with the CC genotype.", "keywords": [ "Chronic Myeloid Leukemia", "High-Performance Liquid Chromatography", "Polymerase chain reaction", "Restriction fragment length Polymorphism" ], "content": "Introduction\n\nThe prognosis of Chronic Myeloid Leukaemia (CML) has changed significantly in the last two decades with the introduction of tyrosine kinase inhibitors (TKIs), such as imatinib mesylate (IM), as the standard treatment. The efficacy of IM is determined by its concentration in the plasma. However, there is a noticeable variability in the response among individuals, and even within the same patient, when blood samples are taken at different times. This variability in drug response could be due to changes in pharmacokinetic processes, along with other factors (Natarajan, Kumar et al. 2019). Single nucleotide polymorphisms (SNPs) or single nucleotide variants (SNVs) may affect the plasma drug concentration and hence the therapeutic response. Genes that encode transporters and metabolizing enzymes are of special interest as SNP for these enzymes may explain the resistance developed against Imatinib Mesylate in CML initially or during treatment. The cytochrome P450 enzyme system extensively metabolizes imatinib in pharmacokinetic processes (Pena, Muriel et al. 2020). The main enzyme involved in vivo metabolism is CYP3A4. Multiple studies have indicated that individuals with minor alleles of SNP rs2242480 of CYP3A4 may have lower plasma concentrations (Pena, Muriel et al. 2020). Considering this, a decreased response to treatment in individuals with minor allele frequencies could be anticipated (Ullah, Ali et al. 2022). The predicted response can lead to the adoption of strategies like therapeutic drug monitoring for Imatinib with individualized adjustment of doses to achieve the therapeutic goal during the early stages of treatment (García-Ferrer, Wojnicz et al. 2019).\n\nThis study aimed to explore the impact of minor allele frequencies of rs2242480 on the response to imatinib and plasma trough concentration with the effects of different genetic models on the outcome of treatment.\n\n\nMethods\n\nIt was a descriptive analytical study and was conducted in the Department of Pharmacology and Therapeutics at Islamic International Medical College from December 2020 to February 2022.\n\nThis study is approved by Islamic International medical college Research Ethics committee, which is in alignment with the international guidelines provided by the declaration of Helsinki and International conference on harmonization –Good Clinical practice (ICH-GCP). The date of approval is July 25th, 2019, and the approval number is Ref#Riphah/IIMC/ERC/19/0265. With the necessary approval from Research Ethics Committee, data collection was started after the informed consent is taken from the participants with no financial burden on the study participants. Study participants are free to access the data and has the right to withdraw themselves from the study at any stage. As this study is observational, so direct drug intervention or therapy was not done by the researcher and no risk or harm is involved with this study. The Declaration of Helsinki was followed in maintaining the confidentiality of the study’s data.\n\nNewly diagnosed patients were selected from the CML clinic at Holy Family Hospital. The inclusion criteria were newly diagnosed patients who were taking imatinib 400 mg daily (Haque, Shah et al. 2022), had no other comorbidities, showed good compliance with treatment, and were not receiving CYP3A4 or CYP3A5 inhibitors or inducers (Sacha 2014). Sampling technique was nonprobability consecutive sampling. Initially sample size (https://csg.sph.umich.edu/abecasis/cats/gas_power_calculator/index.html) was 120 patients, but later, due to non-compliance and findings of comorbidities, the final sample size was 106. The age of these patients ranged from to 18-70 years. Informed written consent was obtained from all participants before the start of the study.\n\nLeukaemia net guidelines were followed to determine the treatment prognosis (Hochhaus, Baccarani et al. 2020). In some patients complete haematological response was achieved after three months of treatment with Imatinib and they were labelled as responders to the treatment of TKIs more specifically to Imatinib (SULTAN, JAFFRI et al. 2021). These patients were followed for the next three months as well to confirm their response towards the same dose of Imatinib. In patients who were labelled as non-responders, the complete haematological response could not be achieved after three months of 400 mg of Imatinib, they were Philadelphia positive as well. Therefore, they were switched to the second generation of the tyrosine kinase inhibitor nilotinib.\n\nGenomic DNA was extracted from the blood using a Thermo Scientific Gene JET Whole Blood Genomic DNA Purification Mini Kit (Thermo Fisher Scientific Inc. Pittsburgh, PA, USA) according to the manufacturer’s protocol (Mumtaz, Ahmed et al. 2020). This method has been previously used with excellent DNA yield of good quality (Al-Saud, Al-Romaih et al. 2020). The genetic polymorphisms of CYP3A4 rs2242480 were determined by using the polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) method (Ozeki, Nagahama et al. 2019). LEFT PRIMER: GAGGTTTTTTACTTAGCAT RIGHT PRIMER: CCCAGTGTACCTCTGAAT and the product size was 554.\n\nWhen the IM plasma concentration reached a steady state, which was achieved by regularly taking IM for at least a month, peripheral blood samples were taken 0.5 hours before the IM dosing (Chen, Dong et al. 2020). These samples were analyzed for IM trough plasma concentration determination and genotyping analysis. The analysis was performed using reverse-high-performance liquid chromatography. The equipment used was a Waters e2695 separation module, along with a 2489 UV/Vis detector and autosampler. A C18 column with a particle size of 5 μm was employed, and the analysis time was 10 min at a flow rate of 1 ml/min. The mobile phase consisted of an aqueous buffer solution of KH2PO4 (0.094 M), K2HPO4 (0.0058 M), and acetonitrile at a v/v ratio of 90:10. The detector wavelength was set at 210 nm (Boovizhikannan, Mahesh et al. 2022).\n\nStatistical analyses were conducted using SPSS software versions 22.0 and Microsoft SPSS-23 (https://www.ibm.com/support/pages/downloading-ibm-spss-statistics-22). Descriptive statistics were used to present the mean ± SEM in groups. The chi-square test was used to compare categorical variables, and the Hardy-Weinberg equilibrium test was performed using an appropriate χ2 test (Zhang, Ge et al. 2022). Binary logistic regression analysis was carried out to determine the impact of genotypes on response, and the association between genotypes was compared. Imatinib levels were compared according to genotype using analysis of variance (ANOVA). Statistical significance was set at P < 0.05.\n\n\nResults\n\nIn total, 120 patients were included in this study. Of these, 14 were excluded because they did not meet the inclusion criteria. complete Haematological response was considered in responders when the WBC count was less than 10×103/μL, basophils were less than 6% with no myelocytes, promyelocytes, or myeloblasts in the differential leukocyte count, and platelets were less than 450×103/μL with non-palpable spleen (Farooq, Khan et al. 2019). 54.7% of patients were male, while 45.3% patients were female. A significant association was found between sex and increased response in females as compared to males (64% vs. 36%). The imatinib trough concentration in males was lower than that in females (875 vs. 1151ng/ml). (Of the total sample size, 11 patients were above 60 years of age). There was an increased percentage of responders with increasing age and imatinib levels of 625 ng/ml in group 1 compared to 1240 ng/ml in group 4. None of the observed genotype frequencies were significantly different from the expected value (p > 0.05), illustrating that these frequencies follow Hardy-Weinberg equilibrium (Table 1).\n\nOf the 106 sample sizes, 49 patients had a CC variant of CY3A4 rs2242480, 38 patients had a CT variant, and 19 patients had a minor TT allele. Plasma HPLC levels of trough concentration of imatinib were calculated in all three variants with the highest trough levels of 1298 ng/ml in patients with the CC variant, while CT levels were 873ng/ml and TT levels were 489 ng/ml (Figure 1). Analysis of variance was used to determine the difference between the polymorphic variants, which was found to be significant (p-value 0.000) (Table 1). The p value between the wild homozygous and heterozygous individuals was 0.015. Similarly, the p-value was again found to be significant (0.003) between heterozygous (CT) and mutant homozygous (TT).\n\nAbbreviations: HPLC: high-Performance Liquid Chromatography; CML: Chronic Myeloid Leukaemia.\n\nCYP3A4 rs2242480 polymorphism in genetic models with impact on Imatinib concentration in non-responders and responders.\n\nAnalyzing responders and non-responders, rs2242480, minor allele TT was associated with decreased response to imatinib as a significant p-value in codominant (p-value 0.005), dominant (p value0.002), recessive (p-value 0.02), and additive models (p-value 0.000), whereas in the over-dominant model, the minor allele TT caused a decrease in response with genotypes CC/TT with a p-value of 0.199 (Table 2).\n\nAbbreviations: CML: Chronic Myeloid Leukaemia; OR: Odds ratio; CI: Confidence Interval.\n\n* Significant that is if p value is less than 0.05.\n\n\nDiscussion\n\nDrug transporters, including entry and efflux transporters, along with enzymes involved in imatinib metabolism, may have a substantial influence on therapeutic response. The pharmacokinetic processes of imatinib depend on the efficiency of a protein involved in drug absorption and disposition. After oral administration of IM, it is mainly metabolized by the Cytochrome P450 enzyme system by CYP3A4 and CYP3A5 enzymes. The entry transporters involved are from the ABC subfamily. Organic cationic transporter 1(OCT), encoded by SLC22A1, cannot be ignored because of its importance in the uptake and extrusion of small toxic by-products produced endogenously. Imatinib has changed the course of this cancer, but it is now widely accepted that resistance to this drug is emerging. In this study, we explored the effect of genetic polymorphisms on imatinib trough concentration determined using HPLC and its association with the outcome of treatment in responders and non-responders. This genetic polymorphism was identified against CYP3A4 rs2242480, and data were collected against each allelic form and its association with response. Sex and age associations were also assessed. Imatinib determined by HPLC was also analyzed in both sexes, in different age groups, and against each allelic form.\n\nDuring the study period, from December 2020 to February 2022, blood samples were collected after steady-state concentration was achieved, and it was revealed that HPLC trough levels of imatinib were higher in the elderly than in the younger age groups, with a highly significant p-value (0.01) among groups. The trough levels of imatinib were 625 mg/ml, 780 mg/ml, 801 mg/ml, and 1240 mg/ml from group 1 to group 4, respectively, showing a gradual increase in the concentration of imatinib with increasing age. The potential mechanism behind this could be attributed to the lower volume of distribution and slower metabolism. This finding may guide treating physicians for therapeutic drug monitoring in both elderly and younger patients for dose adjustments with better treatment outcomes in terms of a decrease in adverse effects and relatively higher doses in young patients to achieve therapeutic concentration (Gao, Wang et al. 2023). Our study was in alignment with the study done in July 2023 by Adattini, Adiwidjaja et al. (2023) which showed increased concentration in the older patient population with earlier achievement of complete molecular response and more adverse effects beyond the therapeutic concentration. Another study conducted in April 2020 by Xia, Chen et al. (2020) concluded that age could be a significant covariate in determining imatinib concentration, which also supports this study for anticipating age-related adverse effects with underlying supra-therapeutic imatinib concentrations. The association of response with age was also determined through X2 and it was found to be significant (p value 0.02) with more responders to the treatment in the elderly, which aligns with the effectiveness of Imatinib in CML as determined by Chen, Dong et al. (2020). In terms of response, it was found out that females have a better response as compared to males with responder’s percentage (64% vs 36%) as shown in Table 1 and highly significant association (p value 0.000). The reason for this better outcome could be differences in pharmacokinetic processes, better immune response, or adherence to the treatment, as shown by Breccia, Molica et al. (2018). Imatinib plasma concentration was also higher in females (1151 ng/ml) vs males (875 ng/ml).\n\nSNPs may contribute to inter-individual variations in IM reactions and disposition among different sexes. The mutant allele T was reported to be associated with a higher CYP3A4 metabolic activity, thus enhancing the clearance of IM, which is mainly metabolized by CYP3A4, leading to a substantial decrease in IM plasma levels, which was in agreement with the study done by Pena, Muriel et al. (2020). Therefore, the mutant allele T of rs2242480 is a significant risk factor for predicting inadequate clinical efficacy of IM, and patients who carry mutant allele T of rs2242480 may be suggested to have a higher dose therapy (Fava, Rege-Cambrin et al. 2021).\n\nThe results of this study were narrowed down to show not only a substantial link with the trough IM concentration, but also differential results in the same single nucleotide polymorphism. This is because the findings are all related to issues that have a strong association within their respective domains of concern. In particular, single nucleotide polymorphism of rs2242480 that showed a notable variation in IM concentration warranted or demanded more samples to confirm if they should be considered before IM administration or dose adjustment.\n\nIn conclusion, for the treatment of CML, individualized medicine requires the identification of specific SNPs linked to low imatinib concentrations. Individuals who possess these genetic variants might need to change their dosage, try different treatment plans, or be closely watched to ensure maximal therapeutic efficacy. Furthermore, by comprehending the genetic underpinnings of Imatinib metabolism, adverse drug reactions can be anticipated and managed, improving therapy overall.\n\nAlthough genetic variants frequently exhibit population-specific differences, their analysis requires a diverse range of patient cohorts to account for various obstacles and restrictions. Additionally, the precise role of individual SNPs in influencing imatinib concentration is difficult to determine because of the multifactorial nature of the medication response. This response is influenced by complex interactions between genetic, environmental, and clinical factors.\n\nFuture studies should focus on expanding our knowledge of the genetic factors that influence imatinib metabolism. To ensure that these findings are accurate and applicable to a wider population, it is essential to conduct large-scale studies involving multiple centers. Combining genomic data with clinical outcomes and long-term surveillance studies will provide a more comprehensive understanding of how SNPs affect imatinib response in specific populations. Moreover, advancements in pharmacogenomics may lead to the development of predictive models that can guide personalized treatment plans for CML.\n\n\nConclusion\n\nThere is a potential way to improve the outcomes of CML treatment by considering the relationship between SNPs and low imatinib levels in patients. Despite these challenges, continuous research and collaboration among healthcare experts can help to develop personalized treatment plans. This, in turn, can lead to better safety and effectiveness of Imatinib treatment for patients suffering from chronic myeloid leukaemia.\n\nThis study can be performed on multisite or multicentre to get more detailed results\n\n\nEthics and consent\n\nThe study protocol was approved by the Islamic International Medical Collegeethical review committee Ref#Riphah/IIMC/ERC/19/0265 dated 25th July 2019. The study protocol were in accordance with the declaration of Helsinki and guidelines provided by good clinical practice.\n\nInformed written consent was obtained from all participants before the start of the study.", "appendix": "Data availability\n\nFig share: Data of demographic features of Chronic myeloid leukaemia patients taking Imatinib (400 mg) with genetic and allelic frequencies of rs2242480 is available with: https://doi.org/10.6084/m9.figshare.25448260.v1 (Khan, 2024a).\n\nFig share: Data for Genetic models for rs2242280 in CML patients taking Imatinib (400 mg) is available with https://doi.org/10.6084/m9.figshare.25458964.v1 (Khan, 2024b).\n\nFig share: Figure for Plasma trough concentration of Imatinib (400 mg) in genotypes of rs2242480 is available with https://doi.org/10.6084/m9.figshare.25458973.v1 (Khan, 2024c).\n\nFig share: SPSS Data for rs2242480 Genotype is shared with link https://doi.org/10.6084/m9.figshare.25464859.v1 (Khan, 2024d).\n\nData are available under the terms of the Creative Commons Attribution: licence CC0.\n\nFig share: Strobe guidelines: Impact of CYP3A4 rs2242480 polymorphisms on Imatinib HPLC determined trough concentration and response in chronic myeloid leukaemia in Pakistani patients: DOI https://doi.org/10.6084/m9. figshare.25465027.v1 (Khan, 2024e).\n\nData are available under the terms of the Creative Commons Attribution: licence CC0\n\n\nReferences\n\nAdattini JA, et al.: Application of physiologically based pharmacokinetic modeling to understand real-world outcomes in patients receiving imatinib for chronic myeloid leukemia. Pharmacol. Res. Perspect. 2023; 11(4): e01082. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Saud H, et al.: Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing. Ann. Saudi Med. 2020; 40(5): 373–381. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoovizhikannan T, et al.: Various analytical methods for estimation of Imatinib: A review. World J. Biol. Pharm. Health Sci. 2022; 12(1): 053–065. Publisher Full Text\n\nBreccia M, et al.: Prognostic factors associated with a stable MR4. 5 achievement in chronic myeloid leukemia patients treated with imatinib. Oncotarget. 2018; 9(7): 7534–7540. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen Y, et al.: Factors influencing the steady-state plasma concentration of imatinib mesylate in patients with gastrointestinal stromal tumors and chronic myeloid leukemia. Front. Pharmacol. 2020; 11: 569843. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFarooq N, et al.: Hematological Response to Imatinib Mesylate in Chronic Myeloid Leukemia in a Tertiary Care Centre. Int. J. Pathol. 2019; 66–71.\n\nFava C, et al.: Imatinib: the first-line CML therapy. Chronic Myeloid Leukemia. Springer; 2021; pp. 49–59. Publisher Full Text\n\nGao D, et al.: Prediction for Plasma Trough Concentration and Optimal Dosing of Imatinib under Multiple Clinical Situations Using Physiologically Based Pharmacokinetic Modeling. ACS omega. 2023; 8(15): 13741–13753. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarcía-Ferrer M, et al.: Utility of therapeutic drug monitoring of imatinib, nilotinib, and dasatinib in chronic myeloid leukemia: a systematic review and meta-analysis. Clin. Ther. 2019; 41(12): 2558–2570.e7. PubMed Abstract \| Publisher Full Text\n\nHaque A, et al.: Comparing Imatinib and Nilotinib in the Treatment of Newly Diagnosed Chronic Myeloid Leukemia in Patients of Sandeman Provincial Hospital, Quetta, Pakistan.J. Pak. Soc. Intern. Med.2022;3(1):36–40.\n\nHochhaus A, et al.: European LeukemiaNet 2020 recommendations for treating chronic myeloid leukemia. Leukemia. 2020; 34(4): 966–984. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan A: Demographic features of Chronic Myeloid Leukaemia patients taking Imatinib (400 mg). Genotype and allele frequencies of rs2242480. figshare. Dataset. 2024a. Publisher Full Text\n\nKhan A: Genetic models for rs2242280 in CML patients taking Imatinib (400mg). figshare. Dataset. 2024b. Publisher Full Text\n\nKhan A: Plasma trough concentration of Imatinib (400mg) in genotypes of rs2242480. figshare. Figure. 2024c. Publisher Full Text\n\nKhan A: SPSS DATA FOR rs2242480 Genotype. figshare. Dataset. 2024d. Publisher Full Text\n\nKhan A: STROBE Reporting guidelinesImpact of CYP3A4 rs2242480 polymorphisms on Imatinib HPLC determined trough concentration and response in chronic myeloid leukemia in Pakistani patients. figshare. Online resource. 2024e. Publisher Full Text\n\nMumtaz S, et al.: Genetic diversity of hepatitis c virus genotype 3A based on complete core protein in Peshawar, Pakistan. Jundishapur J. Microbiol. 2020; 13(3). Publisher Full Text\n\nNatarajan H, et al.: Imatinib trough levels: a potential biomarker to predict cytogenetic and molecular response in newly diagnosed patients with chronic myeloid leukemia. Leuk. Lymphoma. 2019; 60(2): 418–425. PubMed Abstract \| Publisher Full Text\n\nOzeki T, et al.: Influence of CYP3A4/5 and ABC transporter polymorphisms on lenvatinib plasma trough concentrations in Japanese patients with thyroid cancer. Sci. Rep. 2019; 9(1): 5404. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPena MÁ, et al.: Effect of cytochrome P450 and ABCB1 polymorphisms on imatinib pharmacokinetics after single-dose administration to healthy subjects. Clin. Drug Investig. 2020; 40(7): 617–628. PubMed Abstract \| Publisher Full Text\n\nSacha T: Imatinib in chronic myeloid leukemia: an overview. Mediterr. J. Hematol. Infect. Dis. 2014; 6(1).\n\nSultan S, et al.: Chronic Myeloid Leukemia: Clinico-Hematological Profile from Southern Pakistan. P J M H S. 2021;15(11): 3047–3049.\n\nUllah A, et al.: A Review of the Genetic Variants Affecting Efficacy and Adverse Effects of Standard of Care Treatment in Patients with Chronic Myelogenous Leukemia. Precis. Med. Commun. 2022; 2(01): 43–58.\n\nXia Y, et al.: Correlations between imatinib plasma trough concentration and adverse reactions in Chinese patients with gastrointestinal stromal tumors. Cancer. 2020; 126: 2054–2061. PubMed Abstract \| Publisher Full Text\n\nZhang Q, et al.: Polymorphisms in drug metabolism genes predict the risk of refractory myasthenia gravis. Ann. Transl. Med. 2022; 10(21): 1155. Publisher Full Text" }	[ { "id": "295002", "date": "08 Jul 2024", "name": "Aijun Zhang", "expertise": [ "Reviewer Expertise Pediatric oncology and hematology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The selection of polymorphisms maybe need more basis; there are many polymorphisms in the P450 enzyme system, and the authors did not provide a good explanation for why only rs2242480 was selected\n2. When comparing imatinib concentrations, an ANOVA was used, before which it was necessary to test for a normal distribution, as data that did not conform to the normal distribution could affect the accuracy of the results if parametric tests were still applied (in fact, the vast majority of cases did not conform to the normal distribution).\n3. In the statistical analysis, age and gender showed significant correlation with imatinib concentration, so it’s necessary to characterize the distribution of age and gender of the samples among genotypes, otherwise it is difficult to judge whether the differences among genotypes are caused by the chance of uneven distribution of age and gender.\n4.\n\nThe comparison of imatinib concentrations between the responding and non-responding groups are necessary to help unearth a direct link between imatinib concentrations and drug response.\n5. As the results suggest that imatinib concentrations are influenced by multiple factors, further studies need to consider whether polymorphisms have better specificity as markers of imatinib levels and drug response. I suggest that multifactorial analyses would be further refined in different subgroups, and also that consideration be given to whether a more accurate and direct indicator of response to treatment in this case might be drug concentrations rather than polymorphisms.\n6. Table1 has an error in the table header, view here\n7. Inappropriate choice of keywords did not reflect the core content of this article.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "305265", "date": "21 Aug 2024", "name": "Nicholas Cross", "expertise": [], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDr Asma Khan and colleagues describe the relationship between constitutional genetic CYP3A4 status with imatinib trough concentration as determined by HPLC. These findings confirm previously indexed studies but insufficient essential detail. Comments:\nThe title of the paper does not make sense – please rephrase The abstract should include the number of cases studies and P value In addition to gender the study should consider the disease phase of the patients at diagnosis as well as the ELTS score in their analysis. The fact that many patients did not achieve CHR after 3 months suggests a high proportion of cases in advanced phase.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-310
https://f1000research.com/articles/12-293/v1	16 Mar 23	{ "type": "Research Article", "title": "Sargassum sp. extract improve hematological profile of tilapia fish (Oreochromis niloticus)", "authors": [ "Mohamad Gazali", "Irwan Effendi", "Amir Husni", "Nurjanah Nurjanah", "Sri Wahyuni", "Ronal Kurniawan", "Irwan Effendi", "Amir Husni", "Nurjanah Nurjanah", "Sri Wahyuni" ], "abstract": "Background: Strategies to increase body resistance and prevent disease in aquaculture include using vaccines, antibiotics, and probiotics. Today, the use of antibiotics with natural ingredients is becoming a trend. One of the natural ingredients that contain high antioxidants and antibiotics is Sargassum sp. Methods: This research was conducted from March to May 2022 at the Biotechnology Laboratory, Faculty of Fisheries and Marine, Universitas Riau, in two stages: 1) the sensitivity of extracts of Sargassum sp. and 2) the application of Sargassum sp. extract orally in tilapia (O. niloticus). The parameters measured were clear zone, minimum inhibitory concentration, LD50 test of leaf extract of Sargassum sp. in tilapia (O. niloticus), hemoglobin levels, hematocrit, total leukocytes, total erythrocytes, leukocyte differentiation, and survival rate. Data on hematology parameters were tabulated and analyzed using a One-Way ANOVA followed by a Student Newman Keuls (SNK) test when deemed necessary. Results: The results showed that the extract of Sargassum sp. inhibited the growth of Aeromonas hydrophila bacteria with a clear zone of 6.5-15.0 mm, which is classified as resistant. At doses of 2000, 2500, and 3000 ppm, it did not cause death in fish for 96 hours (LD50). Hematological parameters can be a sign of the health status of fish. Tilapia given Sargassum sp. in different doses gave an effect between treatments, both after 30 days of rearing and post-test against A. hydrophila bacteria (p<0.05). The results showed that the hematology of fish fed with Sargassum sp. extract was in the normal or healthy range. Healthy tilapia had erythrocyte counts ranging from 1.34-2.11×106 cells/mm3, hematocrit 26.17-33.19%, hemoglobin 6.26-11.2 g/dL and total leukocytes 1.01-1.50×104 cells/mm3 and total erythrocytes 5.88-9.13×104 cells/ mm3. Conclusions: A dose of 3000 ppm provided the highest health improvement against A. hydrophila bacterial infection.", "keywords": [ "Sargassum sp. extract", "hematology", "A. hydrophila", "fish health status" ], "content": "Introduction\n\nAquaculture is the answer to meeting global nutritional needs of a growing population and ensuring food safety from aquatic sources.1 Tilapia (Oreochromis niloticus) is an omnivorous fish with advantages such as a tolerance to different environments, high economic value, and high market demand.2,3 To meet the demand, intensive aquaculture with high stocking density and artificial feed has become the standard in fish farming.4 Challenges in this aquaculture include feed costs, environmental pollution, climate change, water quality, and pathogen infection,5 which can reduce the productivity and profitability of aquaculture activities.6,7\n\nMotile Aeromonas septicaemia (MAS) caused by Aeromonas hydrophila is a bacterial disease that can cause mass mortality in a culture.7,8 The pathogenicity of A. hydrophila can cause mortality in cultured fish up to 80-100% within one to two weeks.9 Strategies to increase body resistance and prevent disease in cultivation including using vaccines, antibiotics, and probiotics. Antibiotic applications have been widely used to control fish diseases, including MAS. However, its use affects the environment and human health, including through causing the multi-resistance of bacteria and the accumulation of these compounds in foodstuffs.10,11\n\nUnderstanding how specific and non-specific immune responses modulate fish health is key to increasing productivity and reducing losses in the intensive aquaculture sector. Nowadays, the use of antibiotics with natural ingredients is becoming a trend. Some immunostimulants used as additives in feed can enhance the body's defense system and thus prevent losses from disease.12 In addition, enhancing the immune response with environmentally friendly materials is an effective strategy to promote sustainable cultivation.\n\nMarine macroalgae are natural ingredients that contains high antioxidants and antibiotics. Macroalgae contain primary metabolites such as vitamins, minerals, fiber, alginate, carrageenan, and agar that are widely used as cosmetic ingredients for skin care. The brown macroalga Sargassum sp. has an essential function in marine ecosystems.13 One of the most important functions of Sargassum is to provide a nursery habitat for juvenile fish and other marine animals.14 The floating mats of Sargassum provide shelter for young fish and other animals to hide from predators, feed, and grow.15 Sargassum sp. is a brown macroalgae that grows in the mid-littoral to sub littoral zone.16 Sargassum sp. Is mostly unexploited and has been found to contain phenols, alkaloids, triterpenoids,17 saponins, and flavonoids.18 According to Lee et al.,19 the extract of S. horneri, an additional immunostimulant in feed, showed significant results supporting its use in white shrimp culture. Therefore, it is necessary to research the effect of Sargassum sp. as a feed supplement for immune response and prevention of infection with A.hydrophila bacteria in tilapia (O. niloticus).\n\n\nMethods\n\nThis research was conducted from March to May 2022 at the Biotechnology Laboratory, Faculty of Fisheries and Marine, Universitas Riau.\n\nThis research was conducted in two stages, namely 1) the sensitivity test of extracts of Sargassum sp. and 2) the oral administration of extracts of Sargassum sp. in tilapia (O. niloticus). The experiments were carried out within the ethical guidelines provided by the research institution and national or international regulations.\n\nA sensitivity test was performed using the Kirby Bauer disc method. To reduce the error rate, it was repeated three times. Determination of the dose used refers to the study of Ref. 20. The dose of macroalgae extract used is as follows:\n\nOxytetracycline antibiotics as a positive control\n\nD1: 100% macroalgae extract equivalent to 10,000 ppm\n\nD2: 90% macroalgae extract equivalent to 9,000 ppm\n\nD3: 80% macroalgae extract equivalent to 8,000 ppm\n\nD4: 70% macroalgae extract equivalent to 7,000 ppm\n\nD5: 60% macroalgae extract equivalent to 6,000 ppm\n\nD6: 50% macroalgae extract equivalent to 5,000 ppm\n\nD7: 40% macroalgae extract equivalent to 4,000 ppm\n\nD8: 30% macroalgae extract equivalent to 3,000 ppm\n\nD9: 20% macroalgae extract equivalent to 2,000 ppm\n\nD10: 10% macroalgae extract equivalent to 1000 ppm\n\nThe parameters measured during the study were:\n\n1. Clear zone\n\n2. Minimum inhibitory concentration\n\n3. LD50 test of leaf extract of Rhizophora sp. in tilapia (O. niloticus).\n\nObservation of the inhibition zone of Sargassum sp. against bacteria A. hydrophila was conducted using the Kirby-Bauer disc method, using a 6 mm diameter blank disk. In the initial stage, a solution of Sargassum sp. 50 μL and oxytetracycline as a control was applied into a blank disc using a micropipette. Next, the blank disc was left for ±3 minutes to absorb the solution. It was then placed on TSA media containing A. hydrophila bacterial inoculant and incubated for 24 hours at 37°C. After 24 hours, the inhibition zone was observed by measuring the diameter of the clear zone formed using a caliper.\n\nThe dose used in the MIC test was based on the extract dose that produced the smallest inhibition zone to one that did not produce any. Each extract dose was added with 50 μL of bacterial suspension (bacterial density 108 CFU/mL). The solution was then homogenized and incubated for 24 hours at 37°C. The number of colonies was observed by isolating the bacteria from a solution previously incubated for 24 hours into 50 μL of TSA media and then re-incubated. After 24 hours, the bacterial colonies in the dish were counted, containing 30-300 colonies.\n\nThe LD50 toxicity test was initiated by preparing 120 tilapia fish into a container containing Sargassum sp. extract according to the treatment dose, referring to the MIC test. Each container contained 10 L of water, with a stocking density of 1 fish/1 L. LD50 observations were undertaken for 24-96 hours by observing the behavior, clinical symptoms, and fish mortality reaching 50%.\n\nObservation of the immune response was carried out using the experimental method by applying a one-factor completely randomized design (CRD) with five levels of treatment; to reduce the error rate, it was repeated three times so that 15 experimental units were needed. The treatment doses in this study were selected according to the preliminary test as follows:\n\nNC: Negative control (feeding without Sargassum sp. extract and without being infected with A. hydrophila bacteria)\n\nPC: Positive control (feeding without Sargassum sp. extract and infected with A. hydrophila bacteria)\n\nF1: Feed containing sargassum sp. extract at a dose of 2.0 g/kg feed\n\nF2: Feed containing sargassum sp. extract at a dose of 2.5 g/kg feed\n\nF3: Feed containing sargassum sp. extract at a dose of 3.0 g/kg feed\n\nThe parameters measured were hemoglobin levels, hematocrit, total leukocytes, total erythrocytes, leukocyte differentiation and survival rate.\n\nThis study used 300 fingerlings of tilapia, around 5.20±0.03 g BW. The fish specimens were selected based on their performance, indicated by active swimming, no wounds or external parasites. Before the treatment, the fish was adapted for a week. The experiments were carried out within the ethical guidelines provided by the research institution and national or international regulations.\n\nThe macroalgae were dried and crushed using a blender. Once it was smooth, it was extracted, and the products were mixed into commercial feed with the dose according to the treatment. Next, it was printed and dried before a proximate test was carried out to examine the nutritional content of the pellets.\n\nThe fish were reared in a 60 × 30 × 30 cm aquarium filled with 60 L fresh water and the fish density was 1 fish/3 L water. The fish was reared for 30 days and fed three times/day (08.00 AM, 01.00, and 06.00 PM). The total feed provided was 5% of body weight per day.\n\nThe A. hydrophila strain (ATCC 35654) used in this study was obtained from the Fish Quarantine in Pekanbaru, Riau, Indonesia. Fish were infected with A. hydrophila (0.1 mL 108 of A. hydrophila culture). Negative control (Nc) were fish without any treatment, while positive control (Pc) were fish infected with A. hydrophila and not given Sargassum extract. A total of 15 fish from each treatment were studied. Blood sampling was conducted three times: at the beginning, middle and end of the study period, with three fish from each aquarium. They were anesthetized using clove oil (5 drops/L). While they were inactive and unresponsive to touch, blood was then drawn from the tail vein by inserting a 10% moistened EDTA (Merck) syringe. Blood samples were stored in moistened EDTA vials in cold boxes filled with crushed ice. Total erythrocytes and leukocytes were counted using a Neubauer hemocytometer and then counted21 and analyzed.22 Hematocrit and leukocrit levels were determined using heparin capillary micro-hematocrit and centrifuged at 12,000 rpm for three minutes. To calculate the hematocrit or leukocrit level, the length of the column of packed red cells or packed white cells was measured and divided by the length of the entire column of blood (cells and plasma) and multiplied the number by 100%. Hemoglobin levels were measured using Sahli’s method.23\n\nData on hematology parameters (the total erythrocytes, hematocrit level, hemoglobin, total leucocytes, leucocyte differentiation, Phagocytic Index, and survival) were tabulated and analyzed using SPSS 26. Data were analyzed using a one-way ANOVA followed by a Student Newman Keuls (SNK) test if necessary.\n\nAll animals were treated according to animal welfare guidelines that have been established and approved by the Dean of the Faculty of Fisheries and Marine Science, Teuku Umar University, Prof. M. Ali Sarong; Prof. Sarong serves as the ethical commitee who approved the use of vertebrae animal in these experiments with approval number: 0674/UN59.3/TU.00.01/2022.\n\n\nResults\n\nThe results of the sensitivity test showed that the use of Oxytetracycline and extracts of Sargassum sp. with doses of 100%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, and 10% resulted in different inhibitory zones against the growth of A. hydrophila bacteria. Doses of 30-100% can inhibit the growth of A. hydrophila bacteria with an inhibition zone ranging from 6.5-15.0 mm, while doses of 10-20 % are no longer formed inhibition zones. More details can be seen in Table 1.\n\nThe minimum inhibitory concentration (MIC) test was carried out based on the results of the sensitivity test of Sargassum sp. with a dose that produces a minimum zone of inhibition, which was then diluted to obtain 30%, 25%, and 20% doses. The MIC test aimed to determine the minimum concentration to inhibit bacterial growth. The results showed that a dose of 20-30% produced an average number of colonies capable of inhibiting the growth of A. hydrophila bacteria ranging from 155.33-215×108 CFU/mL. A dose of 20% was the minimum dose to inhibit the growth of A. hydrophila bacteria. On the other hand, in the control treatment (0%), the number of growing bacterial colonies was uncountable. The results of the MIC test can be seen in Table 2.\n\nThe LD50 toxicity test of macroalgae extract was carried out to obtain a dose of extract that caused 50% death for 96 hours in 10 tilapia tested per aquarium. The doses used were based on the MIC test results obtained, namely 20% (2000 ppm), 25% (2500 ppm), and 30% (3000 ppm) and control. The results showed that tilapia soaked with Sargassum sp. did not die after 96 hours of experience, indicating that the Sargassum sp. was not toxic to fish. The results of the toxicity test can be seen in Figure 1.\n\nMeasurements of erythrocyte cells of tilapia fed a diet containing extracts of Sargassum sp. with different doses can be seen in Table 3. The administration of Sargassum sp. in the feed with different doses caused an increase in the immune response, which was shown by the increase in total erythrocytes ranging from 1.57-1.93×106 cells/mm3, when compared to fish given the feed without the addition of Sargassum sp. Which ranged from 1.40-1.67×106 cells/mm3 after 30 days of rearing and post-challenge test with A. hydrophila bacteria (p<0.05). Meanwhile, tilapia fed without Sargassum extract could not be examined for erythrocyte cell numbers due to mortality reaching 100%.\n\nThe increase in total erythrocytes was in line with the increase in hemoglobin and hematocrit levels in tilapia fed with Sargassum sp. extract after 30 days of rearing and post-test against A. hydrophila bacteria (p<0.05).\n\nMeasurement of leukocyte cells of tilapia fed a diet containing extracts of Sargassum sp. with different doses can be seen in Table 4. Feed containing extracts of Sargassum sp. increased the immune response of tilapia, indicated by an increase in total leukocytes ranging from 1.91-1.99×104 cells/mm3 when compared to the control treatment ranging from 1.88-1.89×104 cells/mm3 after 30 days of rearing (p<0.05). This range remained in normal conditions. In addition, it also affected the concentration of lymphocytes ranging from 76.67-79.33% (p<0.05). The concentration of monocytes, neutrophils, and platelets was not significantly different between treatments (p>0.05).\n\nAfter the challenge test, the total leukocytes of fish increased between 2.01-2.10×104 cells/mm3 (p<0.05), this range was in normal conditions. The leukogram of PC could not be observed because the mortality reached 100%. Feed with extracts of Sargassum sp. at different doses affected the concentration of lymphocytes, monocytes, neutrophils, and platelets of tilapia (p<0.05).\n\nTilapia survivors were fed with extracts containing Sargassum sp. with doses ranging from 95-98.33% for 30 days of rearing (p>0.05). After the challenge test with A. hydrophila bacteria, tilapia survival ranged from 71.67-83.33%, while the KP (control feed and challenged A. hydrophila) experienced 100% mortality. More details are presented in Figure 2.\n\n\nDiscussion\n\nSargassum sp. extract. at a dose of 100% - 30% inhibited the growth of A. hydrophila bacteria. This can be seen from the average inhibition zone formed for each dose. Wayne24 categorizes the resulting inhibition zones into susceptible, intermediate, and resistant criteria. The CLSI criteria define the sensitivity as susceptible if the diameter of the inhibition zone formed is 21 mm, intermediate if the diameter of the inhibition zone is between 16-20 mm, and resistant if the diameter of the inhibition zone is 15 mm. This study obtained an inhibitory zone of 6.5–15 mm against A. hydrophila bacteria, so the overall treatment group corresponded for the resistant criteria for Sargassum sp. against A. hydrophila bacteria.\n\nCalculation of the growth of the number of bacterial colonies of A. hydrophilla given a solution of the extract of Sargassum sp. with doses of 20%, 25% and 30% resulted in the average number of colonies capable of inhibiting the growth of A.hydrophilla bacteria ranging from 155.33×108 CFU/mL – 215.33×108 CFU/mL. At a dose of 20%, the average number of bacterial colonies was 215.33×108 CFU/mL. It could be said that the minimum dose inhibited the growth of A.hydrophilla bacteria. The best bacterial colony growth in inhibiting bacterial growth is 30-300 colonies.25\n\nThe survival rate of tilapia against Sargassum sp. showed that 2000, 2500 and 3000 ppm doses did not cause fish death. This indicates that Sargassum sp. extract is not a toxic substance. In addition, this type of macroalgae has active ingredients that can inhibit the growth of bacteria, so it is expected to be an alternative disease control in aquaculture in Indonesia.\n\nAccording to Tavares-Dias et al. and Fagbenro et al.,26,27 stress and nutritional imbalance can trigger changes in tilapia blood parameters. Hematological parameters are essential for assessing the health status of fish and evaluating fish physiology, feed impact, and other stressors. Environmental conditions, sex, age, feeding, and fish activity can affect hematological parameters.28\n\nIn this study, the hematological parameters (erythrogram and leukogram) of tilapia that were given to the addition of Sargassum sp. with different doses showed an effect between treatments, both after 30 days of rearing and post-test against A. hydrophila bacteria (p<0.05). This indicates that the administration of Sargassum sp. can affect fish health. A dose of 3000 ppm lead to the highest health improvement against A. hydrophila bacterial infection, thought to be caused by the nutrients and secondary metabolites in the feed capable of meeting the needs in forming the fish's immune system.\n\nFish infected with the bacteria experience changes in the number of erythrocytes, hemoglobin, hematocrit, and total leukocytes. The results showed that the hematology of fish fed with Sargassum sp. extract was within the normal or healthy ranges. Healthy tilapia have erythrocyte counts ranging from 1.34-2.11×106 cells/mm3, hematocrit 26.17-33.19%,29 hemoglobin 6.26-11.2 g/dL,30 and total leukocytes 1.01-1.50×104 cells/mm3,31 5.88-9.13×104 cells/mm3.32 Increased hemoglobin levels are associated with increased oxygen transport capacity and the body's defense mechanism against stress.\n\nThe secondary metabolite contents of Sargassum include vitamin C, fucoidan, and flavonoids. Vitamin C in Sargassum sp. can increase immunity and function and act as a fish immune system booster.33 In addition, fucoidan can stimulate the immune response by producing fish immune cells. However, given its ability to activate immune cells and promote cytokine production, fucoidan may have potential as an immune-boosting supplement.34 Flavonoids function as immunomodulators or substances that can affect the quality and intensity of the immune response. Flavonoids can stimulate the immune system by sending intracellular signals to cell receptors, making cell performance more active. The action of active ingredients, especially flavonoids, in stimulating the immune system is to accelerate the activation of leukocytes and macrophages so that the phagocytosis process against foreign bodies can be carried out quickly.35,36\n\nVitamin C can increase the body's resistance to pathogens; its role in protein synthesis is necessary in immune responses and collagen biosynthesis to accelerate the wound healing process. Leukocytes, in addition to the thymus gland, spleen, and immune cells, store large concentrations of vitamin C. In stressed fish, the number of lymphocyte cells in the blood and lymphoid organs (bone marrow, lymph glands, and spleen) decrease.37 Hazzuli et al.38 stated that fish would respond to vitamin C by increasing the activity and reactivity of cellular and humoral defense cells. Besides, it can increase fish's phagocytic activity (non-specific immune response).\n\nMacroalgae are a valuable source of secondary metabolites, which can increase immune responses and are used as immunostimulants in aquaculture fish feed.39 Sargassum sp. extract application on immune responses has been carried out in several types of aquatic biota such as tiger prawns,40 mullet,41 Asian sea bass,42 and rainbow trout.43,44 Generally, it has been shown that Sargassum extract can be used as an immunostimulant.\n\n\nConclusions\n\nThe results of the present research showed that the extract of Sargassum sp. was able to inhibit the growth of A. hydrophila bacteria with an inhibition zone (clear zone) of 6.5-15.0 mm, which is classified as resistant; at doses of 2000, 2500, and 3000 ppm it did not cause death in fish for 96 hours (LD50). Hematological parameters can be a sign of the health status of fish. Tilapia given Sargassum sp. extract at different doses showed an effect between treatments after 30 days of rearing and post-test against A. hydrophila bacteria (p<0.05). The results showed that the hematology of fish fed with Sargassum sp. was within the normal or healthy range. Healthy tilapia had erythrocyte counts ranging from 1.34-2.11×106 cells/mm3, hematocrit 26.17-33.19%, hemoglobin 6.26-11.2 g/dL, total leukocytes 1.01-1.50×104 cells/mm3 and total erythrocytes 5.88-9.13×104 cells/mm3. A dose of 3000 ppm led to the highest health improvement against A. hydrophila bacterial infection.\n\n\nAuthor roles\n\nGazali M: Conceptualization, Data Curation, Formal Analysis, Methodology, Writing – Original Draft Preparation; Effendi I: Data Curation, Formal Analysis, Supervision, Methodology, Writing – Original Draft Preparation; Husni A: Data curation, Validation, Writing-Review & Editing; Nurjanah N: Data Curation, Validation, Writing-Review & Editing; Wahyuni S: Conceptualization, Investigation, Methodology, Writing – Original Draft Preparation; Kurniawan R: Conceptualization, Investigation, Methodology, Software, Writing – Original Draft Preparation", "appendix": "Data availability\n\nZenodo: Sargassum sp. extract improve Hematological profile of Tilapia fish (Oreochromis niloticus), https://doi.org/10.5281/zenodo.7595715. 45\n\n- Erytrogram, leucogram, survival.xlsx\n\n- Figure 1. docx\n\n- Table 1. docx\n\n- TABLE CLEAR ZONE, COUNT BACTERIA, LD50.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would like to thank the Laboratory of Fisheries University of Riau. This research was funded by Ministry of Education and Republic of Indonesia with Collaboration University Research.\n\n\nReferences\n\nEdwards P, Zhang W, Belton B, et al.: Misunderstandings, myths and mantras in aquaculture: its contribution to world food supplies has been systematically over reported. Mar. Policy. 2019; 106: 103547. Publisher Full Text\n\nDawood MAO, Zommara M, Eweedah NM, et al.: Synergistic effects of selenium nanoparticles and vitamin E on growth, immune-related gene expression, and regulation of antioxidant status of Nile tilapia (Oreochromis niloticus). Biol. Trace Elem. Res. 2019; 195: 624–635. PubMed Abstract \| Publisher Full Text\n\nMagouz FI, Mahmoud SA, El-Morsy RAA, et al.: Dawood MAO,: Dietary menthol essential oil enhanced the growth performance, digestive enzyme activity, immune-related genes, and resistance against acute ammonia exposure in Nile tilapia (Oreochromis niloticus). Aquaculture. 2021; 530: 735944. Publisher Full Text\n\nMastan AS: Use of Immunostimulants in aquaculture disease management. J. Fish. Aquat. Sci. 2015; 2(4): 277–280.\n\nBoyd CE, D'Abramo LR, Glencross BD, et al.: Achieving sustainable aquaculture: Historical and current perspectives and future needs and challenges. J. World Aquacult. Soc. 2020; 51(3): 578–633. Publisher Full Text\n\nArunkumar M, LewisOscar F, Thajuddin N, et al.: In vitro and in vivo biofilm forming Vibrio spp: A significant threat in aquaculture. Process Biochem. 2020; 94: 213–223. Publisher Full Text\n\nEl-Gawad EAA, Esaly AME, Soror EI, et al.: Effect of dietary Moringa oleifera leaf on the immune response and control of Aeromonas hydrophila infection in Nile tilapia (Oreochromis niloticus) fry. Aquac. Int. 2019; 28: 389–402. Publisher Full Text\n\nAshour M, Mabrouk MM, Ayoub HF, et al.: Effect of dietary seaweed extract supplementation on growth, feed utilization, hematological indices, and non-specific immunity of Nile Tilapia, Oreochromis niloticus challenged with Aeromonas hydrophila. J. Appl. Phycol. 2020; 32(5): 3467–3479. Publisher Full Text\n\nNahar S, Rahman MM, Ahmed GU, et al.: Isolation, Identification, and Caracterization of Aeromonas hydrophila from Juvenile Farmed Pangasius (Pangasius hypophthalmus). Int. J. Fish. Aquat. Stud. 2016; 4(4): 52–60.\n\nOmitoyin BO, Ajani EK, Orisasona O, et al.: Effect of guava Psidium guajava (L.) aqueous extract diet on growth performance, intestinal morphology, immune response and survival of Oreochromis niloticus challenged with Aeromonas hydrophila. Aquac. Res. 2019; 50: 1851–1861. Publisher Full Text\n\nHoseinifar SH, Esteban MA, Cuesta A, et al.: Prebiotics and fish immune response: a review of current knowledge and future perspectives. Rev. Fish. Sci. Aquac. 2015; 23(4): 315–328. Publisher Full Text\n\nThy HTT, Tri NH, Quy OM, et al.: Effects of the dietary supplementation of mixed probiotic spores of Bacillus amyloliquefaciens 54A, and Bacillus pumilus 47B on growth, innate immunity and stress responses of striped catfish (Pangasianodon hypophthalmus). Fish Shellfish Immunol. 2017; 60: 391–399.\n\nYang Y, Chai Z, Wang Q, et al.: Cultivation of seaweed Gracilaria in Chinese coastal waters and its contribution to environmental improvements. Algal Res. 2015; 9: 236–244. Publisher Full Text\n\nEggertsen L, Ferraira CEL, Fontoura L, et al.: Seaweed beds support more juvenile reef fish than seagrass beds in a south-westren Atlantic tropical seascape. Estuar. Coast. Shelf Sci. 2017; 196: 97–108. Publisher Full Text\n\nStachowiak C: Assessing the Nursery-Role Function of Pelagic Sargassum for Juvenile Fishes the Northen Gulf of Mexico. Master’s Theses.2020.\n\nHu ZM, Uwai S, Yu SH, et al.: Phylogeographic heterogeneity of the brown macroalga Sargassum horneri (Fucaceae) in the northwestern Pacific in relation to late Pleistocene glaciation and tectonic configurations. Mol. Ecol. 2011; 20: 3894–3909. PubMed Abstract \| Publisher Full Text\n\nGazali M, Nurjanah ZNP: Eksplorasi Senyawa Bioaktif Alga Cokelat Sargassum sp. Agardh Sebagai Antioksidan dari Pesisir Barat Aceh. J. Pengolah. Has. Perikan. 2018; 21(1): 167–178. Publisher Full Text\n\nPrabu DL, Sahu NP, Pal AK, et al.: Immunomodulation and interferon gamma gene expression in sutchi catfish, Pangasianodon hypophthalmus: Effect of dietary fucoidan rich seaweed extract (FRSE) on pre and post challenge period. Aquac. Res. 2016; 47: 199–218. Publisher Full Text\n\nLee PT, Tran HTQ, Huang HT, et al.: Sargassum horneri extracts stimulate innate immunity, enhance growth performance, and upregulate immune genes in the white shrimp Litopenaeus vannamei. Fish Shellfish Immunol. 2020; 102: 276–285. PubMed Abstract \| Publisher Full Text\n\nKurniawan R, Wahyuni S, Armando F: Inhibition Test of Hot Water Extract of Rhizophora apiculata Leaves Against Edwardsiella tarda Bacteria in-vitro. J. Natur Indones. 2022; 20(1): 30–34. Publisher Full Text\n\nBlaxhall PC, Daisley KW: Routine haematological methods for use with fish blood. J. Fish Biol. 1973; 5(6): 771–781. Publisher Full Text\n\nAnderson DP, Siwicki AK: Simplified Assays for Measuring Non-specific Defense Mechanism in Fish. Fish Health Section/American Fisheries Sociaty Meetings. Washington.1994; 26.\n\nPatil PJ, Thakare GV, Patil SP: Variability and Accuracy of Sahli’s Method in Estimation of Haemoglobin Concentration. Natl. J. Integr. Res. Med. 2013; 4(1).\n\nClinical and Laboratory Standards Institute (CLSI): Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fourth Informational Supplement. Wayne: CLSI Document M100-S24; 2014; 34(1).\n\nDwidjoseputro: Dasar-Dasar Mikrobiologi. Penerbit Djembatan: Jakarta.2010.\n\nTavares-Dias M, Mariano WS: Aquicultura no Brasil: Novasperspectivas. Aspectos Biológicos, Fisiológicos e Sanitários de Organismos Aquáticos. São Carlos: Pedro & João Editores; 2015.\n\nFagbenro O, Adeparusi E, Jimoh W: Haematological profile of blood of African catfish (Clarias gariepinus, Burchell 1822) fed sunflower and sesame meal based diets. J. Fish. Aquat. Sci. 2010; 8: 80–86.\n\nIbrahim RE, Amer SA, Shahin SA, et al.: Davies SJ, Attia GA, Effect of fish meal substitution with dried bovine hemoglobin on the growth, blood hematology, antioxidant activity and related genes expression, and tissue histoarchitecture of Nile tilapia (Oreochromis niloticus). Aquac. Rep. 2022; 26: 101276. Publisher Full Text\n\nSuryaningrum LH, Samsudin R: Nutrient digestibility of green seaweed Ulva meal and the influence on growth performance of Nile tilapia (Oreochromis niloticus). Emir. J. Food Agric. 2020; 32(7): 488–494.\n\nPratiwi DY, Pratiwy FM: A review-the effect of dietary supplementation of Ulva on the growth performance and haematological parameters of Nile tilapia (Oreochromis niloticus). Int. J. Fish. Aquat. Stud. 2022; 10(1): 29–32.\n\nEmam MA, Shourbela RM, El-Hawarry WN, et al.: Effects of Moringa oleifera aqueous extract on the growth performance, blood characteristics, and histological features of gills and livers in Nile tilapia. Aquac. Fish. 2021. Publisher Full Text\n\nLukistyowati I: Feliatra, Adelina, Application of Probiotic that are in Isolation From Giant Prawns and Black Tiger Shrimps on the Leukocytes of Nile Tilapia (Oreocromis niloticus) Infected by Streptococcus iniae. Int. J. Oceans Oceanogr. 2019; 13(2): 309–324.\n\nPratiwy FM, Pratiwi DY: The effects of bioactive compound (Antioxidant) from Sargassum extract on the erythrocytes and differential leucocytes of catfish (Clarias sp.). Int. J. Fish. Aquac. Stud. 2020; 8(6): 123–126. Publisher Full Text\n\nCastro RI, Zarrab, Lamas J: Watersoluble Seaweed Extracts Modulate the Pantoea agglomerans lippolysaccharide (LPS). Fish Shellfish Immunol. 2004; 10: 555–558.\n\nSyawal H, Effendi I, Kurniawan R: Improving Haematological Profile of Catfish (Pangasius hypophthalmus) Due to Addition of Herbal Supplements in Feed. Jurnal Veteriner. 2021; 22(1): 16–25. Publisher Full Text\n\nPayung NC, Manoppo H: Peningkatan Respons Kebal Non-Spesifik dan Pertumbuhan Ikan Nila (Oreochromis niloticus) Melalui Pemberian Jahe (Zingiber officinale). Jurnal Budidaya Perairan. 2015; 3(1): 11–18.\n\nAffandi R, Tang UM: Fisiologi Hewan Air. Malang. Intermedia: 70 hlm.2017.\n\nHazzuli NJ, Setyawan A, Harpeni E: Imunogenitas Kombinasi Vaksin Inaktif Whole Cell Aeromonas salmonicida dan Vitamin C pada Ikan Mas (Cyprinus carpio). E-Jurnal Rekayasa dan Teknologi Budidaya Perairan. 2015; 3(2): 359–365.\n\nAraújo M, Rema P, Sousa-Pinto I, et al.: Dietary inclusion of IMTA-cultivated Gracilaria vermiculophylla in rainbow trout (Oncorhynchus mykiss) diets: effects on growth, intestinal morphology, tissue pigmentation, and immunological response. J. Appl. Physiol. 2016; 28: 679–689. Publisher Full Text\n\nImmanuel G, Sivagnanavelmurugan M, Marudhupandi T, et al.: The effect of fucoidan from brown seaweed Sargassum wightii on WSSV resistance and immune activity in shrimp Penaeus monodon (Fab). Fish Shellfish Immunol. 2012; 32: 551–564. PubMed Abstract \| Publisher Full Text\n\nKanimozhi S, Krishnaveni M, Deivasigmani B, et al.: Immunomostimulation effects of Sargassum whitti on Mugil cephalus against Pseudomonas fluorescence. Int. J. Curr. Microbiol. App. Sci. 2013; 2: 93–103.\n\nYangthong M, Hutadilok-Towatana N, Thawonsuwan J, et al.: An aqueous extract from Sargassum sp. enhances the immune response and resistance against Streptococcus iniae in the Asian sea bass (Lates calcarifer Bloch). J. Appl. Phycol. 2016; 28: 3587–3598. Publisher Full Text\n\nYazdanpanah M, Sotoudeh E, Mansouri TH, et al.: Dietary administration of Sargassum angustifolium and Gracilaria pulvinata extracts affect antioxidant enzyme activities and Lactobacillus bacterial population in intestine of rainbow trout (Oncorhynchus mykiss) fry. Iran J. Fish. Sci. 2021; 20(4): 926–944.\n\nSonmez AY, Bilen S, Tastan Y, et al.: Oral administration of Sargassum polycystum extracts stimulates immune response and increases survival against Aeromonas hydrophila infection in Oncorhynchus mykiss. Fish Shellfish Immunol. 2021; 117: 291–298. PubMed Abstract \| Publisher Full Text\n\nGazali M, Effendi I, Husni A, et al.: Sargassum sp extract improve Hematological profile of Tilapia fish (Oreochromis niloticus). [Data set]. Zenodo. 2022. Publisher Full Text" }	[ { "id": "166807", "date": "08 Jun 2023", "name": "Wahidatul Husna Zuldin", "expertise": [ "Reviewer Expertise Seaweed Culture", "Macroalgal Extraction", "Microalgae Culture", "Seaweed Ecology." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract\nThe abstract was clearly written. Easy to comprehend with sufficient information on the research background, applied methods, and data produced from the study.\nIntroduction\nThe introduction section was nicely written. However, the author is suggested to add more on past studies related to the relationship between macroalgal extract and fish hematological profile.\nMethods\nPlease clarify what features of Sargassum sp. were used in the study. Is it include the rhizoids/roots?\nWhen does the author state Sargassum sp., and what potential species were used in the study?\nAlso, further, explain the extraction method. What solvent was used for the seaweed extraction?\nResults and Discussion\nThe results section was clearly presented. Great work on that. The data are highly useful for the tilapia industry. The discussion section was nicely written with a recent literature review included to support the findings.\nConclusions\nThe conclusions are relevant and clearly stated.\nOverall, the article is well written with minor revisions required.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-293
https://f1000research.com/articles/13-309/v1	22 Apr 24	{ "type": "Study Protocol", "title": "Postural control imbalance in individuals with a minor lower extremity amputation: a scoping review protocol.", "authors": [ "Maxime Acien", "Ahmed Dami", "Virginie Blanchette", "Gabriel Moisan", "Ahmed Dami", "Virginie Blanchette", "Gabriel Moisan" ], "abstract": "Introduction Lower extremity amputations (LEA) impact the quality of life and physical abilities and increase the risk of developing secondary health complications. Current literature predominantly focuses on major LEA, leaving a gap in understanding biomechanics related to balance and postural control in minor LEA. The shifts towards increased rates of minor LEA, due to improved quality of care and patient management, highlights the need for a focused exploration of postural control deficits in this population. The scoping review will address this gap in the literature.\n\nObjectives The purpose of the review is to synthesize current research on postural control deficits following a minor foot amputation, focusing on any resections through or distal to the ankle joint, and to evaluate interventions aimed at improving balance in affected individuals.\n\nInclusion criteria The review will encompass individuals of all ages who underwent a minor foot amputation, including various levels and etiologies. It will focus on quantitative data related to standing posture, ability to perform self-balanced activities of daily living, and external aids or treatments to improve postural control. The outcomes will include modifications in the sensation of balance, fall predictors, and biomechanical changes in postural control.\n\nMethods A preliminary search of MEDLINE (PubMed) was conducted to develop a full search strategy aimed at compiling all existing scientific articles on postural control and balance in individuals with a minor LEA. A comprehensive search will be performed across multiple databases and grey literature. Two reviewers will independently extract the data. The Mixed Methods Appraisal Tool will be used to assess risk and quality.\n\nDiscussion By emphasizing the understudied aspects of postural control imbalances induced by minor LEA, the review will highlight potential areas for therapeutic intervention and contribute to a better understanding of rehabilitation for those affected.", "keywords": [ "Ankle", "Amputation", "Biomechanical Phenomena", "Foot", "Lower extremity", "Postural Balance", "Review" ], "content": "Introduction\n\nOver the last decade, the annual number of lower extremity amputations (LEA) has increased considering the aging of the population and the rise of chronic diseases.1 Several studies reported a decreased rate of major LEA and an increased rate of minor LEA.2,3 Commonly, major LEA are characterized by an amputation proximal to the ankle joint, while minor LEA are identified by resection through or distal to the ankle joint.4 The increased rate of minor LEA compared to major LEA is mainly due to team approach to manage underlying cause leading to LEA, easier access with better quality of care, timely assessment and management of ulcers, and improved community-based outreach.5–7 Diabetes, vascular disease and traumatic accidents are the three main causes of LEA.8 In most developed countries, the prevalence of medical conditions such as diabetes and peripheral vascular disease is constantly rising,9,10 leading to a concomitant increase in the risk of LEA.3,10\n\nLEA negatively impacts the quality of life in those affected.11 An important challenge for healthcare professionals, the patients, and their caregivers is to successfully restore their physical abilities and their capacity to perform activities of daily living.11 Individuals who have undergone a LEA, experience alterations in their physical abilities, which may lead to an increased risk of developing secondary comorbidities such as osteoarthritis to the amputated and/or contralateral limb,12 low back pain,13 and even a more proximal secondary LEA.2,14 Some alterations in physical abilities could result in serious long-term biomechanical and neuromuscular deficits, leading to altered postural control,15 which is a direct cause of increased risks of falls.16 Experiencing a fall, in an individual with a LEA significantly reduces self-confidence and perception of balance capability, increases the fear of falling, and thus impacts the quality of life.11,17\n\nScientific literature quantifying postural control in individuals with a LEA still predominantly focuses on major LEA.15–18 Balance confidence to carry out daily activities without fear of falling is known to have a significant impact on individuals with a major LEA quality of life.19 Systematic reviews have also addressed topics such as balance20,21 and the risk of falls22 in individuals with a major LEA. However, nearly half of the LEA are minors2 and there is currently a limited number of studies focusing on better understanding the biomechanical deficits associated with minor foot amputations. Previous reviews highlighted impaired walking abilities.23,24 None have focused on balance and postural control and a preliminary search of PROSPERO, MEDLINE, the Cochrane Database of Systematic Reviews, and JBI Evidence Synthesis was conducted and no current or in-progress scoping reviews or systematic reviews on this topic were identified. Additionally, external aids and treatments (e.g., protheses, ankle-foot orthoses) are commonly prescribed to patients,25 but current knowledge is limited regarding how these devices could mitigate the biomechanical postural impairments resulting from a minor foot amputation. Therefore, the purpose of the scoping review will be to compile published studies that have investigated postural control deficits induced by a minor foot amputation. This will map the knowledge on this topic, which is still relatively understudied in the current literature and identify gaps of knowledge in this field. It will aim to understand the changes in postural control resulting from a minor foot amputation, the external aids and treatments that have been studied with the aim of improving physical condition and quality of life after a LEA.\n\n\nProtocol\n\nConsidering the PCC elements (Participants, Concept, Context), this scoping review is designed to address the following research question: “What quantitative data are available regarding balance deficits (C) in individuals who have undergone a minor foot amputation (P), and what tools/treatments are identified as capable of modifying postural control (C)?” The specific questions that arise from this are as follows:\n\n- What biomechanical variables are affected by a minor foot amputation during balance tasks?\n\n- Are there differences in an individual's ability to maintain balance on the amputated lower extremity compared to the contralateral limb?\n\n- Are there differences in an individual's balance regarding the level of minor LEA?\n\n- What type/nature of treatments improve postural abilities in individuals with a minor foot LEA?\n\nThese questions will guide our review to explore and synthesize the available quantitative data on balance deficits in individuals with a minor foot amputation and identify tools or treatments that may improve posture control.\n\nTable 1 contains information describing the characteristics of the studies included in the review examination.\n\n\n\n- Toe(s)\n\n- Ray(s)\n\n- Metatarsal-phalangeal\n\n- Transmetatarsal\n\n- Tarsometatarsal (Lisfranc)\n\n- Midtarsal (Chopart)\n\n- Ankle (Syme)\n\n\n\n- Transtibial\n\n- Knee\n\n- Transfemoral\n\n- Hip\n\n\n\n- Balance kinetics: GRF, pressure peak, CoP excursion in lateral and antero-posterior plans during quiet or dynamic standing\n\n- Kinematics: body displacement, segments movements\n\n- Electromyography\n\n- Functional test scores\n\n\n\n- Peer-reviewed original articles\n\n- Quantitative and quantitative part of mixed-method articles\n\n- Case reports/case series, dissertation/thesis, annals of congresses, conference proceedings, presentations, posters\n\n\n\n- Qualitative studies\n\n- Study protocol\n\n- Meta-analyses, narrative, and systematic reviews\n\nParticipants. Studies involving individuals of all ages who have undergone a minor foot amputation at the ankle joint or at a more distal level,4 will be included in this review. These levels of LEA will be considered for inclusion:\n\n• Ankle disarticulation (Syme).\n\n• Midtarsal disarticulation (Chopart joint).\n\n• Tarsometatarsal disarticulation (Lisfranc joint).\n\n• Transmetatarsal amputation.\n\n• Ray amputation.\n\n• Metatarsal-phalangeal disarticulation.\n\n• Toe amputation (one or more toe(s)).\n\nNo exclusion criteria will be applied regarding the etiology of LEA such as diabetes, vascular diseases (e.g., arteritis, burger disease, etc.), infectious diseases, tumors, congenital conditions, mechanical trauma (e.g., road or work accidents, etc.), or thermal trauma (e.g., burns, frostbite, etc.). Moreover, no exclusion will be made based on the unilateral or bilateral nature of the LEA. If studies included individuals who had a major LEA on one side and a minor LEA on the other, they will be considered as long as the analysis of postural control was performed separately for each lower extremity. Potential studies may address both unilateral and bilateral LEA, regardless of the level of LEA, whether it occurs in the ankle joint or more distally. If a study focuses on LEA in general, it will be included in the review if one or more clearly identified subgroups meet the inclusion criteria. No restrictions will be made based on sex, gender, race, geographic or ethnic origin of the participants.\n\nConcept. This review will consider studies that quantitatively investigated balance abilities and postural control in one or more individuals who have undergone a minor foot amputation. We will gather information on possible postural biomechanical deficits identified and documented in the current literature as being induced by such LEA. The variables of interest are those related to changes in balance sensation and postural control quantitatively based on experimental conditions measured in the relevant articles. Thus, we will include studies investigating:\n\n- Changes in balance sensation, ability to maintain a balanced posture, as well as the risk of falls. Examples of assessments will include ordinal balance scales (e.g., Tinetti Performance Oriented Mobility Assessment (POMA), Berg Balance Scale (BBS), etc.) or more dynamic functional tests (e.g., Functional Reach Test (FRT), Timed Up and Go Test (TUG), etc.).26 These tests are indicative, and additional assessments will be considered to evaluate individual's capacity to safely balance during predetermined tasks.\n\n- Biomechanical changes measured in a research laboratory during controlled tests. These changes included spatiotemporal aspects (e.g., time and velocity), kinematics (e.g., joint angles and accelerations, body displacement and postural oscillations), kinetics (e.g., ground reaction force, plantar pressures, center of pressure excursion in the mediolateral and anteroposterior planes, distribution/projection of the center of mass), and electromyographic changes, depending on the studies.\n\nContext. This review will consider studies that have explored means implemented to improve the function deteriorated by a minor LEA, from an orthopedic perspective including prosthetics, foot/ankle orthoses, orthopedic insoles, and shoes, as well as sensitization, training, or pre/post-operative exercises. The studies eligible for review will not be limited to any geographical location.\n\nTypes of evidence sources. Published, peer-reviewed quantitative studies and quantitative parts of mixed methods studies will be considered for inclusion in this scoping review. In addition, case reports, case series, theses, annals of congresses, conference proceedings, or posters will be included. Qualitative studies, research protocols, meta-analyses, narrative editorials and comments, and systematic reviews will not be considered in the review.\n\n\nMethods\n\nThe scoping review will be conducted in accordance with the methodology developed by Arksey and O'Malley27 and later revised by Levac and Colquhoun,28 and in line with the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols for scoping reviews (PRISMA-ScR)29 guidelines. The protocol is registered with Open Science Framework (https://osf.io/fvqbc).\n\nThe search strategy will aim to locate both published peer-reviewed original studies, quantitative, and mixed method studies. An initial limited search of MEDLINE (PubMed) was undertaken in December 2023 to confirm the feasibility of this review and pilot our search strategy in identifying studies relevant to our research question. The text words contained in the titles and abstracts of relevant articles, and the index terms used to describe the articles, were used to develop a full search strategy for PubMed (Table 2), in collaboration with the Université du Québec à Trois-Rivières librarian. The search strategy, including all identified keywords and index terms, will be adapted for each included information source. In all cases, the first theme will include all terms related to or synonymous with “amputation”, the second will concern the level of amputation, and the third will include outcomes referring to balance tasks and posture control indices in standing and sitting positions. Terms from these three themes will be combined. The reference lists of articles included in the review will be screened for potential additional studies. No restrictions related to the year of publication will be applied to the search strategies. However, the search will focus on human populations and texts published in French or English.\n\nThe databases to be searched will include SPORTDiscus (EBSCO), CINAHL (EBSCO), MEDLINE (EBSCO), Cochrane Library (CENTRAL) and Physiotherapy Evidence Database (PEDro). Other databases that catalog online trials, such as ClinicalTrials.gov and EudraCT, will also be examined. Additionally, grey literature will be explored using the academic search engine BASE, ProQuest Dissertations and Theses (ProQuest) and Google Scholar.\n\nFollowing the search, all identified records will be collated and uploaded into EndNote software version 21.2 (Clarivate Analytics, PA, USA) and duplicates will be removed. Following a pilot test, titles and abstracts will then be screened by two independent reviewers (MA and AD) for assessment against the inclusion criteria for the review. Potentially relevant papers will be retrieved in full text and will be assessed in detail against the inclusion criteria by two independent reviewers (MA and AD). Reasons for exclusion of full-text papers that do not meet the inclusion criteria will be recorded and reported in the scoping review. Any disagreements that arise between the reviewers at each stage of the selection process will be resolved through discussion or with a third reviewer (GM). The results of the search and the reason for exclusion will be reported in full in the final scoping review and presented in a PRISMA flow diagram.29\n\nData will be extracted from included publications by two independent reviewers (MA and AD) using a data extraction tool developed by the research team. Any disagreements that arise between the reviewers will be resolved through discussion or with a third reviewer (GM). Data will be imported into a table created in a Microsoft Excel version 16.79.1 (Microsoft Corporation, WA, USA) sheet (Table 3). The extracted data will include specific details about the participants, concept, context, study methods, and key findings relevant to the review questions. The following data will be extracted:\n\n• Study characteristics (journal, authors, year, country where the study was conducted).\n\n• Study population (age, sample size, comorbidity/health status, type, level, and reason for amputation, inclusion criteria).\n\n• Study objectives and aims.\n\n• Study design (methods, intervention description, study duration, dependent variables).\n\n• Key findings related to the scope of the review.\n\n• Metatarsal-phalangeal disarticulation.\n\n• Discussion/recommendations for future research/clinical implications.\n\nA draft extraction tool is provided and will be modified and revised as necessary during the process of extracting data from each included paper. Modifications will be detailed in the full scoping review. Authors of papers will be contacted to request missing or additional data, where required.\n\nThe quality of the selected studies will be evaluated using the open-access Mixed Methods Appraisal Tool (MMAT) developed by Hong and colleagues.30 Depending on the study type, each component will be assessed as ‘yes’, ‘no’, or ‘can't tell’ by the two reviewers (MA and AD), and comments may be added to justify the response. In both cases, we will provide a detailed presentation of the scores attributed to each criterion, as well as an overall score based on the evaluation of all criteria, following the methodological guidelines provided by the authors.30 Results will thus be contrasted according to their results. However, a poor methodological quality score will not be considered in determining inclusion. This evaluation will be performed retrospectively after the studies selection.\n\nThe results of the review will be analyzed and displayed in tabular format using charting methods to meet the objective of this scoping review. The results will be presented in a narrative format.\n\nGiven the nature of a scoping review, which involves synthesis and analysis of existing literature, ethical approval is not required. However, it is important to ensure that all data analysed is from reputable sources and that all referenced works are properly attributed. The results of this scoping review will be disseminated through academic channels, including peer-reviewed publications and presentations at relevant conferences. This approach will ensure that the findings can contribute to the wider scientific community and encourage further research and discussion on the topic. In addition, the review will follow the PRISMA-ScR29 guidelines to ensure transparency and repeatability of the methodology used.\n\nWe have completed our search strategy and development of keywords and medical subject headings based on the different databases. Literature searching and article extraction will begin once our search strategy has been peer reviewed.\n\n\nDiscussion\n\nThe postural mechanisms affected by minor foot amputations have received limited attention in the current scientific literature. Our understanding of balance deficits in individuals with a minor foot amputation during daily activities is primarily based on extrapolation from studies conducted in individuals with a major LEA. The scoping review will map the articles that have investigated balance and postural control in one or more individuals who have lost a minor part of their lower extremity. The scoping review will provide an overview of the orthoses, prostheses, technical aids, and other treatments or modalities that have been studied in people with a minor LEA to restore or improve their postural control abilities. Synthesizing knowledge in this area and reviewing of existing treatments, with a particular focus on their impact on balance stability tasks, are essential to better assist individuals who have undergone minor LEA. Therefore, it is important to emphasize the understudied aspects of postural control imbalances induced by these amputations. The review will highlight potential areas for therapeutic intervention and contribute to a better understanding of the rehabilitation for these individuals.\n\nEthical approval and written consent were not required.\n\n\nAuthors contributions\n\nMaxime Acien. Conceptualization, Methodology, Investigation, Writing - Original Draft, Visualization.\n\nAhmed Dami. Writing - Review & Editing.\n\nVirginie Blanchette. Funding acquisition, Writing - Review & Editing.\n\nGabriel Moisan. Supervision, Project administration, Funding acquisition, Writing - Review & Editing.\n\nAll authors approved the final draft.", "appendix": "Data availability statement\n\nNo data is associated with this article.\n\nOpen Science Framework: “Postural Control Imbalance in Individuals with a Minor Foot Amputation: A Scoping Review Protocol” (https://doi.org/10.17605/OSF.IO/FVQBC). 31\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nOpen Science Framework: PRISMA-ScR protocol reporting items 32 for “Postural Control Imbalance in Individuals with a Minor Foot Amputation: A Scoping Review Protocol” (https://doi.org/10.17605/OSF.IO/N49TH).\n\n\nAcknowledgements\n\nWe would like to thank the Université du Québec à Trois-Rivières librarian Benjamin Poulin-Daigle for his help elaborating the search strategy for this scoping review.\n\n\nReferences\n\nEidmann A, et al.: Demographics and Etiology for Lower Extremity Amputations—Experiences of an University Orthopaedic Center in Germany. Medicina. 2023; 59(2): 200. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBehrendt C-A, et al.: International variations in amputation practice: a VASCUNET report. Eur. J. Vasc. Endovasc. Surg. 2018; 56(3): 391–399. PubMed Abstract \| Publisher Full Text\n\nSpoden M, Nimptsch U, Mansky T: Amputation rates of the lower limb by amputation level–observational study using German national hospital discharge data from 2005 to 2015. BMC Health Serv. Res. 2019; 19: 1–9. Publisher Full Text\n\nvan Netten JJ , et al.: Definitions and criteria for diabetes-related foot disease (IWGDF 2023 update). Diabetes Metab. Res. Rev. 2023; 40: e3654. Publisher Full Text\n\nBlanchette V, Armstrong DG: An Approach that Needs Patients and Their Families as Partners. Wound Care Canada. 2022; 20(1).\n\nBlanchette V, Brousseau-Foley M, Cloutier L: Effect of contact with podiatry in a team approach context on diabetic foot ulcer and lower extremity amputation: systematic review and meta-analysis. J. Foot Ankle Res. 2020; 13(1): 1–12. Publisher Full Text\n\nMcDermott KM, Srinivas T, Abularrage CJ: Multidisciplinary approach to decreasing major amputation, improving outcomes, and mitigating disparities in diabetic foot and vascular disease. Seminars in Vascular Surgery. Elsevier; 2023.\n\nImam B, et al.: Incidence of lower limb amputation in Canada. Can. J. Public Health. 2017; 108: 374–380. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnimaw W, Seyoum Y: Increasing prevalence of diabetes mellitus in a developing country and its related factors. PLoS One. 2017; 12(11): e0187670. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEid MA, Mehta KS, Goodney PP: Epidemiology of peripheral artery disease. Seminars in Vascular Surgery. Elsevier; 2021.\n\nQuigley M, Dillon MP: Quality of life in persons with partial foot or transtibial amputation: a systematic review. Prosthetics Orthot. Int. 2016; 40(1): 18–30. Publisher Full Text\n\nFarrokhi S, et al.: A narrative review of the prevalence and risk factors associated with development of knee osteoarthritis after traumatic unilateral lower limb amputation. Mil. Med. 2016; 181(suppl_4): 38–44. PubMed Abstract \| Publisher Full Text\n\nHighsmith MJ, et al.: Low back pain in persons with lower extremity amputation: a systematic review of the literature. Spine J. 2019; 19(3): 552–563. PubMed Abstract \| Publisher Full Text\n\nThorud JC, et al.: Reoperation and reamputation after transmetatarsal amputation: a systematic review and meta-analysis. J. Foot Ankle Surg. 2016; 55(5): 1007–1012. PubMed Abstract \| Publisher Full Text\n\nViton JM, et al.: Equilibrium and movement control strategies in trans-tibial amputees. Prosthetics Orthot. Int. 2000; 24(2): 108–116. PubMed Abstract \| Publisher Full Text\n\nSteinberg N, et al.: Fall incidence and associated risk factors among people with a lower limb amputation during various stages of recovery–a systematic review. Disabil. Rehabil. 2019; 41(15): 1778–1787. PubMed Abstract \| Publisher Full Text\n\nMandel A, Paul K, Paner R, et al.: Balance confidence and activity of community-dwelling patients with transtibial amputation. J. Rehabil. Res. Dev. 2016; 53(5): 551–560. PubMed Abstract \| Publisher Full Text\n\nMoisan G, et al.: Balance control deficits in individuals with a transtibial amputation with and without visual input. Prosthetics Orthot. Int. 2022; 46(2): 134–139. PubMed Abstract \| Publisher Full Text\n\nMiller WC, et al.: The influence of falling, fear of falling, and balance confidence on prosthetic mobility and social activity among individuals with a lower extremity amputation. Arch. Phys. Med. Rehabil. 2001; 82(9): 1238–1244. PubMed Abstract \| Publisher Full Text\n\nKu PX, Osman NAA, Abas WABW: Balance control in lower extremity amputees during quiet standing: a systematic review. Gait Posture. 2014; 39(2): 672–682. PubMed Abstract \| Publisher Full Text\n\nSeth M, Lamberg E: Standing balance in people with trans-tibial amputation due to vascular causes: A literature review. Prosthetics Orthot. Int. 2017; 41(4): 345–355. PubMed Abstract \| Publisher Full Text\n\nHunter SW, et al.: Risk factors for falls in people with a lower limb amputation: a systematic review. PM R. 2017; 9(2): 170–180.e1. PubMed Abstract \| Publisher Full Text\n\nDe Oliveira FCL, et al.: Association between the level of partial foot amputation and gait: a scoping review with implications for the minimum impairment criteria for wheelchair tennis. Br. J. Sports Med. 2023; 57(4): 237–248. Publisher Full Text\n\nDillon MP, Fatone S, Hodge MC: Biomechanics of ambulation after partial foot amputation: a systematic literature review. J. Prosthet. Orthot. 2007; 19(8): P2–P61.\n\nJanisse DJ, Janisse EJ: Shoes, orthoses, and prostheses for partial foot amputation and diabetic foot infection. Foot Ankle Clin. 2010; 15(3): 509–523. PubMed Abstract \| Publisher Full Text\n\nLangley FA, Mackintosh SF: Functional balance assessment of older community dwelling adults: A systematic review of the literature. Internet J. Allied Health Sci. Pract. 2007; 5(4): 13. Publisher Full Text\n\nArksey H, O'Malley L: Scoping studies: towards a methodological framework. Int. J. Soc. Res. Methodol. 2005; 8(1): 19–32. Publisher Full Text\n\nLevac D, Colquhoun H, O'Brien KK: Scoping studies: advancing the methodology. Implement. Sci. 2010; 5: 1–9.\n\nTricco AC, et al.: PRISMA extension for scoping reviews (PRISMA-ScR): checklist and explanation. Ann. Intern. Med. 2018; 169(7): 467–473.\n\nHong QN, et al.: Mixed methods appraisal tool (MMAT), version 2018. Registration of Copyright. 2018; 1148552(10).\n\nAcien M: Postural Control Imbalance in Individuals with a Minor Foot Amputation: A Scoping Review Protocol. OSF. January 18, 2024. Publisher Full Text\n\nPeters MD, et al.: Best practice guidance and reporting items for the development of scoping review protocols. JBI Evid. Synth. 2022; 20(4): 953–968. PubMed Abstract \| Publisher Full Text" }	[ { "id": "306690", "date": "06 Sep 2024", "name": "Humberto Omana", "expertise": [ "Reviewer Expertise Literature reviews", "Rehabilitation research", "Falls prevention", "Biomechanics" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for allowing me the opportunity to review this manuscript. Overall, I believe that there are important changes in both the writing and methodology that should be considered. The writing and rationale would benefit from added information. For example, knowing the biomechanics viewpoint used, then there should be writing that details why people living with LEAs have worse balance and gait. If intervention studies are also part of the scoping review, then the introduction should reflect this information. Due to the numerous ways in which balance control can be assessed, the authors would benefit from using a balance framework to present their findings. The authors need to also better explain why the MMAT is being used (for intervention studies also?). Below I will detail my feedback to the authors for consideration:\nAbstract: The argument for the need to complete this scoping review is not fully developed. What is it about a minor LEA that leaves people with a lower ability to maintain balanced? This is something that I will bring up again in the Introduction section.\nAbstract: What is the argument for including people of all ages? Can you really generalize your results to all people living with a minor LEA? This, knowing the research presented at the top of the abstract is likely related to middle aged or older adults...\nAbstract: The abstract is specific to balance control but from reading the protocol I know that interventions studies are also being included. The reasoning for this addition into the scoping review is never explained.\nIntroduction: \"Some alterations in physical abilities could result in serious long-term biomechanical and neuromuscular deficits, leading to altered postural control, which is a direct cause of increased risks of falls.\" : This sentence is vague. The authors need to explain the reason why people living with LEAs have impaired balance (how does this change according to levels of amputation?). The stance of the manuscript appears to be from neuromechanics in which canse that viewpoint should be used.\nIntroduction: \"Experiencing a fall, in an individual with a LEA significantly reduces self-confidence and perception of balance capability, increases the fear of falling, and thus impacts the quality of life.\": Falls also lead to physical injuries and set backs regarding rehab. Although falls are mentioned throughout it would be difficult for the reader to understand how people living with LEAs would compare relative to other populations. Consider sharing falls rate.\n\nIntroduction: \"However, nearly half of the LEA are minors...\": As in younger adults? minor amputations? Revise.\n\nIntroduction: \"Therefore, the purpose of the scoping review will be to compile published studies that have investigated postural control deficits induced by a minor foot amputation.\": The introduction needs to better explain what do know about balance control in people living with LEAs, and then explain what you think you will find through your scoping review.\n\nMethods: \"...and what tools/treatments are identified as capable of modifying postural control (C)?”: This was never explained in the abstract or the introduction, and makes this scoping review much bigger than what was initially stated. What is the reasoning behind this? If this is one of the goals then I would expect that the gaps in the literature would also be shared.\nMethods (Table 1): The outcomes shared are broad. My suggestion would be to organize the scoping review based on a framework to help you with the many different types of variables you will come upon. Consider reviewing the following manuscripts:[1],[2],[3],[4],[5],[6].\nMethods: There is a lot of redundancy between what is on the tables and what is on the text of the methods. Please make revisions to have one or the other.\nMethods: By index terms do you mean MeSH terms?\nMethods (Table 2): This search bubble is problematic because most studies will state amputation + balance but not the level of amp. Why not combine bubbles 2 and 3 using OR? The number of items found for the combined bubbles does not seem high... but his only one database.\nMethods: Usually for reviews we also review the reference section of previous literature reviews and relevant papers. Consider adding this into your methodology as it is best practices.\n\nMethods: How will duplicates be removed? If an automatic system is used, please consider also manually reviewing the removed articles as automated system can sometimes remove articles in error (which increases the more articles you gather).\n\nMethods: \"Authors of papers will be contacted to request missing or additional data, where required.\": How? How many contact emails will be sent? What if they don't answer?\nMethods: \"...Mixed Methods Appraisal Tool (MMAT)\": Can you expand on this tool? what criterions does it cover? validity? for intervention studies you will be using the same tool?\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-309
https://f1000research.com/articles/12-1024/v1	22 Aug 23	{ "type": "Research Article", "title": "“The person was like the glue in the cracked pot which was no longer there”: Family-focused support for bereavement via co-production of a web-based intervention", "authors": [ "Natasha Campling", "Susi Lund", "Alison Allam", "Gail Precious", "Michelle Myall", "Susi Lund", "Alison Allam", "Gail Precious", "Michelle Myall" ], "abstract": "Background: Families, friends and support networks are key to managing bereavement. COVID-19 social restrictions prevented families and friends from being with the dying and participating in usual rituals to honour the dead. This resulted in social disconnection, feelings of guilt, and difficulty in making sense of the death and reconstructing relationships. In response to this context a theoretically informed, co-produced web-resource to facilitate meaning-making, which situates bereavement in the context of family and friends, was developed. This paper describes the development of the web-based intervention.\n\nStudy aims: To co-produce a web-based intervention theoretically informed by the family level extension Dual Process Model and Family Sense of Coherence, and pilot the intervention gaining user feedback to inform refinements in readiness for adoption and implementation. Methods: Following a scoping review, a mixed methods study was undertaken using an online survey via questionnaire and virtual co-production workshop with bereaved people and bereavement professionals.\n\nResults: Survey respondents reported the pandemic negatively affected bereavement (guilt, isolation, inability to bear witness) but also presented new opportunities to celebrate the deceased and support the bereaved (new funeral rituals, technology, remote contact, social acknowledgement of grief). Sense-making and managing bereavement were helped through information-giving, support networks, and relocating the person within the family context. A web-resource to facilitate collective grief was viewed positively and endorsed. Key content including family activities to stimulate support, information regarding the range of grief experience and dealing with the practicalities, along with other sources of support was agreed by workshop participants to form the basis of the intervention.\n\nConclusion: The Families in Bereavement intervention encourages consideration of bereavement in the context of close social networks. It enables grief to be understood and managed within a shared experience by promoting communication and meaning-making.", "keywords": [ "bereavement", "grief", "family-focused", "theoretically-informed", "web-based intervention", "co-production", "COVID-19" ], "content": "Introduction\n\nCOVID-19 first emerged in December 2019 and spread rapidly, becoming a global pandemic resulting in an unprecedented level of deaths, causing mass bereavement worldwide. While significant focus has been on deaths from COVID-19, the impact has been far reaching affecting all those bereaved from any cause during the pandemic. Estimates suggest. Before COVID-19, 60% of bereaved people managed their bereavement with the help of family, friends and support networks (Penny, 2020). Social restrictions resulted in significant disruption and inability to provide these usual forms of support. Furthermore restrictions, including those applied to funerals and lack of opportunity to spend time or visit the dying, disrupted social rituals marking the death leaving family members feeling they were unable to bear witness and honor their dying and dead. The ensuing social disconnections (Smith et al., 2020) and guilt (Bear et al., 2020; Torrens-Burton et al., 2022) exacerbated the challenge of bereavement. For many, death became unexpected, out of time and place.\n\nThe social disconnection between a dying person and family, caused by social distancing precautions, meant the construction of family narratives of end-of-life was compromised. A review of the international literature, across 13 countries during COVID-19, found that whilst there was diversity of experience based on culture and belief systems all countries identified significant impact on family bereavement (Stroebe & Schut, 2021). Almost half (49%) of respondents to a survey of 2,000 UK adults, carried out by Dying Matters, agreed that being unable to be with someone as they died, or attend their funeral, would make it harder for them to process the death (Penny, 2020). It is narratives that serve to link the biography of a living family member with the death and which are important in the process of making sense of what has happened, paying tribute to the deceased and in reconstructing bonds between the bereaved and their deceased family member (Klass et al., 2014; Walter, 1996). This meaning-making process is essential for family wellbeing and resilience (Gilbert, 1996), yet it was challenged by varying COVID-19 control measures.\n\nMost Western focused professional bereavement support interventions and services are underpinned by grief theories which concentrate predominately on the individual, mitigating psychological distress, and identifying and preventing complicated grief (Laranjeira et al., 2022). (It is difficult to determine if this is the case beyond Western societies due to paucity of evidence, and further research is required to understand the focus of interventions globally). Services are often delivered face-to-face or by telephone, others are group-based, with inequitable access dependent on the setting in which the death occurred. To address these gaps in provision, de-professionalizing bereavement for those individuals not at risk of complicated grief and shifting the focus to the wider family, this study co-produced a web-based intervention Families and Friends in Bereavement adopting a family-focused approach.\n\nFamily support is recognized as key to managing bereavement, yet most grief theories focus on individual rather than collective experience (Stroebe and Schut, 2015). A notable exception is the family-level extension to the Dual Process Model of Coping with Bereavement, in which Stroebe and Schut (2015) describe family level tasks influencing loss and restoration orientated coping. Loss orientation refers to dealing with processing the stressful aspects of a loss experience and focusing on the deceased (e.g. memorializing and thinking about the person who has died), restoration orientation refers to coping with other losses which manifest as a result of the bereavement (e.g. financial hardship, adapting to new routines and roles). Restrictions during the pandemic contributed to significant additional stressors and precluded the usual oscillation between loss and restoration orientated processes by disrupting everyday living which in usual times offers a degree of respite and distraction from confronting or avoiding family stressors (Stroebe and Schut, 2021).\n\nFamily Sense of Coherence provides an additional theoretical foundation for family-focused support (Antonovsky and Sourani, 1988) and has informed a family support intervention in the context of life-limiting illness (Duke et al., 2020). Rather than focusing on distress (ill health), Family Sense of Coherence is concerned with family strengths, resilience and meaning. In the context of bereavement, it is influenced by the comprehensibility, manageability and meaningfulness of the death. Combined, Family Sense of Coherence theory and the focus offered in the family level extension to the Dual Process Model, provided a theoretical framework to guide family orientated bereavement support.\n\nThe Families and Friends in Bereavement intervention was developed to encourage users to consider their bereavement experience in the context of family, friends and close social networks, to promote communication and meaning-making, fostering coherence and resilience (McKnight, 2015). Web-based interventions are known to provide effective and accessible psychological support (Cowpertwait & Clarke, 2013; Knowles et al., 2017; Stroebe et al., 2008); and they have the advantage of enabling users to access support when needed, increasing the potential effectiveness of bereavement support (Hewison et al., 2020). Furthermore, recent evidence has highlighted the need for a family centered and online approach for bereavement support (Harrop et al., 2020).\n\nThis paper provides a detailed description of the stages of development of the Families and Friends in Bereavement intervention including piloting.\n\nThe aims of the study were to:\n\n1. Co-produce a web-based intervention with patient and public contributors (PPI) and bereavement professionals, theoretically informed by the family level extension Dual Process Model and Family Sense of Coherence.\n\n2. Pilot the intervention and gain user feedback to inform refinements.\n\n3. Evaluate the intervention capturing users’ experiences of accessibility, acceptability, usability and utility in readiness for adoption and implementation.\n\nFindings from the evaluation (aim 3) will be published in a forthcoming paper.\n\n\nMethods\n\nOur approach to intervention-development was underpinned by co-production and theoretically informed by Family Sense of Coherence (Antonovsky & Sourani, 1988) and the family-level extension to the Dual Process Model (Stroebe & Schut, 2015) which were used to develop the family-focused intervention. The co-production approach (Grindell et al., 2022) developed partnerships between the research team, people with real world experience of bereavement, and community and national stakeholders. Involving people with lived experience of this specific context, leveraging their knowledge, experience and insights, to enable a deep understanding of the challenges they face; and encouraging the uptake of outputs was used to help ensure “contextual fit” (Goodyear-Smith et al., 2015) and findings that have relevance to end users of the web-resource.\n\nThe study received endorsement and support from the National Bereavement Alliance (the largest UK umbrella bereavement organization with over 80 member organizations). In consultation with people with lived experience of bereavement (personal and/or professional) and in line with UK palliative and end of life care policy (National Palliative and End of Life Care partnership, 2021), we defined family as relatives, friends, neighbors or anyone important to the bereaved.\n\nThis was a mixed methods study. Firstly, we explored in-depth the underpinning theories (Family Sense of Coherence and the family level extension to the Dual Process Model). Secondly, we carried out scoping work of the COVID-19 family-focused bereavement literature published between January 2020 and March 2021. This was specifically to identify and understand key elements of family bereavement support. Thirdly, findings from the scoping work and our theoretical framework were used to inform an online survey to gather data on personal and/or professional experiences of bereavement during the pandemic. Fourthly, the survey findings were taken to an online co-production workshop attended by members of the public with experience of bereavement and bereavement professionals working in hospice bereavement services, frontline and umbrella charities, to co-produce key content for the web-based intervention. Data gathered from the workshop discussion was used by the research team, in collaboration with an expert web designer, to produce and launch the intervention. Fifthly, users of the intervention were invited to provide feedback via a short survey embedded within a web-page of the intervention. Lastly, this feedback informed refinements to the intervention.\n\nThe process of intervention development (illustrated in Figure 1) is described below using the GUIDance for rEporting intervention Development studies in health research (GUIDED) (Duncan et al., 2020). Whilst GUIDED recommends use of the Template for Intervention Description and Replication (TiDieR) checklist (Hoffmann et al., 2014) the open accessibility and flexibility of an online intervention precluded specifying the who, how, when, how much, and where of use, therefore this checklist was not used.\n\nTheoretical framework\n\nFamily support is key to managing bereavement and in our previous work we drew on Family Sense of Coherence as a theoretical lens to facilitate family-focused support (Duke et al., 2020). Sense of coherence refers to the extent to which individuals perceive their world as meaningful, comprehensible and manageable (Antonovsky & Sourani, 1988). Antonovsky and Sourani advanced sense of coherence by applying the concept to families, demonstrating that successful coping with family stressors is associated with adaptation within the family and wider community networks.\n\nFor the purpose of the intervention development, we applied the three Family Sense of Coherence constructs to bereavement: defining meaning as wanting to respond and create meaning as a family, comprehensibility as the ability to understand and make sense, and manageability as the ability to utilize available resources to respond to the bereavement (Figure 2).\n\nStroebe and Schut (2015) expansion of their seminal theory of bereavement to include the collective family response (family level extension to the Dual Process Model) explains family level tasks both loss and restoration focused that relate to adjustment of the family as a whole as well as its individual members. For families to attend to these tasks, adaptation to these at both an individual and family level is required.\n\nTogether the models comprehensively describe the processes required as a family, in both attending to the bereavement and the consequences of the death, in order to make sense, create meaning and utilize available resources to adapt to the loss (Figure 3).\n\nCombined, Family Sense of Coherence and the family level extension to the Dual Process Model, were used to create a robust theoretical framework to guide family orientated bereavement support.\n\nScoping work\n\nTo identify and understand key elements of family bereavement support during COVID-19 we scoped the emerging evidence. This was underpinned by the question: what is known about family experiences of bereavement during the COVID-19 pandemic?\n\nSearches were carried out in MEDLINE (EBSCO) CINAHL, Web of Science and PsycINFO using search terms related to “family bereavement” “grief” “loss” and “social support, “coping” and “resilience”. Searches were carried out in March-April 2021 (of literature published between January 2020 to March 2021) and it provided an initial indication of family experience prior to the proliferation of publications regarding bereavement during COVID-19.\n\nFrom the limited evidence available at this time on bereavement during COVID-19 papers explored the nature of family experiences and support needs (see Table 1).\n\nOnline survey\n\nThe online survey was informed by the scoping work and focused on experiences of people who had been bereaved and the theories we applied. Survey items addressed family experiences of bereavement during COVID-19; views on supporting family bereavement via a web-based intervention and collected demographic data from respondents (see Table 2 for key questions, responses were unlimited free text).\n\nThe online survey was piloted via distribution to seven patient and public contributors (PPI) and two bereavement organizations in February 2021. Three PPI contributors and one representative of a bereavement organization responded (n=4). Changes to language and terminology to improve clarity were made following these pilot responses.\n\nThe survey was distributed via the National Bereavement Alliance; Hospice UK; a large patient and public involvement network; and social media. It ran for three months between April and July 2021 using Microsoft Forms.\n\nThirty-two responses were received with an average completion time of 32 minutes. Thirteen completed the survey from a professional perspective, 12 from a professional and personal perspective, and the remaining seven from a personal perspective. Respondents who were bereavement professionals (those with professional experience), or those with both professional and personal experience reported working in health care, including hospices (n=19); third sector (n=4) and other (n=4) which included private and digital technology sectors. One respondent did not provide details. They worked in a range of roles, with varying levels of seniority and length of experience. Demographic information for bereaved respondents (those with personal experience, or those with both personal and professional experience) is provided in Table 3.\n\nData analysis\n\nSurvey results were analyzed using Framework Analysis (Ritchie et al., 1994) by NC, SL, MM following the five stages of data familiarization, framework identification, indexing, charting, and mapping and interpretation, and generated key themes outlined below.\n\n\nResults\n\nFindings demonstrated that family tasks in bereavement included managing practicalities around the death including organizing the funeral and sorting the estate, living with the loss and learning to adapt, and acknowledging that family members experience and move through grief in different ways utilizing a variety of coping strategies.\n\n…Family tasks have been interrupted due to COVID - for example not being able to meet to care and support each other, to talk about the loved one, to go through possessions and keep sakes, to sort out the affairs of the loved ones etc. - this has all been difficult due to family members not being able to mix, to go indoors etc. It was also hard at the funeral having to be socially distanced and not able to talk with and hug family members. At the same time, it was amazing we had over 1000 people watch the live streamed/recorded funeral service for my dad… (Participant 08, personal and professional)\n\n…I found that my siblings and myself all had different grief stages and experiences when our parents died (Dad then Mum a few months later), and we did not really support each other as we were at different stages. We also had different ways of coping and this caused issues (i.e. drinking heavily)… (Participant 17, personal)\n\nCOVID-19 impacted bereavement in a number of ways. For example, feelings of guilt, an inability to bear witness, putting grief on hold as a result of the imposed lockdowns, and the impact of media reporting of daily death tolls led to feelings of their loss being seen ‘as just a number’. Isolation resulting from social restrictions resulted in lack of control and choice over mourning including an inability to share collective memories and undertake cultural rituals and rites of passage usually enacted by a death.\n\n…Instances where the family have not been able to be present have caused increases in distress and have factored into the complexity of feelings that must be managed in grief. Bereaved people being more often alone and isolated also adds more space for rumination. Having said this, I think many bereaved families have created support bubbles, moved in together, or just elected to ignore some restrictions for the greater good of caring for one another. Frequent phone calls and virtual meetings have also been prevalent… (Participant 05, professional)\n\n…Due to rapid deterioration often experienced, these [COVID] deaths have not been good and are not seen as good deaths at the time as people close to the patient don’t have time to process what’s happening. The restrictions on funeral numbers have been particularly challenging especially for some cultures who would normally have had large gatherings as a result of death… (Participant 06, professional)\n\n…For some it has a negative impact due to limited support networks and opportunities for meaningful activity as a distraction etc., but for others there can have a positive impact as pace of life has slowed down, people are at home more, etc… (Participant 18, professional)\n\n…I feel that I wasn’t able to give him the celebration in life he deserved in the final weeks as friends and family could not visit. I do not feel that I was able to give him the funeral he deserved because of restrictions in numbers. Everyday there was a change in government restrictions. The three weeks in planning were a nightmare. I was able to have a pretty pathetic excuse for a Wake. I feel I failed him, but my friends and family say I did all I could under the restrictions… (Participant 21, personal)\n\n…We are left with thinking we ‘should’ have another remembrance event, with an expectation from people who couldn’t be there, but this just feels stressful. Had we had a ‘normal’ funeral, then this would be over, and no one would expect another event.\n\nMy friends didn’t visit me in a way that I suspect they would have done pre pandemic. I received lots of text/WhatsApp messages, but few people actually picked up the phone and called me which I really wanted. I felt very isolated and as if it had to be me that contacted people, but I just couldn’t… (Participant 22, personal)\n\n…Humans are social, we grieve together, and our grief is healed by being with others who understand. Despite restrictions being all but gone, people are still out of step with seeing each other. Their support networks have shrunk… (Participant 31, professional)\n\nSurvey analysis confirmed findings from the scoping review that the pandemic presented opportunities to express grief and support the bereaved in different ways. Technology was utilized in novel and diverse ways both by professionals and the bereaved to enable social connections and facilitate support, this included online streaming of funerals and increased use of digital platforms. For some the social restrictions were viewed positively, such as smaller scale funerals and protected time to grieve.\n\n…Live streaming the funeral - it gave the opportunity for many more people to attend than we would ever of (sic) had in person. We also have a recording of the service as a memory and have looked back at it on several occasions… (Participant 08, personal and professional)\n\n…I think it has given people space and an “excuse” to not be sociable - and take more time in their grief. I think for most, the pandemic has shown them who is really important and who is really there for them… (Participant 12, professional)\n\n…Virtual meeting has meant that miles are no object in being able to have conversations with support people (friends and family). It’s not the same as meeting in person, but there are some people I couldn’t have had contact with otherwise… (Participant 28, personal)\n\nRespondents identified factors that helped make sense of and manage bereavement. Having information and guidance about the practical tasks that needed to be taken following a death was felt to be essential. Information on the emotional impact of grief, how it can affect families and the diversity and commonality of experience was equally necessary. Being able to relocate the person who had died within the family context and ensure an ongoing bond was considered important in helping to adapt to the loss. The ability to draw on support networks, share stories to help make sense of the death, and having time to reflect as well as legacy projects to remember and honor the dead were also valued.\n\n…Mostly support from other members of the family and people who shared memories and good times with the departed, talking about the condition and how we were or were not able to intervene and make a difference for our loved one… (Participant 32, personal and professional)\n\nThe idea of a web-based intervention was positively viewed and acknowledged as a means to widen access. However, it was recognized that this was reliant on possessing some level of IT literacy. To ensure accessibility respondents desired ease of navigation, and succinct information utilizing varied media (images and music). Regarding content, information on the experience and range of manifestations of grief, signposting to other organizations and support, and information on how to support one another were deemed important. Respondents thought, for the intervention to facilitate a family response to grief, it should include questions and prompts for conversations and activities for capturing and sharing memories and feelings. Respondents offered suggestions for encouraging use of the intervention, these included images, use of colors, and avoidance of clichés. Essentially the intervention should be simple, straightforward and honest, relatable, and clear in what it adds and how it differs from existing resources.\n\n…It would be helpful to have sections on emotional support - what kind of things people need and how to get them, links to relevant organizations, and practical support on how to face tackling the things you have to do because the person has died. Also, some ideas, both for the bereaved person and those supporting them of things they might be able to do to help them feel a bit better. For example, a friend gave me a bag of ‘crap day’ presents, so if I was having a particularly awful day, I could open one. I’ve done that for other friends since, and it was something I really valued as it reminded me that my friend was supporting me even at the worst times. Other ideas of activities that allow people to talk about their loved one without feeling awkward would be helpful… (Participant 28, personal)\n\nParticipants were sought through respondents to the survey (who were asked to indicate their interest in the workshop), social media e.g., Twitter, patient and public involvement networks, professional bereavement organizations, and carers’ organizations. Twelve individuals expressed an interest to participate, eight were able to attend on the date set, with five attending on the day (one was unwell, one had technical issues and one had unanticipated work pressures on the day).\n\nThe two-hour online workshop (via Microsoft Teams) was held in September 2021. Of the five participants, one was a person with lived experience, one was representative of a carers’ organization, two were from hospice bereavement services (one professional and one volunteer) and was one from a bereavement organization. The workshop was facilitated by the research team, and in response to the survey findings that highlighted the importance of creative activities, an artist and musician contributed to the intervention content.\n\nThe aim of the workshop was to co-produce the content of the intervention. To do so the research team provided an overview of the study, presented findings from the survey, and discussed potential content including family ‘activities’ to stimulate family interactions and communication describing how these linked to the study’s theoretical underpinnings. It was explained that the survey had endorsed the following content: a landing page – what the web-resource is about (the unique selling point of the resource); about grief – outlining the range of experience; dealing with practicalities; what to say (or not); and links to other sources of information and advice (for specific types of bereavement). However, the focus of the co-production discussion was on the theoretical underpinning of the intervention (and why this helps to support family bereavement), views on a reflective zone consisting of music and art, and family ‘activities’ to aid support.\n\nAn outline of the underpinning theories (as in the theoretical framework above) was presented and participants endorsed the value of the theories and their understanding of them in relation to family bereavement. They wanted the theoretical underpinning to be available on the intervention site to show users the robust foundations of the intervention, as well as the links between the family ‘activities’ and theory. Workshop participants supported the value of art (and music) in aiding ‘time out’ from considering bereavement, rather than necessarily aiding reflection. For some the images and music encouraged a sense of calm and mindfulness. Nonetheless, it was recognized that art preferences are individual and therefore there was support for maximizing options such as the ability to look at different visual images, with or without music.\n\nThe mainstay of the discussion revolved around potential family ‘activities’ of which three (mapping family networks, creating a family repository of memories, and questions to support families to talk together) were presented to the participants. For each activity the participants were asked to consider whether it made sense to them, if they could see it working with families and others to facilitate communication, and finally what changes they would suggest.\n\nI. Mapping family networks (Family Sense of Coherence – Manageability)\n\nParticipants supported asking intervention users to consider who is in their family network, then using this to identify the strengths and coping strategies of those identified, including the benefits of each relationship, and what effect the bereavement has had on each member of the network. Participants suggested completed exemplars of family maps would be useful and that one exemplar should be for an individual with limited family (i.e. representing the diversity of family and social networks such as neighbors/friends not just kin).\n\n…Family mapping might be quite useful to encourage people to think, oh yes, I can see how I could put members of my family on a piece of paper and I can see how it works…, by just putting one or two little examples. And I think I personally would feel confident enough to continue and do the task if I had that…. (Hospice bereavement service provider – volunteer)\n\n…If several family members actually drew this map separately and then sort of brought them together… You could have a think about it and see how similar or different they were and that might help people to understand that each person’s family maps are different even though they’re in the same group….” (Hospice bereavement service provider – professional)\n\n\n\nII. Creating a family repository of memories (Family Sense of Coherence – Meaning)\n\nThe workshop participants felt that encouraging families to create collections of memories and stories was important. With the increasing use of and familiarization with technology during the pandemic, there was recognition that this did not need to be a physical collection. Instead, digital memorialization such as legacy walls were viewed as a sharing innovation developed through COVID-19 which could be shared with distant family members in other countries.\n\n…Encouraging each individual to supply something that they feel is important to remember the person…” (Hospice bereavement service provider – volunteer)\n\n“…Whether it’s a physical or a digital thing… if families are overseas for example, or the things that people want to keep are of a particular nature that might make it easier for them to be digitized for sharing… I do think that there’s a place for both of those things… (Hospice bereavement service provider – professional)\n\n\n\nIII. Questions to help families talk together (Family Sense of Coherence – Meaning, Comprehensibility and Manageability)\n\nThe questions in Table 4 were taken to the workshop as suggestions linked to the theoretical constructs of Family Sense of Coherence to aid family coping via creating meaning, sense making, and the management of resources. The person with lived experience, and representative of a carers’ organization liked the questions but suggested some shortening of wording and refinements to more everyday language.\n\nBereavement service participants also liked the questions as prompts to start and encourage families to talk together.\n\n…I liked the prompts. The questions that you asked or suggested for families to think about, and I particularly like the fact that you’ve included some balance in there. You know that actually acknowledgement that there may be things that you won’t miss and there might be things that you wish had been different and that might vary between family members… that actually sometimes there is a sense of relief when someone dies, particularly if they’ve suffered, or if the relationships been very difficult, perhaps towards the end or long term, and it’s something that often people feel very guilty for admitting that they feel anything but sadness… So relief, maybe even anger… We know that those are normal parts of grieving, and I wonder if perhaps some questions that just give permission for people to speak about those feelings that they feel a little bit taboo… (Hospice bereavement service provider – professional)\n\nIt was suggested that using prompts to explore secondary losses as a result of the bereavement would be of value too:\n\n…Secondary losses that you might have as a result, you might want to explore that a little bit. So if there’s been an additional loss because that person has died, so perhaps somebody has had to move house or they’ve had to move the communities. They’re not just losing their loved one… (Bereavement organization participant)\n\nFollowing the workshop, the research team further developed the content of the respective webpages and their format/appearance (addressing all the suggestions highlighted above) based on Framework Analysis of the workshop transcript. The expert web designer then implemented these, followed by a cycle of amendments. The web-based intervention was then launched to coincide with National Grief Awareness Week (2-8 December 2021) following an invitation from the National Bereavement Alliance to publicize and demonstrate the intervention at their monthly webinar the previous week.\n\nFeedback on the intervention was invited through a dedicated page on the pilot website. Respondents were asked to complete a questionnaire via Microsoft Forms between December 2021 and January 2022. A total of 13 anonymous responses were returned. Bereavements were reported as resulting from COVID-19 (n=1); COVID-19 alongside other illness (n=2), other illnesses (n=8) and two did not provide details of the cause of death. Bereavement related to both family members and friends. A further nine respondents (six professionals, two bereaved and one bereaved professional) contacted the research team via email rather than completing the feedback form.\n\nAdditional feedback was provided from 18 participants when the intervention was presented at a national bereavement webinar. Comments were positive and constructive, and those supporting the bereaved highlighted the family activities as being something they would use with clients.\n\nQuestions related to accessibility, acceptability, usability and perceived benefits of the resource. A summary of key responses is provided below in Table 5.\n\nFollowing analysis of the feedback, the first cycle of iterative changes was undertaken. Webpages were condensed, so that a separate page on ‘how to support each other’ was removed, with the information incorporated into the ‘about grief’ page. The standalone ‘activities to support grief’ page was added to the ‘home’ page, to emphasize the intervention’s unique focus and content. A new page was inserted called ‘bereavement during COVID’ which drew on the survey findings to outline personal experiences of bereavement during the pandemic (including the positive developments that occurred). Text refinements were made to all webpages to break-up sections of text using images and edited for succinctness. In terms of appearance the font size across the site was increased to enhance readability.\n\n\nDiscussion\n\nThis paper reports on a study to co-produce a theoretically informed web-based intervention to support family and friends’ bereavement. The intervention was developed during COVID-19 as a resource to bridge an existing gap in bereavement support that became apparent during the social restrictions at the time. Our findings showed that the pandemic impacted bereavement in a variety of ways. Participants felt unable to prepare for the death of the person because of enforced separations, guilt at being unable to bear witness, or participate in goodbye rituals. There was a sense of disbelief and for some disconnection to the extent it was like “the person [who] was like the glue in the cracked pot was no longer there”(Participant 15, personal and professional). The disruption to these inherently important customs resulted in a loss of agency (Vieveen et al., 2023) and powerlessness for families and friends who were prevented from participating in the care of their relative or being present as end of life approached. This combined with a lack of connectedness with usual support networks resulted in disruption to the meaning-making process to enable families and friends to understand and make sense of the death. Meaning-making has been shown to be essential to bereavement in terms of wellbeing, resilience and emotionally adjusting to the loss (Barboza et al., 2022; Breen et al., 2019; Cardoso et al., 2020). Being able to attribute meaning to a death also enables the bereaved to reconstruct bonds with the deceased (Rothaupt & Becker, 2007) and begin to move forward with their lives following an unwanted and unexpected life transition (Fuchs, 2018; Shear, 2012).\n\nThe COVID-19 pandemic prevented many families and friends from accessing and assimilating the ‘active ingredients’ of meaning-making and threatened their capacity to experience the meaning of a death (Derkx et al., 2020). Findings from our study demonstrated the importance placed on the exchange of experiences with others within their social network and highlighted the need to discuss feelings and emotions in order to make sense of the death, regain a level of control in their lives, and “hold on to things differently” (Vieveen et al., 2023). They also highlighted the use of technology to enable social connections and facilitate support online at a time when this was prohibited face to face. It is in response to these insights that the Families and Friends in Bereavement intervention was co-produced. However, while the web-resource was developed during COVID-19 the content is designed to ensure ongoing relevance and legacy beyond this specific context.\n\nThe intervention is novel in shifting the professional gaze of bereavement to one that strengthens a social response to grief through family, friends and social networks. While every bereavement is experienced individually the intervention promotes ways to understand, make meaning and manage the bereavement collectively. While family relationships can add complexity to meaning-making in the grief process, they have also been shown to provide an invaluable resource for dealing with it (Kissane et al., 2008). Activities offered within the intervention stimulate social interactions and encourage communication to enable users to consider the strengths of their network and how reciprocal support may be realized. In doing so, the loss of agency experienced during the death of the person can be re-gained as the web-resource offers a mechanism for agency in the bereavement process through flexibility in how it can be used and engaged with.\n\nFeedback obtained during intervention development and piloting has indicated that it is accessible, acceptable, usable and importantly has value and benefit. We are now undertaking a qualitative evaluation utilizing semi-structured interviews and focus groups. Evaluation data will inform a second cycle of refinements to develop the final version of the intervention, including metrics on the use of the resource, in readiness for adoption and implementation.\n\nAn important strength of this study is the combined use of the two underpinning theories, Family Sense of Coherence (Antonovsky & Sourani, 1988) and the family level extension to the Dual Process Model (Stroebe & Schut, 2015) which have provided a robust framework for data collection, analysis and intervention development. The explicit use of the two theories identified key constructs and mechanisms to guide our focus and informed the content of the intervention. A further strength is the use of co-production to develop the intervention. We approached the study from the position that those who are affected by the research and potential users of its outputs have experiences and knowledge that can offer invaluable insights to inform understanding. By drawing on the views and experiences of those who are bereaved, and bereavement professionals who support them, has ensured the intervention has relevance and utility for those it seeks to support. As with all studies there are limitations. It might be argued that the scoping work undertaken was partial. At the time we reviewed the literature, the evidence base on bereavement experience and support needs during COVID-19 was emerging and the plethora of papers which have been published since were not available to us at the time the intervention was under initial development. We recognize that this may be considered a potential limitation but would argue it does not compromise the robustness of the resource due to it being theoretically informed and grounded in real world experience. In addition, literature that has been published subsequently concurs with our findings (Burrell & Selman, 2022; Mayland et al., 2020; Selman et al., 2021, 2022; Torrens-Burton et al., 2022).\n\n\nConclusion\n\nFamilies, friends and support networks are essential to managing bereavement. COVID-19 social restrictions prevented families and friends from being with the dying and participating in usual rituals to honor the dead. This resulted in social disconnection, feelings of guilt, and difficulty in making sense of the death and reconstructing relationships. The Families and Friends in Bereavement intervention was developed during the pandemic with the aim of promoting communication and meaning-making, fostering coherence and resilience. However, while designed during COVID-19 the content has continuing relevance beyond this context. We have provided a platform (with family-focused tools) to process the death and family narrative, and begin to make sense of what has happened, and reconstruct bonds and adjust to altered family roles and structure. The web-resource provides a framework to promote meaning-making, comprehensibility and manageability, therefore providing a mechanism to rebuild, reconfigure and begin to glue back the pieces of the cracked family pot.\n\nThe study was approved via the Faculty Research Ethics Committee at the University of Southampton (Ethics/ERGO number: 63208). At the start of both the online survey and feedback form on the pilot website respondents had to indicate that they had read and understood the study information sheet, were 18 or over and agreed to take part. Full written consent was obtained for participation in the co-production workshop.", "appendix": "Data availability\n\nThe underlying data is not available as study participants consented only to their data being used for the sole purpose of this study and not to sharing for secondary analysis purposes.\n\nOSF: Supporting families and friends bereaved during COVID-19 and beyond. https://doi.org/10.17605/OSF.IO/H6TNX\n\nThis project contains the following extended data:\n\n- Online survey.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe study team are grateful to Mark Livermore who expertly designed and produced the web-based intervention. We would also like to thank artist and musician Cindy Brooks for her contributions to the Space to Pause web-page.\n\n\n\n\nReferences\n\nAntonovsky A, Sourani T: Family sense of coherence and family adaptation. J. Marriage Fam. 1988; 50: 79–92. Publisher Full Text\n\nBarboza J, Seedall R, Neimeyer RA: Meaning co‐construction: Facilitating shared family meaning‐making in bereavement. Fam. Process. 2022; 61(1): 7–24. PubMed Abstract \| Publisher Full Text\n\nBear L, Simpson N, Angland M, et al.: ‘A good death’during the Covid-19 pandemic in the UK: a report on key findings and recommendations. London: London School of Economics and Political Science; 2020.\n\nBorghi L, Menichetti J: Strategies to Cope With the COVID-Related Deaths Among Family Members. Front. Psych. 2021; 12. PubMed Abstract \| Publisher Full Text Reference Source\n\nBreen LJ, Szylit R, Gilbert KR, et al.: Invitation to grief in the family context. Death Stud. 2019; 43(3): 173–182. PubMed Abstract \| Publisher Full Text\n\nBurrell A, Selman LE: How do funeral practices impact bereaved relatives’ mental health, grief and bereavement? A mixed methods review with implications for COVID-19. Omega (Westport). 2022; 85(2): 345–383. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCardoso ÉA d O, Silva BC d A d, Santos JHD, et al.: The effect of suppressing funeral rituals during the COVID-19 pandemic on bereaved families. Rev. Lat. Am. Enfermagem. 2020; 28: e3361. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCowpertwait L, Clarke D: Effectiveness of web-based psychological interventions for depression: a meta-analysis. Int. J. Ment. Heal. Addict. 2013; 11(2): 247–268. Publisher Full Text\n\nDerkx P, Bos P, Laceulle H, et al.: Meaning in life and the experience of older people. Int. J. Ageing Later Life. 2020; 14(1): 37–66.\n\nDuke S, Campling N, May CR, et al.: Co-construction of the family-focused support conversation: a participatory learning and action research study to implement support for family members whose relatives are being discharged for end-of-life care at home or in a nursing home. BMC Palliat. Care. 2020; 19(1): 146. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDuncan E, O’Cathain A, Rousseau N, et al.: Guidance for reporting intervention development studies in health research (GUIDED): an evidence-based consensus study. BMJ Open. 2020; 10(4): e033516. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFernández Ó, González-González M: The Dead with No Wake, Grieving with No Closure: Illness and Death in the Days of Coronavirus in Spain. J. Relig. Health. 2022; 61: 703–721. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFox M, McIlveen J, Murphy E: Death, dying and bereavement care during COVID-19: Creativity in hospital social work practice. Qual. Soc. Work. 2021; 20(1): 131–137. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFuchs T: Presence in absence. The ambiguous phenomenology of grief. Phenomenol. Cogn. Sci. 2018; 17(1): 43–63. Publisher Full Text\n\nGilbert KR: “We’ve had the same loss, why don’t we have the same grief?” Loss and differential grief in families. Death Stud. 1996; 20(3): 269–283. Publisher Full Text\n\nGoodyear-Smith F, Jackson C, Greenhalgh T: Co-design and implementation research: challenges and solutions for ethics committees. BMC Med. Ethics. 2015; 16(1): 1–5. Publisher Full Text\n\nGrindell C, Coates E, Croot L, et al.: The use of co-production, co-design and co-creation to mobilise knowledge in the management of health conditions: a systematic review. BMC Health Serv. Res. 2022; 22(1): 877. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHanna JR, Rapa E, Dalton LJ, et al.: A qualitative study of bereaved relatives’ end of life experiences during the COVID-19 pandemic. Palliat. Med. 2021; 35(5): 843–851. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarrop E, Farnell D, Longo M, et al.: Supporting people bereaved during COVID-19: study report 1. Report, Cardiff University and the University of Bristol. 2020; 27.\n\nHewison A, Zafar S, Efstathiou N: Bereavement support in the UK–a rapid evidence assessment. Bereavement Care. 2020; 39(2): 69–78. Publisher Full Text\n\nHoffmann TC, Glasziou PP, Boutron I, et al.: Better reporting of interventions: template for intervention description and replication (TIDieR) checklist and guide. BMJ. 2014; 348. PubMed Abstract \| Publisher Full Text\n\nKissane D, Lichtenthal WG, Zaider T: Family care before and after bereavement. Omega (Westport). 2008; 56(1): 21–32. Publisher Full Text\n\nKlass D, Silverman PR, Nickman S: Continuing bonds: New understandings of grief. Taylor & Francis; 2014.\n\nKnowles LM, Stelzer E-M, Jovel KS, et al.: A pilot study of virtual support for grief: Feasibility, acceptability, and preliminary outcomes. Comput. Hum. Behav. 2017; 73: 650–658. Publisher Full Text\n\nLaranjeira C, Moura D, Salci MA, et al.: A Scoping Review of Interventions for Family Bereavement Care during the COVID-19 Pandemic. Behav. Sci. 2022; 12(5): 155. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMayland CR, Harding AJ, Preston N, et al.: Supporting adults bereaved through COVID-19: a rapid review of the impact of previous pandemics on grief and bereavement. J. Pain Symptom Manag. 2020; 60(2): e33–e39. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcKnight A: Perspectives on grief: psychoanalytical evolutionary and family systems. Family systems. 2015; 11(1): 31–48.\n\nMoore SE, Jones-Eversley SD, Tolliver WF, et al.: Six feet apart or six feet under: The impact of COVID-19 on the Black community. Death Stud. 2020; 46: 891–901. Publisher Full Text Reference Source\n\nNational Palliative and End of Life Care partnership: Ambitions for Palliative and End of Life Care: A National Framework for local action 2021–2026. NHS England; 2021. Retrieved 13th March 2023. Reference Source\n\nPearce C, Honey JR, Lovick R, et al.: ‘A silent epidemic of grief’: a survey of bereavement care provision in the UK and Ireland during the COVID-19 pandemic. BMJ Open. 2021; 11(3): e046872. PubMed Abstract \| Publisher Full Text Reference Source\n\nPenny A: [COVID-19 Palliative and End of Life Care Weekly Update Webinar]. Bereavement during the outbreak, lockdown, and beyond. NHS England and NHS Improvement; 2020, 21 May. [Webinar]. Reference Source\n\nRitchie J, Spencer L, Bryman A, et al.: Analysing qualitative data. London: Routledge; 1994.\n\nRothaupt JW, Becker K: A literature review of Western bereavement theory: From decathecting to continuing bonds. Fam. J. 2007; 15(1): 6–15. Publisher Full Text\n\nSelman LE, Farnell D, Longo M, et al.: Risk factors associated with poorer experiences of end-of-life care and challenges in early bereavement: Results of a national online survey of people bereaved during the COVID-19 pandemic. Palliat. Med. 2022; 36(4): 717–729. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSelman LE, Sowden R, Borgstrom E: ‘Saying goodbye’during the COVID-19 pandemic: A document analysis of online newspapers with implications for end of life care. Palliat. Med. 2021; 35(7): 1277–1287. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShear MK: Grief and mourning gone awry: pathway and course of complicated grief. Dialogues Clin. Neurosci. 2012; 14(2): 119–128. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSmith KV, Wild J, Ehlers A: The Masking of Mourning: Social Disconnection After Bereavement and Its Role in Psychological Distress. Clin. Psychol. Sci. 2020; 8(3): 464–476. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStroebe M, Schut H: Family matters in bereavement: Toward an integrative intra-interpersonal coping model. Perspect. Psychol. Sci. 2015; 10(6): 873–879. PubMed Abstract \| Publisher Full Text\n\nStroebe M, Schut H: Bereavement in times of COVID-19: A review and theoretical framework. Omega (Westport). 2021; 82(3): 500–522. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStroebe MS, Van Der Houwen K, Schut H: Bereavement support, intervention, and research on the Internet: A critical review.2008.\n\nTorrens-Burton A, Goss S, Sutton E, et al.: ‘It was brutal. It still is’: a qualitative analysis of the challenges of bereavement during the COVID-19 pandemic reported in two national surveys. Palliat. Care Soc. Pract. 2022; 16: 263235242210924. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVieveen MJM, Yildiz B, Korfage IJ, et al.: Meaning-making following loss among bereaved spouses during the COVID-19 pandemic (the CO-LIVE study). Death Stud. 2023: 1–9. PubMed Abstract \| Publisher Full Text\n\nWalter T: A new model of grief: Bereavement and biography. Mortality. 1996; 1(1): 7–25. Publisher Full Text" }	[ { "id": "240907", "date": "19 Feb 2024", "name": "Lorenza Entilli", "expertise": [ "Reviewer Expertise online grief support", "traumatic bereavement support", "qualitative studies" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate the opportunity to review this manuscript, as the topic holds significant importance for clinical practices related to grief.\nIntroduction section: the narrative is notably straightforward and comprehensible.\na) the section might be enhanced with more recent literature references and a deeper elucidation of the concept of meaning-making in the context of grief: - [1],[2],[3]\n\nb) The statement “(It is difficult to determine if this is the case beyond Western societies due to paucity of evidence, and further research is required to understand the focus of interventions globally).” is pivotal in the study. Therefore, it merits emphasis without the use of brackets.\nc) The assertion that \"Web-based interventions are known to provide effective and accessible psychological support\" is significant. However, the cited literature, such as Cowpertwait & Clarke (2013) and Stroebe et al. (2008), might not be entirely relevant or current. I suggest revisiting the literature to incorporate recent studies on this subject, along with a detailed analysis of the advantages and disadvantages of such tools. Given the abundance of literature on this topic, it would be beneficial to assist the reader in evaluating the current state of the art to better understand the novelty of your contribution.\nRecommendations:\n[4],[5],[6],[7],[8],[9] [10],[12]\n\nAs for the last recommended article, it would be useful for the authors to specify whether they believe certain types of losses may benefit more or less from online support, such as traumatic loss. Furthermore, it is important to consider whether authors classify COVID-19 deaths as traumatic. This kind of clarification is significant, particularly if the authors advocate for a family-centered approach, as existing literature indicates that certain losses may have a more disruptive (or generative in the long term) impact on family bonds than others.\n\nMethod section.\na) The co-production approach presents intriguing possibilities alongside limitations. It would be beneficial to reference works that have already employed this approach within the context of COVID-19 grief.[11]\n\nb) The population under study appears to be homogeneous in certain aspects but heterogeneous in others, as evidenced by literature indicating, for instance, that women tend to seek help more frequently than men. It would be insightful for the authors to elaborate on whether they are satisfied with the level of saturation achieved. Did they conclude data collection when saturation or homogeneity was attained (if this was their intent), or were other factors such as time and resources the determining factors?\nLastly, it is crucial to understand how the survey was disseminated. Is there a possibility that primarily professionals and patients closely associated with the funding institute were reached? While not inherently a limitation, this factor needs to be discussed in terms of representativeness to ensure a comprehensive understanding of the study's findings.\n\nd) data analysis\n“Survey results were analysed using Framework Analysis (Ritchie et al., 1994) by NC, SL,MMfollowing the five stages of data familiarization, framework identification, indexing, charting, and mapping and interpretation, and generated key themes outlined below.” Critical pieces of information are absent in the manuscript and need clarification. For instance:\n- who between the authors conducted the analysis? - how was consensus reached between authors?\n\ne) Considering the emphasis on family bonds, it would be beneficial to include the relationship status with the deceased in the participant descriptions following the quotation. For example, \"Participant 17, daughter, personal.\" Furthermore, it is important to briefly discuss or at least consider in the analysis and discussion throughout the paper how different family roles might have influenced the experience of loss.\n\nf) The summary of feedback from the pilot website provides valuable and informative insights for the reader.\n\nI trust that the recommendations offered will prove useful in enhancing the impact of the research and its contributions.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11176", "date": "22 Apr 2024", "name": "Natasha Campling", "role": "Author Response", "response": "Introduction section: the narrative is notably straightforward and comprehensible. Thank you. a) the section might be enhanced with more recent literature references and a deeper elucidation of the concept of meaning-making in the context of grief:- [1],[2],[3] Thank you we have added additional references into the introduction specific to the challenges of meaning-making in the context of COVID-19. We have not cited references 1 and 2 as they are concerned with 1. online communities and 2. prolonged grief which have not been the foci of our work. The social disconnection between a dying person and family, caused by social distancing precautions, meant the construction of family narratives of end-of-life was compromised. A review of the international literature, across 13 countries during COVID-19, found that whilst there was diversity of experience based on culture and belief systems all countries identified significant impact on family bereavement (Stroebe & Schut, 2021). Almost half (49%) of respondents to a survey of 2,000 UK adults, carried out by Dying Matters, agreed that being unable to be with someone as they died, or attend their funeral, would make it harder for them to process the death (Penny, 2020) . It is narratives that serve to link the biography of a living family member with the death and which are important in the process of making sense of what has happened, paying tribute to the deceased and in reconstructing bonds between the bereaved and their deceased family member (Klass et al., 2014; Walter, 1996). This meaning-making process is essential for family wellbeing and resilience (Gilbert, 1996), yet it was challenged by the chaos and confusion of the pandemic and variance of COVID-19 control measures (Milner & Echterling 2021). As highlighted by Walsh (2020) during COVID-19 families experienced multiple stressors and needed help to build resilience in their grief, strengthen family bonds, accommodate uncertainty and navigate challenges. Meaning-making processes necessitated shared attempts to make sense of loss, identify previously utilised coping strategies and develop a sense of coherence. b) The statement “(It is difficult to determine if this is the case beyond Western societies due to paucity of evidence, and further research is required to understand the focus of interventions globally).” is pivotal in the study. Therefore, it merits emphasis without the use of brackets. Thank you we agree and have removed the brackets. c) The assertion that \"Web-based interventions are known to provide effective and accessible psychological support\" is significant. However, the cited literature, such as Cowpertwait & Clarke (2013) and Stroebe et al. (2008), might not be entirely relevant or current. I suggest revisiting the literature to incorporate recent studies on this subject, along with a detailed analysis of the advantages and disadvantages of such tools. Given the abundance of literature on this topic, it would be beneficial to assist the reader in evaluating the current state of the art to better understand the novelty of your contribution. Thank you we have added recent references. We understand that outlining the benefits and drawbacks of online tools is helpful for the reader to understand the current state of knowledge. However, given the diversity of web-based interventions and the vast literature we consider this would be more appropriate as a standalone review as it would not be possible to do this justice in an introduction. The Families and Friends in Bereavement intervention was developed to encourage users to consider their bereavement experience in the context of family, friends and close social networks, to promote communication and meaning-making, fostering coherence and resilience (McKnight, 2015). Web-based interventions are known to provide effective and accessible psychological support (Dominguez-Rodriguez et al 2023; Brog et al 2022; Heckendorf et al 2022; Cowpertwait & Clarke, 2013; Knowles et al., 2017; Stroebe et al., 2008); and they have the advantage of enabling users to access support when needed, increasing the potential effectiveness of bereavement support (Hewison et al., 2020). Furthermore, recent evidence has highlighted the need for a family centered and online approach for bereavement support (Harrop et al., 2020). Recommendations: [4],[5],[6],[7],[8],[9] [10],[12] As for the last recommended article, it would be useful for the authors to specify whether they believe certain types of losses may benefit more or less from online support, such as traumatic loss. Furthermore, it is important to consider whether authors classify COVID-19 deaths as traumatic. This kind of clarification is significant, particularly if the authors advocate for a family-centered approach, as existing literature indicates that certain losses may have a more disruptive (or generative in the long term) impact on family bonds than others. Our web-based intervention is specific to the 60% of bereaved people who manage their bereavement with the help of family, friends and support networks alone. We state that the intervention is complimentary to other bereavement support and acknowledge certain types of loss particularly those that can result in complex or prolonged grief may require professional intervention. Method section. a) The co-production approach presents intriguing possibilities alongside limitations. It would be beneficial to reference works that have already employed this approach within the context of COVID-19 grief.[11] Thank you we have added this into the following paragraph. Our approach to intervention-development was underpinned by co-production and theoretically informed by Family Sense of Coherence (Antonovsky & Sourani, 1988) and the family-level extension to the Dual Process Model (Stroebe & Schut, 2015) which were used to develop the family-focused intervention. The co-production approach (Grindell et al., 2022) developed partnerships between the research team, people with real world experience of bereavement, and community and national stakeholders. Involving people with lived experience of this specific context, leveraging their knowledge, experience and insights, to enable a deep understanding of the challenges they face; and encouraging the uptake of outputs was used to help ensure “contextual fit” (Goodyear-Smith et al., 2015) and findings that have relevance to end users of the web-resource. Co-production offered an opportunity to enhance individual’s agency and COVID-19 as an unprecedented event made the inclusion of experts by experience imperative, as a result co-production has been used as a methodological approach in COVID-19, grief and and death related studies (Booth et al 2021, Entilli et al 2024). b) The population under study appears to be homogeneous in certain aspects but heterogeneous in others, as evidenced by literature indicating, for instance, that women tend to seek help more frequently than men. It would be insightful for the authors to elaborate on whether they are satisfied with the level of saturation achieved. Did they conclude data collection when saturation or homogeneity was attained (if this was their intent), or were other factors such as time and resources the determining factors? Whilst resource and time factors were a consideration it was not our intent to achieve data saturation (we felt that this would be impossible due to the individual nature of grief) but the reason for selecting co-production as an approach was to enable the robust underpinning of the web-resource design informed by lived experience. Lastly, it is crucial to understand how the survey was disseminated. Is there a possibility that primarily professionals and patients closely associated with the funding institute were reached? While not inherently a limitation, this factor needs to be discussed in terms of representativeness to ensure a comprehensive understanding of the study's findings. As stated in the paper the survey was distributed via the National Bereavement Alliance; Hospice UK; a large patient and public involvement network; and social media. None of these routes were aligned to or linked to the funders. d) data analysis “Survey results were analysed using Framework Analysis (Ritchie et al., 1994) by NC, SL, MM following the five stages of data familiarization, framework identification, indexing, charting, and mapping and interpretation, and generated key themes outlined below.” Critical pieces of information are absent in the manuscript and need clarification. For instance: - who between the authors conducted the analysis? - how was consensus reached between authors? Thank you we have added the following. Survey results were analyzed using Framework Analysis (Ritchie et al., 1994) by NC, SL, MM following the five stages of data familiarization, framework identification, indexing, charting, and mapping and interpretation, and generated key themes outlined below. NC, SL, and MM conducted the analysis and agreement was reached on coding and theme generation via team analysis workshops. Findings were shared to check interpretation and gain consensus with the co-production group. e) Considering the emphasis on family bonds, it would be beneficial to include the relationship status with the deceased in the participant descriptions following the quotation. For example, \"Participant 17, daughter, personal.\" Furthermore, it is important to briefly discuss or at least consider in the analysis and discussion throughout the paper how different family roles might have influenced the experience of loss. Thank you for this comment. We made the decision not to include relationship status in the descriptor as it would have been challenging to address this equitably as respondents had personal and/or professional experiences, and for many these were cumulative experiences. Furthermore, our work focuses on a collective (family) approach to grief and the theoretical underpinning of the web-resource (Dual Process Model, family extension) highlights that roles are not static but evolve and new ones develop. f) The summary of feedback from the pilot website provides valuable and informative insights for the reader. Thank you. Added references: Booth, J., Croucher, K., & Bryant, E. (2021). Dying to talk? Co-producing resources with young people to get them talking about bereavement, death and dying. Voluntary Sector Review, 12(3), 333-357. Brog, N. A., Hegy, J. K., Berger, T., & Znoj, H. (2022). Effects of an internet-based self-help intervention for psychological distress due to COVID-19: results of a randomized controlled trial. Internet interventions, 27, 100492. Entilli, L., Kõlves, K., De Leo, D., & Cipolletta, S. (2024). Human-Computer Interaction in Times of Grief: Unveiling Support Processes Among COVID-19 Bereaved Users in a Facebook Group Through Netnography. International Journal of Human–Computer Interaction, 1-11. Heckendorf, H., Lehr, D., & Boß, L. (2022). Effectiveness of an internet-based self-help intervention versus public mental health advice to reduce worry during the COVID-19 pandemic: a Pragmatic, parallel-group, randomized controlled trial. Psychotherapy and psychosomatics, 91(6), 398-410. Milner, R. J., & Echterling, L. G. (2021). Co-constructing meaning in the time of coronavirus. Journal of Constructivist Psychology, 34(3), 295-308. Dominguez-Rodriguez, A., Sanz-Gomez, S., González Ramírez, L. P., Herdoiza-Arroyo, P. E., Trevino Garcia, L. E., de la Rosa-Gómez, A., ... & Miaja, M. (2023). The Efficacy and Usability of an Unguided Web-Based Grief Intervention for Adults Who Lost a Loved One During the COVID-19 Pandemic: Randomized Controlled Trial. Journal of Medical Internet Research, 25, e43839. Walsh, F. (2020). Loss and resilience in the time of COVID‐19: Meaning making, hope, and transcendence. Family process, 59(3), 898-911." } ] }, { "id": "246498", "date": "21 Mar 2024", "name": "Anne Finucane", "expertise": [ "Reviewer Expertise Palliative care", "psychological support." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper describes the development of an online family-focused bereavement support intervention underpinned by family sense of coherence and the dual process model. This is a useful paper describing prototype development. The intervention - Families in Bereavement - will be further tested and evaluated. Well done to the research team on their timely, interesting, and valuable work. I have noted some minor points below in relation to clarification and possible restructuring.\nTitle: The quotation in the title at first suggests that this paper is a qualitative study of the experiences of bereaved people as opposed to an intervention development study. You might consider including the name of the actual intervention in the study in place of the quote.\nAbstract It is not entirely clear from the abstract whether an invention prototype was actually developed. Clarification would be helpful. Please note the number of survey respondents and workshop participants. A sentence relating to next steps would be a useful addition to the Conclusion.\nIntroduction The introduction clearly introduces the proposed interventions, describes the background literature and theoretical basis informing the content, and outlines the aim of this paper. Review or delete the two-word sentence “Estimates suggest”.\nMethods “We applied the three Family Sense of Coherence constructs to bereavement: defining meaning and wanting to respond and create meaning as a family…” Perhaps add a little more detail in this paragraph to explain Family Sense of Coherence, especially for readers unfamiliar with family Sense of Coherence and how it applies to bereavement. Or perhaps clarify what is meant using brief examples. Figure 3, paragraph starting “Together the models….” Which models – dual process and sense of coherence – please specify. Figure 3 is named “The theories combined”. Are theories and models being interchangeably? Please choose term for consistency or clarify. It would be useful if you would specify the theories/models for the reader to avoid any confusion. “Combined, Family Sense of Coherence and the family level extension to the Dual Process Model, were used to create a robust theoretical framework to guide family orientated bereavement support.” This sentence comes after the models/theories are displayed – should it come earlier?\nRevise sentence to flow better: “From the limited evidence available at this time on bereavement during COVID-19 papers explored the nature of family experiences and support needs.”\n\nScoping review\n\nPlease clarify the number of papers identified and briefly summarise any key characteristics (eg country where data was gathered, type of bereavement or bereaved populations included etc). I think Table 1 would work better as two paragraphs in the scoping review section as opposed to a Table. Given the number of papers identified on ‘support needs’ the text could elaborate on findings. For instance, there were 5 papers on service response and willingness to adapt – it would be good to see some further insights for intervention development based on this evidence.\nSurvey\nThe results of the scoping work and survey might sit better in the Results section rather than the methods. Please describe PPI input in a separate paragraph somewhere in the paper – good to see the contribution of PPI at different points in the study. Please say something more about the “Large patient and public involvement network”. Who are these? Was it a pre-existing network or one developed for the study? Information on survey completion would fit better in the results section than in the Methods. Characteristics of respondents would also fit better in the Results section.\nPlease add some information the co-design workshop in the Methods section – who were recruited and how. What was discussed. How long did it last. Who facilitated.\nResults The qualitative data, analysed using framework analysis, could be better presented using categories or themes, or by presenting a matrix. At present the whole section is narrative in form and would benefit from some structure. See Gale 2013.\nTypically only one or two quotes are needed to evidence a key point in the text, though other quotes can be usefully included in appendices. Seven quotes to illustrate a general paragraph seems like too many (unless each is linked to a different point which should then be clearly stated).\nDetails on recruitment for the co-production workshop should be moved to the Methods. The section on the co-production workshop describes the practical recommendations from the survey on intervention content (e.g. description of what the resource is about on the landing page). This should appear in the results relating to the survey, as opposed to the section on the co-production workshop. A box or table highlighting the practical recommendations that were identified from survey data would be very helpful and useful for to anyone organizations involved in the development of online bereavement support resources.\n“The workshop was facilitated by the research team, and in response to the survey findings that highlighted the importance of creative activities, an artist and musician contributed to the intervention content.” Please specify how the artist and musician contributed.\nTable 4 would be better placed in the methods in a paragraph describing the format and content etc of the co-production workshop (These are not results). On p13 the authors say that framework analysis was then conducted, however to the reader it might appear that the section above that had been analysed using framework analysis. And no further findings are noted in relation to this additional framework analysis. Some clarification is needed. Please add a paragraph clearly describing the final intervention prototype, how it is navigated, how bereaved people can find it (how will they know about it), what platform is it on, will it be moderate or is it fully self-guided and so on.\nDiscussion A paragraph on what would be useful regarding the development of online bereavement support interventions in general would be very helpful for organisations providing bereavement support or those involved in service development. This could go under an “Implications for practice” heading.\nAny implications for researchers conducting intervention development work in this area would also be useful.\nA paragraph on ideas regarding future plans for sustainability, implementation and funding would be relevant here. Even though this is the first phase of development, thinking about implementation, moderation, sustainability from the onset of intervention development is recommended. (Skivington et al 2021).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11377", "date": "26 Apr 2024", "name": "Natasha Campling", "role": "Author Response", "response": "This paper describes the development of an online family-focused bereavement support intervention underpinned by family sense of coherence and the dual process model. This is a useful paper describing prototype development. The intervention - Families in Bereavement - will be further tested and evaluated. Well done to the research team on their timely, interesting, and valuable work. I have noted some minor points below in relation to clarification and possible restructuring. Thank you, we note that you think there are some minor points and possible restructuring to be addressed. Title: The quotation in the title at first suggests that this paper is a qualitative study of the experiences of bereaved people as opposed to an intervention development study. You might consider including the name of the actual intervention in the study in place of the quote. Thank you we have amended the title to include the name of the intervention. Abstract It is not entirely clear from the abstract whether an invention prototype was actually developed. Clarification would be helpful. Thank you, the intervention was developed and piloted as outlined in the abstract. It is publicly available at: www.familiesandfriendsinbereavement.org.uk Please note the number of survey respondents and workshop participants. This has been added. A sentence relating to next steps would be a useful addition to the Conclusion. We have clarified in the conclusion that the intervention is live and publicly accessible. Introduction The introduction clearly introduces the proposed interventions, describes the background literature and theoretical basis informing the content, and outlines the aim of this paper. Review or delete the two-word sentence “Estimates suggest”. Thank you, this has been removed. Methods “We applied the three Family Sense of Coherence constructs to bereavement: defining meaning and wanting to respond and create meaning as a family…” Perhaps add a little more detail in this paragraph to explain Family Sense of Coherence, especially for readers unfamiliar with family Sense of Coherence and how it applies to bereavement. Or perhaps clarify what is meant using brief examples. Thank you we have clarified this further in the introduction (paragraph 5). Figure 3, paragraph starting “Together the models….” Which models – dual process and sense of coherence – please specify. Thank you we have now consistently referred to our 'theoretical framework' which draws from both the Family Sense of Coherence and the family extension to the Dual Process Model. Figure 3 is named “The theories combined”. Are theories and models being interchangeably? Please choose term for consistency or clarify. It would be useful if you would specify the theories/models for the reader to avoid any confusion. This has been altered for clarity to 'theoretical framework'. “Combined, Family Sense of Coherence and the family level extension to the Dual Process Model, were used to create a robust theoretical framework to guide family orientated bereavement support.” This sentence comes after the models/theories are displayed – should it come earlier? Thank you this has been moved. Revise sentence to flow better: “From the limited evidence available at this time on bereavement during COVID-19 papers explored the nature of family experiences and support needs.” Thank you this has been altered. Scoping review Please clarify the number of papers identified and briefly summarise any key characteristics (eg country where data was gathered, type of bereavement or bereaved populations included etc). Thank you the number of papers have been added but the scoping work was to inform the intervention development and was not intended as a formal scoping review and is therefore not reported as such. I think Table 1 would work better as two paragraphs in the scoping review section as opposed to a Table. Thank you we put this as a Table due to the word limit for the journal but as recommended we have altered this in the revised paper. Given the number of papers identified on ‘support needs’ the text could elaborate on findings. For instance, there were 5 papers on service response and willingness to adapt – it would be good to see some further insights for intervention development based on this evidence. Thank you see Table 2, questions 2 and 3 which were directly informed by the scoping work focusing on family experiences and support needs. Survey The results of the scoping work and survey might sit better in the Results section rather than the methods. Thank you the paper was written initially in a traditional format however internal peer review recommended situating the methods and findings of the respective stages together to avoid confusion. We feel that this enhances the flow of the paper and improves the overall narrative. Please describe PPI input in a separate paragraph somewhere in the paper – good to see the contribution of PPI at different points in the study. Please say something more about the “Large patient and public involvement network”. Who are these? Was it a pre-existing network or one developed for the study? Thank you we have explained this was a national network, but to ensure anonymity we have avoided further details. In keeping with the above point we have retained the PPI involvement in the respective sections. Information on survey completion would fit better in the results section than in the Methods. Characteristics of respondents would also fit better in the Results section. Please refer to the point above. Please add some information the co-design workshop in the Methods section – who were recruited and how. What was discussed. How long did it last. Who facilitated. Please see co-production workshop p14. As stated above we feel that information about recruitment, content and facilitation work best here. We acknowledge this is not traditional but for the sake of flow have opted for this approach throughout. Results The qualitative data, analysed using framework analysis, could be better presented using categories or themes, or by presenting a matrix. At present the whole section is narrative in form and would benefit from some structure. See Gale 2013. Thank you. For the survey data we have added sub-headings to clarify the themes generated. For the workshop data as we applied Framework Analysis utilising a theoretical lens it was most appropriate for the data to be mapped to the three core constructs of Family Sense of Coherence. Typically only one or two quotes are needed to evidence a key point in the text, though other quotes can be usefully included in appendices. Seven quotes to illustrate a general paragraph seems like too many (unless each is linked to a different point which should then be clearly stated). We have drawn on multiple quotes due to the rich and diverse perspectives – personal, voluntary and professional, and to highlight the diversity and individuality of grief itself. As authors we wanted to ensure their voices were heard and this was imperative to our co-production methodology. The quotes cited build on one another increasing understanding of experience, rather than duplicating. Details on recruitment for the co-production workshop should be moved to the Methods. The section on the co-production workshop describes the practical recommendations from the survey on intervention content (e.g. description of what the resource is about on the landing page). This should appear in the results relating to the survey, as opposed to the section on the co-production workshop. Please refer to our response above re. the narrative flow and format. A box or table highlighting the practical recommendations that were identified from survey data would be very helpful and useful for to anyone organizations involved in the development of online bereavement support resources. Thank you some practical recommendations could be drawn by readers from Table 5. “The workshop was facilitated by the research team, and in response to the survey findings that highlighted the importance of creative activities, an artist and musician contributed to the intervention content.” Please specify how the artist and musician contributed. Thank you this has been added. Table 4 would be better placed in the methods in a paragraph describing the format and content etc of the co-production workshop (These are not results). Please refer to our response re. narrative flow and format. On p13 the authors say that framework analysis was then conducted, however to the reader it might appear that the section above that had been analysed using framework analysis. And no further findings are noted in relation to this additional framework analysis. Some clarification is needed. Thank you we recognise that this was confusing, we have therefore amended the wording. Please add a paragraph clearly describing the final intervention prototype, how it is navigated, how bereaved people can find it (how will they know about it), what platform is it on, will it be moderate or is it fully self-guided and so on. Thank you we have amended and updated the paragraph at the end of the discussion. Discussion A paragraph on what would be useful regarding the development of online bereavement support interventions in general would be very helpful for organisations providing bereavement support or those involved in service development. This could go under an “Implications for practice” heading. Any implications for researchers conducting intervention development work in this area would also be useful. Thank you. As our focus, co-production, data collection and analysis was specific to family support we have been cautious not to suggest the transferability of our findings to the development of other online bereavement support interventions. A paragraph on ideas regarding future plans for sustainability, implementation and funding would be relevant here. Even though this is the first phase of development, thinking about implementation, moderation, sustainability from the onset of intervention development is recommended. (Skivington et al 2021). Thank you. We have provided further information in the paragraph at the end of the discussion section." } ] } ]	1	https://f1000research.com/articles/12-1024
https://f1000research.com/articles/12-292/v1	16 Mar 23	{ "type": "Research Article", "title": "Pharmacists’ readiness and willingness to vaccinate the public in United Arab Emirates community pharmacies: A cross-sectional study", "authors": [ "Dixon Thomas", "Amal Abdalla", "Saeed Hussein", "Jean Joury", "Amin Elshamy", "Sherief Khalifa", "Ziad Saleh", "Amal Abdalla", "Saeed Hussein", "Jean Joury", "Amin Elshamy", "Sherief Khalifa", "Ziad Saleh" ], "abstract": "Background: Pharmacist-administered vaccination is currently implemented in many countries worldwide. It has contributed to increased vaccine access and vaccine uptake. This observational cross-sectional study assessed community pharmacists’ willingness, and readiness to administer vaccines to the public in the United Arab Emirates (UAE) and relate it to national and international policies on vaccination. Methods: This research was an online survey of 24-questions that was made available to community pharmacists via social media and WhatsApp. The survey was open for six weeks (from April to June 2022). Descriptive and inferential analysis was performed.\n\nResults: The questionnaire was completed by 374 of 575 (65%) respondents. More than half (64.2%) of the respondents agreed or strongly agreed that pharmacists should be able to vaccinate and 68.4% responded that they were willing to administer vaccines if local regulations allowed them to vaccinate. Most (81.8%) expressed willingness to complete training required to be able to administer vaccines in their pharmacies. Logistic regression showed that pharmacists defined as having high readiness were significantly more willing to undergo all essential training to start a vaccination service in their pharmacies than were pharmacists with poor readiness (OR 2.647; 95% CI: 1.518–4.615; p=0.001). High readiness was also significantly associated with agreement on safety of pharmacy-based vaccination (p=0.027). Conclusions: The majority of community pharmacists surveyed showed readiness to commence pharmacy-based vaccination services. Those with high readiness characteristics are amenable to receiving essential training and consider that vaccination in the community pharmacy setting would be safe.", "keywords": [ "community pharmacists", "pharmacy-based vaccinations", "readiness", "cross-sectional study", "United Arab Emirates" ], "content": "Introduction\n\nPharmacists are amongst the most accessible and trusted healthcare professionals in the community.1–3 Community pharmacists are highly trained but possibly underutilised public health professionals.4\n\nThe coronavirus 2019 (COVID-19) pandemic exposed challenges in the provision of some healthcare services, including vaccination5,6; yet also highlighted the ability of community pharmacists to remain accessible to the public and provide essential services despite unprecedented demand.2,5 Allowing pharmacy-based vaccination is a healthcare strategy that many countries followed to enhance access and thus increase vaccination uptake in the community.7\n\nCommunity pharmacies are one of the first points of contact for ambulatory patients and members of the public with relatively mild health concerns,8 especially as they are conveniently located and offer extended working hours.5,9 By virtue of their accessibility and reach in local communities, community pharmacists are ideally positioned to promote and provide vaccination services.10 Although vaccine administration is not yet a service provided by the majority of community pharmacists in the United Arab Emirates (UAE), studies from Jordan and Saudi Arabia suggest that community pharmacists in the region have shown great willingness to deliver pharmacy-based vaccination services.9,11,12\n\nConsidering the international and regional shifts towards pharmacy-based vaccinations, the objectives of this study were: i) to assess the readiness of community pharmacies in the UAE to start pharmacy-based vaccination services; ii) analyse if community pharmacists are willing to undertake relevant training; and iii) explore factors influencing pharmacists’ initiation of community-based vaccination.\n\nThis study has its origins in an ongoing project to advance pharmacist-provided vaccination services in the UAE, which is being led by a working group of professionals from academia, the pharmaceutical industry, pharmacy practice and regulation, and professional societies in the UAE. The project consists of three phases: research, advocacy, and dissemination of new services. This study is a product of the research phase of the project, which involves generating an evidence base to support advocacy efforts in obtaining permission for some pharmacists to administer COVID-19 vaccination in the UAE. Aim of this research was to assess community pharmacists’ willingness and readiness to administer vaccines to the public in the United Arab Emirates (UAE) and relate it to the policy factors nationally and internationally.\n\n\nMethods\n\nThis observational cross-sectional study surveyed licensed pharmacists practicing in community pharmacies in the UAE. The survey consisted of 24 questions grouped into eight categories: i) demographics; ii) employment details; iii) patient demand at the pharmacy; iv) interest and willingness to vaccinate at the pharmacy; v) willingness to receive training to administer vaccines; vi) perception toward vaccination; vii) factors influencing the decision to administer vaccines; and viii) perceived readiness of pharmacy to administer vaccines.\n\nThe questions were informed in part by those of a recent survey of Jordanian community pharmacists’ readiness to provide vaccination services.11 The questions were reviewed by members of the expert group. This paper was written using the format provided by STROBE statements for cross-sectional studies.13\n\nThe study setting was community pharmacies in the UAE. It was an online study.\n\nPharmacists are administering many vaccines through their pharmacies around the world, and the number of such services is increasing. When this study started in early 2022, pharmacists were not allowed to vaccinate the public in their pharmacies in the UAE. The authors of this paper are from multiple backgrounds and conducted this research and advocacy efforts to initiate pharmacist-administered vaccination in the UAE. As a result, one of the authors of this paper, who owns a chain pharmacy group in the UAE, became one of the first providers of pharmacist-administered vaccination. At the time of submission of this paper on February 2023, 14 pharmacies in the UAE were administering flu or COVID-19 vaccines to the public: https://www.doh.gov.ae/en/Abu-Dhabi-pharmacies. This paper is part of a critical change that happened in the public health of the UAE and a model to many other countries globally where pharmacists are yet to vaccinate people.\n\nOnly responders who completed all questions were included in the analysis. The self-administered survey was created using the Survey Monkey online platform and distributed across networks of community pharmacists in the UAE. The online survey link was sent via email and WhatsApp messages. The survey was open from 22 April to 3 June 2022 (42 days). Those eligible were community pharmacists practicing in UAE who could read English and gave consent to take part in the survey.\n\nThe 11 readiness domain of the survey had the following items; vaccination specific place/room, refrigerator specific for vaccines, temperature monitor, portable refrigerator in case of power failure, anaphylaxis response kit, anaphylaxis management poster/guidance, safety box, medical waste bin, materials for hand sanitization and surface cleaning, means to store patients’ records, and access to nearby hospital if patient needs to be referred.\n\nThe seven agreement domain of the survey had the following items; pharmacists should be able to vaccinate patients, pharmacy-based vaccination would be safe, patients would prefer to get their vaccines at the pharmacy to save time, patients would trust the pharmacist to vaccinate them, pharmacists should be trained on how to vaccinate patients, pharmacists should encourage patients to get vaccinated, and pharmacists should be fully equipped to administer vaccinations.\n\nBased on the Federal Competitiveness and Statistics Authority (FCSA), 8,469 pharmacists were working the health sector in 2018.14 Considering the potential changes in more pharmacies being opened in the country due to COVID-19, the study investigators rounded up the pharmacist population to be 10,000. With 95% confidence interval (CI), 5% margin of error, and an effect size of 55% pharmacists being amenable to providing vaccination services in the future (derived from the recent Jordanian survey,11 a sample size of 370 was calculated. A non-probabilistic sampling strategy of convenience sampling was used by disseminating survey through email and WhatsApp groups.\n\nThe Institutional Review Board of the Gulf Medical University (Academic Health Center), Ajman, United Arab Emirates, reviewed and approved this study (Ref. no. IRB/COP/FAC/55/March-2022, dated March 23, 2022). The Review Board reviewed to ensure potential bias with the study would be minimal and the participants’ confidentiality and consent were reviewed for their compliance with good clinical practice guidelines. Written informed consent was obtained for participating in the study.\n\nSurvey responses were collated and processed using a Microsoft Excel® version 16.70 spreadsheet. The following categorisation was performed to meet the assumptions of statistical tests:\n\n• The Readiness domain included 11 items with ratings ranging from 0–1. Therefore, the scores ranged from 0 to 11. Hence, the total readiness score was grouped into <5.5 (poor readiness) and ≥5.5 (high readiness).\n\n• The Agreement domain included seven items with ratings ranging from 0–4. Therefore, the total scores ranged from 0 to 28. Hence, the total agreement score was grouped into <14 (poor agreement) and ≥14 (better agreement). For individual agreement items, strongly agree and agree were combined as agreement; strongly disagree and disagree were combined as disagreement. Responses as neutral were removed from the analysis.\n\nIBM® SPSS® Statistics Version 26 Armonk, NY was used to perform Fisher's Exact Test, Pearson Chi-squared test, and logistics regression. The Mann-Whitney U test was used to find statistical significance at p-value 0.05.\n\n\nResults\n\nThe calculated sample size was met in 42 days with 374 quality-checked responses being analysed for the results from a total of 575 pharmacists that responded (i.e., 65% response rate).13 Of the 201 respondents not included in the analysis, 186 gave consent but did not finish the survey (32%) while 15 did not agree to the consent form (3%).\n\nTwo respondents who completed the survey entered erroneous ages in the demographics questions category. These data were excluded when calculating the mean age, as they were considered to be data entry errors as participants were asked to type in their age. The two respondents’ answers to all other questions were included in the analysis.\n\nThe demographic characteristics of the 374 community pharmacists who completed the survey are summarised in Table 1. More than half of the respondents were female. All Emirates were represented in the survey respondents, with almost half (45.4%) being from Abu Dhabi. Over three-quarters of the respondents (78.3%) worked at or were owners of a chain community pharmacy. The majority of respondents (92.8%) stated that they worked in an urban setting, which is representative of the UAE population (2022 population statistics15). A majority of the participants were BPharm qualified while others held higher PharmD or MPharm qualifications.\n\n† Two erroneous answers were excluded.\n\n¥ Consolidated data for Ajman, Fujairah, Ras Al Khaimah, Sharjah, and Umm Al Quwain.\n\nMore than half of the respondents (55%) had at least six years’ experience working as a pharmacist. Nearly all respondents (94.4%) were employees rather than owners of a pharmacy and more than half (51.6%) either worked in or owned a pharmacy that employed ≥5 people. In terms of customer facing time, almost two-thirds (63.4%) of the respondents reported that they interacted with at least 20 customers per day.\n\nMost of the respondents (85.6%) reported encountering customers who had vaccine-related queries on a daily basis, and 11.2% of respondents provided advice, answers to questions, and/or education on vaccines and vaccination for more than half of their customers. Slightly more than half of respondents (51.8%) reported spending more than five minutes per customer providing an explanation for a vaccine-related question. Respondents answered customer vaccine-related questions about the COVID-19 and influenza vaccine most often and about pneumococci and meningococci vaccines least often.\n\nIf local regulations allowed pharmacy-based vaccinations, 68.4% of respondents were willing to administer vaccines. Nearly two-thirds (64.2%) of respondents agreed or strongly agreed that pharmacists should be able to vaccinate the public. In terms of enabling pharmacists to be able to administer vaccines, 82.1% of respondents agreed or strongly agreed that pharmacists should receive appropriate training.\n\nRespondents considered health regulatory authority support (95.2%) and a pharmacy’s ability to accommodate vaccine administration (93.0%) as being highly influential in the decision to administer vaccines at the pharmacy. More than half of respondents (68.4%) agreed or strongly agreed that pharmacists should be remunerated for administering vaccines.\n\nFewer than one in 10 pharmacists (7.8%) responded that they would not be ready to perform vaccinations within a 6- to 12-month timeframe compared with 42.0% reporting that they would be fully ready (Figure 1).\n\nRegarding willingness to complete training essential to be able to administer vaccines at their pharmacy, the majority of respondents responded ‘Yes’ to each of first aid training, cardiopulmonary resuscitation (CPR) training, and certification to administer vaccines. Overall, 81.8% responded ‘Yes’ to completing all three types of training and 4.0% people responded ‘No’ to all three (Figure 2).\n\nIn terms of the association of readiness with willingness to undertake training, Fisher's Exact Test showed significant readiness by those who were willing to obtain all three essential training regarding vaccination (Table 2).\n\nOn further evaluation, the results of the logistic regression model demonstrated that pharmacists with high readiness (≥5.5 of the following: having space for vaccination, refrigerator specific for vaccines, temperature monitor, portable refrigerator in case of power failure, anaphylaxis response kit, anaphylaxis management literature, safety box, medical waste bin, materials for hand sanitisation and surface cleaning, means to store patients’ records, and access to nearby hospital if a patient needs to be referred) were significantly more willing to undergo all essential training (i.e., first aid, CPR, certification to administer vaccines) than were pharmacists with poor readiness (OR 2.647; 95% CI: 1.518–4.615; p=0.001).\n\nReadiness and agreement of pharmacists that pharmacy-based vaccination would be safe (Table 3) was significantly associated with pharmacists at high readiness compared to those at poor readiness (p=0.027).\n\n* Neutral responses of 83 are removed from the total 374 ending with 291.\n\n\nDiscussion\n\nThe survey shows that the UAE community pharmacy workforce is well-qualified and has a high degree of relevant customer-facing experience. From the survey responses, many of the community pharmacies in the UAE are adequately staffed and equipped to deliver vaccination services in addition to providing their traditional services. The readiness and willingness expressed by the surveyed pharmacists to vaccinate the public was promising. Collectively, these findings indicate the preparedness of community pharmacies in the UAE to provide vaccination services.\n\nNearly 70% of respondents supporting payment to community pharmacists for vaccination services was lower than expected. It is possible that respondents misinterpreted the question, e.g., payment to the pharmacy versus to pharmacist directly and/or due to cultural norms pharmacists may be reluctant, as healthcare professionals, to demand payment for providing vaccinations. Additionally, respondents may have believed that vaccine administration was a complementary service to selling the vaccine or that they might not be reimbursed by payers for providing the service.\n\nThe majority of the study population showing readiness to initiate pharmacy-based vaccination services in the UAE is consistent with similar studies conducted in the region.11,12 In the cross-sectional survey that assessed Jordanian community pharmacists’ readiness and willingness to deliver vaccination services, 64.5% of qualified pharmacists were willing to vaccinate patients and 65.0% of unqualified participants were willing to receive the required training and qualifications to be able to vaccinate.11 Another cross-sectional online survey of Jordanian community pharmacists found that that 86.6% of respondents had a high level of willingness to administer vaccines in the community pharmacy setting.12\n\nThe proportion of pharmacists expressing willingness to provide vaccines services in our study and the two Jordanian studies is higher than the proportion of community pharmacists (55%) in a Saudi Arabia study who expressed willingness to vaccinate.9 The difference between the studies could be explained by the Saudi Arabia survey being conducted earlier in the pandemic, when pharmacists were less certain about what was required to support public health and when they may have been more fearful of contracting COVID-19 themselves and its consequences.12\n\nRelevant training is required to equip pharmacists with the skill, knowledge, and confidence to deliver vaccination services.16,17 A suitably outfitted pharmacy is also required to ensure appropriate and safe delivery of vaccination services. Necessary items include a purpose-built vaccine refrigerator, dedicated vaccination service area, general equipment necessary for vaccine administration, and an anaphylaxis response kit.\n\nEmphasizing the importance of training, 82.5% of untrained community pharmacists in the Jordanian survey believed that pharmacists should be trained to deliver vaccination services and 80.8% of those working in unsuitably equipped pharmacies believed that community pharmacists should be sufficiently equipped to deliver vaccinations.11 In reality, only 13.4% of the Jordanian pharmacists reported receiving all required training and only 8.2% reported that they worked in adequately equipped pharmacies. In our study, almost all respondents were ready to undertake specific types of training (i.e., first aid, CPR, certification) and pharmacists with high readiness characteristics were more willing to undergo all essential training to start a vaccination service in their pharmacies than were pharmacists with poor readiness.\n\nIn the Saudi Arabia survey, 67.4% of community pharmacists stated that concern about patient safety was a barrier to providing vaccination services,9 and in one of the two Jordanian surveys, 40.3% of community pharmacists strongly agreed that concern about patient safety was a barrier to providing vaccination services.12\n\nIn addition to receiving the relevant training, pharmacist-vaccinators need to operate in settings that are equipped to ensure the safety of patients. In one of the two Jordanian surveys, only a quarter (26.6%) of pharmacist-vaccinators reported having anaphylaxis response kits in their pharmacies and only one-fifth (20.3%) had access to anaphylaxis management literature.11\n\nIn our study, pharmacists with high readiness characteristics agreed that pharmacy-based vaccinations would be safe. Moreover, the association between high pharmacist readiness and agreement on the safety of pharmacy-based vaccination was statistically significant when compared with poor readiness. In July 2022, the Department of Health (DOH) announced that community pharmacies in Abu Dhabi that have received authorisation on successful completion of a DOH-certified training course would be able to provide COVID-19 vaccination free of charge to eligible adults.18,19\n\nEvidence of the benefits of pharmacist-administered vaccination is growing internationally and in the region. Substantial evidence of the benefits of pharmacists as vaccinators is provided by a meta-analysis of 36 studies that assessed the impact of pharmacists as educators, facilitators, or administrators of vaccines on immunization rates.20 All studies found an increase in vaccine coverage when pharmacists were involved compared with vaccine services provision by traditional providers. Expanding the role of the pharmacists also has the potential to reduce pressure on other healthcare providers.21\n\nIt is against this background that a growing number of middle- and high-income countries have expanded the role of pharmacists to incorporate vaccination services, including the US, Australia, New Zealand, and European countries.8,22 Pharmacist-administered vaccination has also been reported in low-income countries.23\n\nVaccination is one of the most cost-effective healthcare interventions for reducing the burden of vaccine-preventable diseases.24,25 Economic analyses conducted in US have demonstrated a lower mean direct cost per adult vaccination in pharmacies compared with vaccination in physician offices from the healthcare plan and patient perspectives (for zoster, pneumococcal, and influenza vaccination),26 as well as from the societal perspective (for influenza vaccination).27 Using pharmacies to deliver routine influenza vaccination to adults is likely to be either cost saving or relatively cost effective from a societal perspective, depending on the target population.27 Moreover, administering influenza vaccines via pharmacies in addition to traditional locations during an influenza epidemic in the US was found to increase vaccination coverage, avoid up to 23.7 million influenza cases, and yield cost savings up to $US2.8 billion to third-party payers and $US99.8 billion to society.28\n\n\nConclusions\n\nThe majority of the study population demonstrated readiness and willingness to initiate pharmacy-based vaccination in the UAE. Pharmacists who agreed that pharmacy-based vaccinations would be safe was significantly associated with those who also showed readiness for starting the vaccination service. Importantly, the willingness to undertake essential training was also found among pharmacists who showed readiness. In this case, we recommend dissemination of pharmacy-based vaccination services throughout UAE.\n\nThe study population was considered to be a good demographic representation of community pharmacists in the UAE as a whole. It is also a strength of our study that the association of pharmacists with higher readiness and greater willingness to undergo essential training was statistically significant as was the association of pharmacists with higher readiness with agreement of the safety of pharmacy-based vaccination.\n\nThe absence of open-ended questions, which would have allowed respondents to provide greater explanation of their answers, was a limitation of the study. Also, community pharmacists not being allowed to vaccinate the public during collection of the study data might have influenced the responses of the pharmacists, though the survey mentioned ‘if approved by the ministry’.", "appendix": "Data availability\n\nOpen Science Framework: Vaccination. https://doi.org/10.17605/OSF.IO/ZQ8VC. 28\n\nThis project contains the following underlying data:\n\n• Vaccination study raw data for analysis.xlsx\n\nOpen Science Framework: STROBE checklist for ‘Pharmacists’ readiness and willingness to vaccinate the public in United Arab Emirates community pharmacies: A cross-sectional study’. https://doi.org/10.17605/OSF.IO/ZQ8VC. 28\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nMedical writing/editorial support was provided by Steve Holliday, Rebecca Neilson, and Laura D’Castro at Innovaacom LLC. Innovaacom LLC also covered the APC of this article. Innovaacom LLC is funded by Pfizer Gulf FZ LLC. Statistical analysis was conducted by Aji Gopakumar.\n\n\nReferences\n\nMerks P, Jakubowska M, Drelich E, et al.: The legal extension of the role of pharmacists in light of the COVID-19 global pandemic. Res. Soc. Adm. Pharm. 2021; 17(1): 1807–1812. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaidment I, Young E, MacPhee M, et al.: Rapid realist review of the role of community pharmacy in the public health response to COVID-19. BMJ Open. 2021; 11(6): e050043. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStratoberdha D, Gobis B, Ziemczonek A, et al.: Barriers to adult vaccination in Canada: A qualitative systematic review. Can. Pharm. J. Rev. Pharm. Can. 2022; 155(4): 206–218. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMossialos E, Courtin E, Naci H, et al.: From “retailers” to health care providers: Transforming the role of community pharmacists in chronic disease management. Health Policy. 2015; 119(5): 628–639. PubMed Abstract \| Publisher Full Text\n\nAruru M, Truong HA, Clark S: Pharmacy Emergency Preparedness and Response (PEPR): a proposed framework for expanding pharmacy professionals’ roles and contributions to emergency preparedness and response during the COVID-19 pandemic and beyond. Res. Soc. Adm. Pharm. 2021; 17(1): 1967–1977. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNawas GT, Zeidan RS, Edwards CA, et al.: Barriers to COVID-19 Vaccines and Strategies to Improve Acceptability and Uptake. J. Pharm. Pract. April 23, 2022; 089719002210816. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNational Institute for Health and Care Excellence (NICE): Overview\|Vaccine uptake in the general population\|Guidance. NICE; May 17, 2022. Accessed July 23, 2022. Reference Source\n\nInternational Pharmaceutical Federation (FIP): FIP Global Vaccination Advocacy Toolkit: Supporting and Expanding Immunisation Coverage through Pharmacists. International Pharmaceutical Federation; 2019. Reference Source\n\nBalkhi B, Aljadhey H, Mahmoud MA, et al.: Readiness and willingness to provide immunization services: a survey of community pharmacists in Riyadh, Saudi Arabia. Saf Health. 2018; 4(1): 1. Publisher Full Text\n\nSingh T, Taitel M, Loy D, et al.: Estimating the Effect of a National Pharmacy-Led Influenza Vaccination Voucher Program on Morbidity, Mortality, and Costs. J. Manag. Care Spec. Pharm. 2020; 26(1): 42–47. PubMed Abstract \| Publisher Full Text\n\nAlnahar SA, Gkountouras G, Darwish RM, et al.: Community pharmacists workforce readiness to deliver vaccination services: A cross-sectional study from Jordan. Pharmacol. Res. Perspect. 2022; 10(2): e00943. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJarab AS, Al-Qerem W, Mukattash TL: Community pharmacists’ willingness and barriers to provide vaccination during COVID-19 pandemic in Jordan. Hum. Vaccin. Immunother. 2022; 18(1): 2016009. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThomas D: Vaccination. [Dataset]. OSF. 2023. osf.io/kp4yx.\n\nFederal Competitiveness and Statistics Authority: Population and Demography, Health, Pharmacists UAE.2019.\n\nUnited Arab Emirates (UAE) Population Statistics 2022\|GMI. Official GMI Blog: March 18, 2022. Accessed August 9, 2022. Reference Source\n\nBushell M, Frost J, Deeks L, et al.: Evaluation of Vaccination Training in Pharmacy Curriculum: Preparing Students for Workforce Needs. Pharmacy. 2020; 8(3): 151. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarroll PR, Chen Y, Vicheth P, et al.: Evaluation of a vaccination training program for pharmacy graduands in Australia. Curr. Pharm. Teach. Learn. 2020; 12(7): 850–857. PubMed Abstract \| Publisher Full Text\n\nAbu Dhabi Government Media Office: Abu Dhabi to provide COVID-19 vaccines and PCR tests in the emirate’s pharmacies.July 29, 2022. Accessed September 19, 2022. Reference Source\n\nDepartment of Health - Abu Dhabi: Abu Dhabi pharmacies can now offer Covid vaccines and PCR tests. What’s On. July 29, 2022. Accessed August 4, 2022. Reference Source\n\nIsenor JE, Edwards NT, Alia TA, et al.: Impact of pharmacists as immunizers on vaccination rates: A systematic review and meta-analysis. Vaccine. 2016; 34(47): 5708–5723. PubMed Abstract \| Publisher Full Text\n\nOECD: Beyond containment: Health systems responses to COVID-19 in the OECD. OECD; March 16, 2020. Accessed August 14, 2022. Reference Source\n\nCosta S, Romão M, Mendes M, et al.: Pharmacy interventions on COVID-19 in Europe: Mapping current practices and a scoping review. Res. Soc. Adm. Pharm. 2022; 18(8): 3338–3349. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYemeke TT, McMillan S, Marciniak MW, et al.: A systematic review of the role of pharmacists in vaccination services in low-and middle-income countries. Res. Soc. Adm. Pharm. 2021; 17(2): 300–306. PubMed Abstract \| Publisher Full Text\n\nRodrigues CMC, Plotkin SA: Impact of Vaccines; Health, Economic and Social Perspectives. Front. Microbiol. 2020; 11. Accessed July 22, 2022. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRémy V, Largeron N, Quilici S, et al.: The economic value of vaccination: why prevention is wealth. J. Mark. Access Health Policy. 2015; 3(1): 29284. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSinghal PK, Zhang D: Costs of Adult Vaccination in Medical Settings and Pharmacies: An Observational Study. J. Manag. Care Pharm. 2014; 20(9): 930–936. PubMed Abstract \| Publisher Full Text\n\nProsser LA, O'Brien MA, Molinari NA, et al.: Non-Traditional Settings for Influenza Vaccination of Adults: Costs and Cost Effectiveness. PharmacoEconomics. 2008; 26(2): 163–178. PubMed Abstract \| Publisher Full Text\n\nBartsch SM, Taitel MS, DePasse JV, et al.: Epidemiologic and economic impact of pharmacies as vaccination locations during an influenza epidemic. Vaccine. 2018; 36(46): 7054–7063. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "194557", "date": "25 Sep 2023", "name": "Hardika Aditama", "expertise": [ "Reviewer Expertise Social and administrative pharmacy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nINTRODUCTION\nClarify the gaps from previous research that will be filled by this research\n\nWhat is the current role of community pharmacies in the UAE regarding vaccination?\nMETHOD\nAdd information regarding the validity and reliability of the instrument used\n\nMention about chi square, but does not appear in the results\nRESULT\nPresent mean with SD\n\nShow all demographics and characteristics in the table 1\n\nShow the results of logistic regression in the table\n\nReadiness result?\nDISCUSSION\nWhy was the 6 month framework chosen?\n\nAre the questions specific to a particular vaccine? What types of vaccines will be prioritized for provision?\n\nBased on the results of your research, what barriers are the main obstacles to immunization in pharmacies? How to deal?\n\nIs there a difference in readiness and willingness for pharmacists in rural-urban areas and in all characteristics/demographics?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10502", "date": "09 Nov 2023", "name": "Dixon Thomas", "role": "Author Response", "response": "Many thanks for the review comments. We believe making modifications based on this review will provide further clarity for the readers. The modifications will be performed soon." } ] }, { "id": "225189", "date": "15 Dec 2023", "name": "Muna Barakat", "expertise": [ "Reviewer Expertise Pharmacy and public health" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for inviting me to review this work entitled “Pharmacists’ readiness and willingness to vaccinate the public in United Arab Emirates community pharmacies: A cross-sectional study” which aimed to assess the community pharmacists’ willingness, and readiness to administer vaccines to the public in the United Arab Emirates (UAE) and relate it to national and international policies on vaccination. I believe this is very important study and will enrich the scientific background in terms of perception toward vaccines among UAE population. However, minor comments were raised and needs to be addressed\n1. Introduction section is too short, needs to be elaborated and mentioning the most important headlines covered in the title and objective, ending with the context of UAE and rationale of the study. 2. Methods:\nPlease add inclusion and exclusion criteria. What do you mean by “The questions were informed in part by those of a recent survey of Jordanian community pharmacists’ readiness to provide vaccination services.11” ? did you use the same tool? Or did you adopt it? Clarify If you implement any modifications, did you assess the reliability and face validity? Regarding “The Readiness domain included 11 items with ratings ranging from 0–1. Therefore, the scores ranged from 0 to 11. Hence, the total readiness score was grouped into……….. Responses as neutral were removed from the analysis” Please elaborate more and tell the reader about score calculations and the cut-off points? Add references. Please add the CI for the logistic regression tables and Odds ratio Please add study limitations at the end of the study\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11404", "date": "21 Jun 2024", "name": "Dixon Thomas", "role": "Author Response", "response": "Many thanks for the review comments. We made the following modifications based on the comments. The introduction is expanded to clarify the topic of study. The context of UAE and the rationale of the study are added. Inclusion and exclusion criteria are provided in the study population section. The process of adopting and adapting the survey instrument and its content validation is provided. In the interpretation of 'readiness,' midpoint 5.5 was taken to categorize poor and high, which is below or above 5.5. It is mentioned, and this is a usual practice statisticians follow, not particularly based on any reference. For 'agreement,' the total score is 28, so 14 is taken as the midpoint. The midpoint keeps changing based on the number of items. The confidence interval (CI) is already there for regression (which is not in table format). The odds ratio is also there. Tables 2 and 3 were showing association for which CI or OR are not required. Study limitations were already provided after the conclusion following the journal format." } ] } ]	1	https://f1000research.com/articles/12-292
https://f1000research.com/articles/13-69/v1	15 Jan 24	{ "type": "Review", "title": "Micro(nano)plastics: invisible compounds with a visible impact", "authors": [ "Prabhakar Sharma", "Prateek Sharma", "Prateek Sharma" ], "abstract": "The plastic related research has been an epicentre in recent times. The presence and spread of micro (nano) plastics (MNPs) are well-known in the terrestrial and aquatic environment. However, the focus on the fate and remediation of MNP in soil and groundwater is limited. The fate and bioaccumulation of ingested MNPs remain unknown within the digestive tract of animals. There is also a significant knowledge gap in understanding the ubiquitous organic environmental pollutants with MNPs in biological systems. Reducing plastic consumption, improving waste management practices, and developing environmentally friendly alternatives are some of the key steps needed to address MNP pollution. For better handling and to protect the environment from these invisible substances, policymakers and researchers urgently need to monitor and map MNP contamination in soil and groundwater.", "keywords": [ "Micro(nano)plastics", "groundwater", "separation method", "remediation" ], "content": "Introduction\n\nThe invention of plastic was a terrific innovation; now, it has penetrated everywhere, and the estimated plastic production reached 367 million tonnes in 2020 globally.1 Plastic is a synthetic polymer made from crude oil and natural gas. The dependence of the public on plastic merchandise has inevitably led to a prompt rise in plastic manufacturing volume. Plastic-related research is increasingly in focus in recent times and more volume of studies are being pursued. Due to the presence of different forms of plastics, the waterbodies (ocean, river, lake, wetland, etc), the atmosphere, the terrestrial environment, and even the groundwater are being polluted by microplastics (<5 mm) and nanoplastics (<100 nm) (Figure 1).2 Plastics fragment into smaller pieces and get converted into MNPs through various processes. At the same time, the hydrocarbon chains in plastic compounds make them difficult for plastic wastes to decompose in the environment. MNPs are reaching either directly into the environment or after the degradation of plastic debris. Although the MNPs have different sizes (1 nm to 5 mm), various shapes (fibre, film, foam, etc.), and unique chemical structures (polyethene, polypropylene, polyethene terephthalate, etc.), they are generally invisible in nature. However, the MNPs interact with the neighbouring compounds and microorganisms, which is crucial for animal, human, and plant health; i.e., these invisible compounds comfortably react/interact with the surrounding environment, including soil, organic and inorganic compounds, microorganisms, heavy metals, and plants.3 As a result, MNPs-related research has been getting significant attention in recent years, both in societies and in scientific communities, due to their potential impacts on ecological systems and human health. Groundwater contamination by plastic microfibers is a pressing concern in environmental science (Figure 2).4 These tiny, nearly invisible plastic fibres shed from clothing, textiles, and other sources can infiltrate the soil and eventually reach groundwater reserves. Once there, they pose a risk of contamination, potentially affecting both aquatic ecosystems and human drinking water sources.4 Understanding and mitigating this hidden threat is essential for safeguarding our precious groundwater resources and the overall health of our environment. However, the current research on interactions of these invisible MNPs is in its early stages and data are limited in the important connected sectors. The objective of this article is to highlight the perspectives of current characterization methodologies, health impact, important source pathways, and available remediation options for the invisible MNPs present in the environment.\n\n\nMNPs Separation and Quantification Methods\n\nThe quantitation and analysis of MNPs are essential for accurately assessing their existence and intensity in different environmental samples.5 A number of techniques are employed for quantification depending on the type of MNPs sample and the size range of MNPs being investigated such as density separation and filtration,6 microscopic and spectroscopic techniques,5 chromatographic approach,7 nanoparticle tracking analysis (NTA),8 quantitative polymerase-chain-reaction (qPCR) approach9 (Figure 3).\n\nDensity separation and filtration are common tools to isolate and concentrate MNPs from soil or water samples. It is employed to segregate MNPs from the collected soil or water samples for further characterization. Optical microscopy is a traditional method of visualization of MNPs. In this method of direct visualization, the segregated MNP samples are collected and prepared on glass slides, and they are manually counted and quantified. Although this method can provide valuable information about the presence of MNPs, it may not be suitable for quantifying relatively small particles or dealing with large sample sizes. However, infrared or Raman spectroscopy is being used for identifying and quantifying MNPs based on unique molecular vibrations of plastic compounds to better understand the polymeric types of these invisible plastic compounds present in the environmental sample.5\n\nMore recently, a combination of microscopy and infrared spectroscopy has been employed to identify and quantify MNPs in individual samples.5 They provide spatial distribution and allow for a more detailed characterization of MNPs in complex soil or water samples. The pyrolysis-gas chromatography-mass spectrometry is also used to identify and quantify MNPs based on the polymer’s chemical breakdown (pyrolysis process).7 It conveniently provides information about the types and concentrations of plastics in the soil or water sample.\n\nIn addition, nanoparticle tracking analysis (NTA) has also been considered an optical technique for tracking individual MNP particles based on their Brownian motion.8 It provides information on particle size distribution and concentration as well. More recently, quantitative polymerase chain reaction (qPCR), a technique within molecular biology based on MNP ingested by microorganisms or organisms, has also been practised.9 All of these techniques for quantifying and analysing MNPs have benefits and drawbacks, but the choice of technique mostly depends on the kind of sample, the goals of the research, and the resources at hand. In order to do more thorough analyses of these invisible plastic compounds in environmental samples, a combination of various approaches is frequently used. To guarantee the accuracy and comparability of MNP data across the globe, these methodologies must be standardised.\n\n\nImpact of MNPs on the Environment\n\nThe potential impact of MNPs on the environment and human health is a noble area of research.10 The extent of the health impacts of MNPs is not yet fully understood, several potential pathways of exposure and adverse health outcomes have been recognised. It is important to note that the current scientific understanding of MNP toxicity on human health is still in its early stages,10 and much more research is needed to fully understand the extent of the risk. The presence of these invisible plastic compounds in the human body and their potential health effects have prompted calls for more comprehensive studies, improved waste management, and the development of sustainable alternatives to reduce plastic pollution and potential human exposure.\n\nMicro (nano) plastics can directly impact the aquatic animal and the human food chain. More recently, they occurred in human blood and other organs with a massive implication for human health in causing cancer or other diseases.11,12 Generally, MNPs accumulation in marine organisms at the lower trophic levels poses potential health risks as they are being consumed by the higher trophic levels and by humans mostly relying on seafood. The intake of MNPs causes oxidative stress, inflammatory reactions, fitness disturbances, and endocrine disorders in humans.13 As they penetrate the body cells, they create cytotoxicity, DNA oxidative damage, genotoxicity, reactive oxygen species (ROS) increase, and increased stream in genes. Micro (nano) plastics induce oxidative stress in the body by releasing chemicals and ROS which leads to cancer development by causing mechanical and genetic damage.14 The accumulation of MNPs in the digestive tract of animals is a growing environmental concern. When animals mistakenly ingest plastic materials like bags, bottles, or other MNP compounds, they can become lodged in their stomach or intestine, causing a range of serious health issues. These foreign objects not only obstruct the digestive process but can also leach harmful chemicals into the animal's body. In many cases, this plastic ingestion can be fatal, posing a significant threat to wildlife populations and highlighting the urgent need for global efforts to reduce plastic pollution and protect our ecosystems. These invisible plastic compounds infiltrate directly into the intestinal mucosa while mingling with other intestinal content and causing inflammations and reduction in intestinal mucus secretion, intestinal barrier dysfunction, increased gut mucosa permeability, and imbalance of gut microbiota.15 Micro (nano) plastics also enter the gastrointestinal tract via the epithelial route then they cause physical damage in the gastrointestinal tract of humans. In animal studies, ingested MNPs could cause inflammation, tissue damage, and alterations in gut microbiota, which could impact overall gut health.16 Exposure to MNPs may trigger immune responses in the body, leading to inflammation and potential immune system dysregulation. Long-term immune system perturbations could also increase susceptibility to infections and other health issues. Some studies suggest that MNPs may have endocrine-disrupting properties in the affected animals, interfering with hormone signalling in the body.12 This interference potentially leads to reproductive and developmental issues for humans and animals. The existing literature suggests that MNPs can accumulate in various organs and tissues, raising concerns about potential long-term health effects related to chronic exposure.12 The ingestion of these invisible plastic compounds by a human lead to cytotoxicity and similar colonic cancer, as stool samples are a potent source of identification of MNPs.17\n\nMicro (nano) plastics have been found in a wide range of food items, including seafood, drinking water, and even salt (Figure 1).18 These items may pose health risks due to their potential to release not only MNPs but also the associated chemical additives and adsorbed toxic substances. As the heavy metals or organic pollutants increase in the environment, the large specific surface area and porous structure of MNPs make them easier to adsorb and enrich other environmental pollutants. These MNPs-contaminant complexes may lead to ecological disturbances.3 Morphologically, these MNPs may act together with other stressors (environmental contaminants, drought stress, or salinity) to produce a combined effect; however, it is unknown whether this combined effect is the sum of the individual effects or a synergistic or antagonistic effect, i.e., the effects of MNPs-contaminant complexes on ecosystem structures and functions or their response thresholds.19\n\nThe synergistic effect occurs when the combination of MNPs with other stressors or pollutants leads to a more substantial impact than the sum of their individual effects. Synergistic effects of MNPs with pollutants may enhance their toxic effects on animals or humans by reducing the biodegradation rate after entering their bodies.20 Micro (nano) plastics can adsorb and accumulate chemical pollutants from the environment, such as pesticides, heavy metals, and persistent organic pollutants.19 In this case, MNPs act as carriers by facilitating the transfer of harmful chemicals into the food web or to the organisms. The combined toxicity of MNPs and adsorbed chemicals can result in more severe health effects on aquatic organisms and potentially humans when consuming contaminated seafood.20 In some instances, the presence of MNPs may encourage the development of toxic algal species, resulting in harmful algal blooms that have a negative impact on the water quality and marine life.21 Micro (nano) plastics can physically injure organisms by abrading their surfaces or obstructing their gastrointestinal tracts.22 The detrimental effect on an organism's health and survival is exacerbated when combined with other environmental stresses, such as temperature changes or decreased food supply. Antagonistic effects occur when the presence of MNPs transforms the behaviour or uptake of other pollutants, potentially reducing their toxicity.23 While some studies have suggested that MNPs might reduce the bioavailability of certain contaminants, leading to lower uptake by organisms, the overall antagonistic impact is not yet fully understood. The presence of MNPs might reduce the bioavailability of harmful chemicals by creating a physical barrier that limits the direct contact between contaminants and organisms. This could lead to reduced uptake of toxins by organisms, potentially mitigating some of the toxic effects as well.\n\n\nSource Pathways of MNPs\n\nAlthough the current literature had properly covered the source, pathways, quantification, and even interaction of these invisible MNPs. It is crucial to understand the sources and pathways of MNPs of the contaminated sites to develop effective mitigation strategies and prevent further pollution.24 For example, the release of fibre from textiles, the presence of microbeads in cosmetic products, and the degradation of plastic debris could be potential sources of MNPs. Most of this research emphasizes the amount and degradation of plastics, recognition and quantification of MNPs in the environment and in the microorganisms, toxicological effects on single species, and combined effects with others. However, there are still some critical issues that urgently need to be addressed. Such as the impact of these invisible plastic compounds on the structural stability of ecosystems or their remediation, especially from the soil and groundwater, is limited.25 The land-use pattern and soil types play a critical role in the infiltration of MNPs into subsurface systems and groundwater.26\n\nThe leaching of MNPs can happen predominantly from agricultural soils or from urban infrastructure wastes. The improper disposal of plastic waste, such as plastic bags, bottles, and packaging materials, is a significant source of MNPs in the environment. Plastics that end up as litter on land can be transported by wind, rain, and water runoff into water bodies. Generally, larger plastic items, such as bottles and bags, break down into MNPs through processes like photodegradation, mechanical weathering, and chemical degradation. They are called secondary MNPs. However, the primary MNPs have resulted from synthetic textiles, like polyester and nylon, shed microfibers during laundering, wear down of vehicle tires over time, industrial wastes containing plastic pellets (known as nurdles), as well as microbeads from personal care products. The biosolids treated from sewage sludge applied on agricultural fields are also a critical source of these invisible plastic compounds in soil and groundwater.27\n\nAlthough a large volume of literature has focused on the presence of invisible MNPs in marine and freshwater systems, some of the recent studies have started focusing on soil, groundwater, and remote locations.25,26 Surface water bodies such as rivers, lakes, and oceans are often the first recipients of MNPs from various sources, including urban runoff, industrial discharges, and plastic debris from land. All of these investigations have shown that MNP pollution of surface waterways is widespread, with significant concentrations occurring around urban areas or plastic manufacturing facilities.\n\nThe studies on MNPs in soil are relatively new and not as abundant as those of surface water, soil contamination by MNPs also occurs through various pathways, including the direct application of plastic mulches, sewage sludge, and atmospheric deposition. A common methodology of MNPs separation and characterization is being adopted for soil as well. While MNP concentrations in soil may not be as high as in surface waters, they can still pose a risk to terrestrial ecosystems and potentially enter the food chain through plant uptake.25 Further, groundwater contamination can occur through the percolation of MNPs from surface soils, landfills, and septic systems which raises concern about their potential impacts on drinking water quality and groundwater-dependent ecosystems.28,29 Due to the challenges of accessing and sampling groundwater, research in this area has been relatively challenging.25,30 To investigate MNP content in groundwater, researchers have used well water sampling and then proceeded with common filtration, separation, and microscopic techniques.26\n\nIn short, studies on MNPs in surface water are more extensive and established compared to those in soil and groundwater but the potential source and the presence of MNPs in all three compartments have been confirmed, and each environment poses unique challenges for research and monitoring. To create efficient mitigation methods and protect both human health and the environment, it is crucial to keep researching the source pathways, fate, and potential effects of MNPs on these environmental compartments.\n\n\nRole of MNPs on Ecosystem Functions\n\nPlastics are polymers based on chains of carbon atoms and carbon as the main component. Micro (nano) plastic releases in the dissolved form as organic carbon or as a greenhouse gas (such as CO2) while degrading in the ecosystem. So, MNPs are also closely associated with the current climate crisis because they are directly or indirectly involved in greenhouse gas emissions from their production to disposal stages.31\n\nMicro (nano) plastics have a significant effect on ecosystem functions, leading to ecological disruptions and alterations in natural processes.32 These effects can impact both aquatic and terrestrial ecosystems. They alter the nutrient cycling of the ecosystem when ingested by organisms. Micro (nano) plastics have an impact on biodiversity, community structure, and the distribution of species within ecosystems. Other species that rely on them for food or ecological interactions are affected in a cascade manner by this. The accumulation of MNPs in sediments, soils, and water bodies modifies the habitat, bioaccumulates the hazardous substances around it, changes how different animals feed and reproduce, and lowers the ecosystem's ability to withstand environmental stressors.32 All these have long-term consequences for population dynamics and ecosystem stability. Organisms exposed to MNPs may be more vulnerable to other ecological pressures, such as changes in temperature, salinity, or pollution, leading to greater susceptibility to diseases and overall ecosystem instability. Micro (nano) plastics also affect the delivery of ecosystem services to human populations and decrease agricultural productivity and fisheries yield, and affect the carbon sequestration capacity of ecosystems.33 Micro (nano) plastics influence the carbon burial rates in marine sediments and ultimately affect the carbon sequestration capacity of ecosystems and alter the global carbon cycle. The intentional and unintentional input of these invisible plastic compounds into the environment may have a latent impact on global carbon stocks. So, a strong commitment is required to find a replacement for plastic products.\n\n\nRemediation Strategies for MNPs\n\nThe remediation of MNPs is a challenging task due to their widespread distribution, small size, persistence in terrestrial and aquatic ecosystems and their consequent impacts on natural systems.34 The removal of MNPs from the contaminated ecosystem is necessary for a benign environment. Two strategies have been used in practice to systematically manage or minimise the pollution caused by MNPs: the first is to block the natural ecosystem's access points, and the second is to remove MNPs in situ from the already contaminated bodies. However, researchers are further exploring various other strategies to address the issue. For example, the upgradation of existing wastewater treatment technologies using granular activated carbon filtration, membrane filtration, and ozonation has a significant impact on MNPs removal. At the same time, stormwater management and beach clean-up initiatives have a promising outcome for preventing the generation of secondary MNPs. Some microorganisms and specialized filter-feeding organisms have also shown the ability to consume and break down MNPs.34 The development and use of biodegradable and environmentally friendly plastics can help reduce the accumulation of MNPs in the environment. Increasing public awareness about MNP pollution and educating people about the sources and impacts of MNPs can help reduce their release into the environment.\n\nThe reduction of MNPs using biochar is another emerging area of research and holds promise as a potential solution to tackle MNP pollution.35 According to Wang et al.,36 biochar is an effective and affordable investment in the removal of MNPs. They observed that sand filters mediated with biochar enhanced the removal efficiency of MNPs. The porous nature of biochar offers a lot of binding sites and a lot of surface area, making it a good adsorbent for MNPs.35 Biochar attracts and traps MNP after being added to contaminated settings, such as soil or water, by limiting its mobility and availability to living things. To lessen the movement of these invisible plastic compounds from sediments to water columns during erosion events or tidal action, biochar can be used as a sediment amendment in coastal locations. It was observed that biochar can help MNPs degrade more quickly by enhancing the vital microbial communities.35\n\n\nInnovative Solutions and Ongoing Efforts for Mitigation of MNPs\n\nIn the ongoing battle to mitigate the detrimental effects of MNP on our environment, innovative solutions and concerted efforts have emerged as critical strategies. Cutting-edge wastewater treatment technologies are being developed to capture and filter out these minuscule plastic particles before they reach our water bodies, significantly reducing their input.28 Biodegradable plastics are also under development to curtail the persistence of MNPs in the environment, though challenges remain in their widespread adoption. Nanotechnology offers promise with materials like magnetic nanoparticles that can attract and remove microplastics from water sources. Furthermore, regulatory bodies are increasingly implementing bans and restrictions on single-use plastics, while citizen science initiatives and educational campaigns are raising awareness and contributing to data collection efforts. Innovations in cleanup technologies for oceans and waterways, as well as a shift towards a circular economy, underscore the diverse range of approaches being pursued to combat the MNP crisis. These collective endeavours aim to safeguard ecosystems and human health from the pervasive impact of these invisible plastic compounds.\n\n\nStrategies and Future Recommendations\n\nAs plastic-related research is an epicentre from the past decade, this paper emphasizes the technological advancements in MNP research and development with their health implications, types, sources, and environmental implications.\n\n1. Although the presence and spread of MNPs are well-known in the terrestrial and aquatic environment, the focus on the fate of MNP in groundwater and their remediation process is scarce. More studies are required to understand the properties, concentrations, and types of MNPs in soil and groundwater in order to assess the public health risks. Therefore, it is urgently required to delineate MNP pollution by the policymaker and researcher for their monitoring, assessment, and handling to safeguard the environment from these invisible compounds.\n\n2. A local-to-global scale mapping of MNP pollution is required in the future by the policymakers, and society must act on their reduction at the local to global level from daily uses.\n\n3. To address the impacts of MNPs on the environment and human health, it is crucial to continue research, implement proper waste management practices, reduce plastic use and promote sustainable alternatives, and develop innovative remediation technologies. A proper understanding of the interactions between MNPs and ecosystems is essential for developing effective conservation and mitigation strategies to safeguard ecosystem health and the services they provide.\n\n4. Addressing the impact of MNPs on ecosystem functions requires a holistic approach, including reducing plastic pollution at its source, implementing effective waste management, and promoting sustainable practices to minimize plastic usage.\n\n5. Even today, there is still a lack of effective technical means to accurately quantify these invisible MNPs in the environment, which hinders their assessment of toxicological effects and ecological risks. So, the standardization of plastics pollution and its remediation from the environment is required across the globe. Overall, the adverse environmental impact of MNPs and their standard treatment strategies should urgently be practised by different stakeholders across the globe.\n\n\nDeclarations\n\n\n\n\nAuthors’ contributions\n\nPrabhakar Sharma and Prateek Sharma conceived and planned the study, wrote the main manuscript text, and reviewed the manuscript. Prabhakar Sharma prepared the figure.\n\n\nEthical approval and consent to participate\n\nNot applicable.\n\n\nConsent for publication\n\nNot applicable.", "appendix": "Data availability\n\nThere are no data associated with this article. All the data used in this paper has been provided.\n\n\nAcknowledgements\n\nNot applicable.\n\n\nReferences\n\nPlastics Europe: Plastics — the Facts 2021: An analysis of European plastics production, demand and waste data.2021.\n\nRochman CM: Microplastics research—from sink to source. Science. 2018; 360: 28–29. Publisher Full Text\n\nKumar R, Ivy N, Bhattacharya S, et al.: Coupled effects of microplastics and heavy metals on plants: uptake, bioaccumulation, and environmental health perspectives. Sci. Total Environ. 2022; 836: 155619. PubMed Abstract \| Publisher Full Text\n\nRe V: Shedding light on the invisible: addressing the potential for groundwater contamination by plastic microfibers. Hydrogeol. J. 2019; 27: 2719–2727. Publisher Full Text\n\nRaj D, Maity SK: Critical assessment of approach towards estimation of microplastics in environmental matrices. Land Degrad. Dev. 2023; 34(10): 2735–2749. Publisher Full Text\n\nHan X, Lu X, Vogt RD: An optimized density-based approach for extracting microplastics from soil and sediment samples. Environ. Pollut. 2019; 254(A): 113009. PubMed Abstract \| Publisher Full Text\n\nXu Y, Qu Q, Jiao M, et al.: Identification and quantification of nanoplastics in surface water and groundwater by pyrolysis gas chromatography-mass spectrometry. Environ. Sci. Technol. 2022; 56(8): 4988–4997. PubMed Abstract \| Publisher Full Text\n\nPeters RJW, Relou E, Sijtsma ELE, et al.: Evaluation of nanoparticle tracking analysis (NTA) for the measurement of nanoplastics in drinking water. International Journal of Food Contamination. 2023. Publisher Full Text\n\nPizzoferrato R, Li Y, Nicolai E: Quantitative detection of microplastics in water through fluorescence signal analysis. Photonics. 2023; 10(5): 508. Publisher Full Text\n\nVethaak AD, Legler J: Microplastics and human health. Science. 2021; 371: 672–674. Publisher Full Text\n\nLeslie HA, van Velzen MJM , Brandsma SH, et al.: Discovery and quantification of plastic particle pollution in human blood. Environ. Int. 2021; 163: 107199.\n\nKumar R, Manna C, Padha S, et al.: Micro (nano) plastics pollution and human health: How plastics can induce carcinogenesis to humans? Chemosphere. 2022; 298: 134267. PubMed Abstract \| Publisher Full Text\n\nWang W, Gao H, Jin S, et al.: The ecotoxicological effects of microplastics on aquatic food web, from primary producer to human: A review Ecotoxicology and environmental Safety.2019; 173: 110–117.\n\nSchirinzi GF, Pérez-Pomeda I, Sanchís J, et al.: Cytotoxic effects of commonly used nanomaterials and microplastics on cerebral and epithelial human cells. Environ. Res. 2017; 159: 579–587. PubMed Abstract \| Publisher Full Text\n\nRahman A, Sarkar A, Yadav OP, et al.: Potential human health risks due to environmental exposure to microplastics and knowledge gaps: a scoping review. Sci. Total Environ. 2020; 757: 143872. Publisher Full Text\n\nGruber ES, Stadlbauer V, Pichler V, et al.: To waste or not to waste: Questioning potential health risks of micro- and nanoplastics with a focus on their ingestion and potential carcinogenicity. Expo Health. 2023; 15: 33–51. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIbrahim YS, Tuan Anuar S, Azmi AA, et al.: Detection of microplastics in human colectomy specimens. JGH Open. 2021; 5: 116–121. Publisher Full Text\n\nAltunisik A: Prevalence of microplastics in commercially sold soft drinks and human risk assessment. J. Environ. Manag. 2023; 336: 117720. Publisher Full Text\n\nBudhiraja V, Urh A, Horvat P, et al.: Synergistic adsorption of organic pollutants on weathered polyethylene microplastics. Polymers. 2022; 14(13): 2674. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMartin J, Santos JL, Aparicio I, et al.: Microplastics and associated emerging contaminants in the environment: Analysis, sorption mechanisms and effects of co-exposure Trends in Environmental Analytical Chemistry.2022; 35: e00170.\n\nPasqualini V, Garrido M, Cecchi P, et al.: Harmful algae and pathogens on plastics in three mediterranean coastal lagoons. Heliyon. 2023; 9(3): e13654. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRodrigues ACB, de Jesus GP , Waked D, et al.: Scientific evidence about the risks of micro and nanoplastics (MNPLs) to human health and their exposure routes through the environment. Toxics. 2022; 10(6): 308. Publisher Full Text\n\nKaur H, Rawat D, Poria P, et al.: Ecotoxic effects of microplastics and contaminated microplastics - Emerging evidence and perspective. Sci. Total Environ. 2022; 841: 156593. PubMed Abstract \| Publisher Full Text\n\nAbbasi S: Routes of human exposure to micro (nano)plastics. Current Opinion in Toxicology. 2021; 27: 41–46. Publisher Full Text\n\nLi S, Ding F, Flury M, et al.: Macro- and microplastic accumulation in soil after 32 years of plastic film mulching. Environ. Pollut. 2022; 300: 118945. PubMed Abstract \| Publisher Full Text\n\nSangkham S, Islam MA, Adhikari S, et al.: Evidence of microplastic contamination in groundwater and human health risk assessment perspectives: A review. Groundw. Sustain. Dev. 2023; 23: 100981. Publisher Full Text\n\nManikanda BK, Natesan U, Vaikunth R, et al.: Spatial distribution of microplastic concentration around landfill sites and its potential risk on groundwater. Chemosphere. 2021; 277: 130263. Publisher Full Text\n\nChia RW, Lee JY, Kim H, et al.: Microplastic pollution in soil and groundwater: a review. Environ. Chem. Lett. 2021; 19: 4211–4224. Publisher Full Text\n\nSingh S, Bhagwat A: Microplastics: a potential threat to groundwater resources. Groundw. Sustain. Dev. 2022; 19: 100852. Publisher Full Text\n\nKhant N, Kim H: Review of current issues and management strategies of microplastics in groundwater environments. Water. 2022; 14(7): 1020. Publisher Full Text\n\nBergmann M, Collard F, Fabes J, et al.: Plastic pollution in the Arctic. Nature Reviews Earth and Environment. 2022; 3(5): 323–337. Publisher Full Text\n\nGreen DS, Boots B, O’Connor NE, et al.: Microplastics affect the ecological functioning of an important biogenic habitat. Environ. Sci. Technol. 2017; 51(1): 68–77. PubMed Abstract \| Publisher Full Text\n\nShafea L, Yup J, Beriot N, et al.: Microplastics in agroecosystems: A review of effects on soil biota and key soil functions. J. Plant Nutr. Soil. Sci. 2023; 186(1): 5–22. Publisher Full Text\n\nMishra SR, Ahmaruzzaman M: Microplastics: identification, toxicity and their remediation from aqueous streams. Sep. Purif. Rev. 2022; 52: 283–304. Publisher Full Text\n\nKumar R, Verma A, Rakib MRJ, et al.: Adsorptive behavior of micro (nano) plastics through biochar: Co-existence, consequences, and challenges in contaminated ecosystems. Sci. Total Environ. 2023; 856: 159097. PubMed Abstract \| Publisher Full Text\n\nWang Z, Sedighi M, Lea-Langton A: Filtration of microplastic spheres by biochar: removal efficiency and immobilisation mechanisms. Water Res. 2020; 184: 116165. PubMed Abstract \| Publisher Full Text" }	[ { "id": "239979", "date": "18 Mar 2024", "name": "Mansoor Ahmad", "expertise": [ "Reviewer Expertise microplastics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe title is interesting. The abstract can be more brief, and authors should highlight the article's aim. The micro (nano)plastics keyword can be removed as it is already in the title and replaced with another keyword.\nIntroduction\nAdd reference to this line Plastic related research is increasingly in focus in recent times and more volume of studies are being pursued. [1],[2]. Add reference to this line Plastics fragment into smaller pieces and get converted into MNPs through various processes.[3],[4]. Add reference to this line As a result,MNPs-related research has been getting significant attention in recent years, both in societies and in scientific communities, due to their potential impacts on ecological systems and human health. [5],[6]. Add reference to this line For example, the release of fiber from textiles, the presence of microbeads in cosmetic products, and the degradation of plastic debris could be potential sources of MNPs.[7] Add more information to the introduction about micro and nano plastics.\n\nI suggest the authors add more information about the sources, impacts and remediations of micro and nano plastics.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [ { "c_id": "11423", "date": "29 Apr 2024", "name": "Prabhakar Sharma", "role": "Author Response", "response": "The title is interesting. Response: We appreciate the reviewer for considering the importance of our paper. The abstract can be more brief, and authors should highlight the article's aim. Response: We have attempted to revise the abstract by highlighting the paper objectives and reduced the length to some extent. The micro (nano)plastics keyword can be removed as it is already in the title and replaced with another keyword. Response: Thanks. We have removed the micro(nano)plastics keyword from the paper. Introduction Add reference to this line Plastic related research is increasingly in focus in recent times and more volume of studies are being pursued. [1],[2]. Response: Both references are added as suggested by the reviewer. Add reference to this line Plastics fragment into smaller pieces and get converted into MNPs through various processes.[3],[4]. Response: Both references are added as suggested by the reviewer. Add reference to this line As a result,MNPs-related research has been getting significant attention in recent years, both in societies and in scientific communities, due to their potential impacts on ecological systems and human health. [5],[6]. Response: Both references are added as suggested by the reviewer. Add reference to this line For example, the release of fiber from textiles, the presence of microbeads in cosmetic products, and the degradation of plastic debris could be potential sources of MNPs.[7] Response: The suggested reference has been included. Add more information to the introduction about micro and nano plastics. Response: Many thanks. We have attempted to expand this aspect and included more discussion about MNPs in the Introduction section. I suggest the authors add more information about the sources, impacts and remediations of micro and nano plastics. Response: We have included more discussion about sources and impact in “Source Pathways of MNPs” section and remediation part in “Innovative Solutions and Ongoing Efforts for Mitigation of MNPs” section. References 2. Bhat M, Eraslan F, Gaga E, Gedik K: Scientometric Analysis of Microplastics across the Globe. 2023. 1-13 Publisher Full Text 3. Bhat MA, Gedik K, Gaga EO: Atmospheric micro (nano) plastics: future growing concerns for human health.Air Qual Atmos Health. 2023; 16 (2): 233-262 PubMed Abstract \| Publisher Full Text 5. Bhat M: Unveiling the overlooked threat: Macroplastic pollution in indoor markets in an urban city. Case Studies in Chemical and Environmental Engineering. 2024; 9. Publisher Full Text 6. Bhat M, Gedik K, Gaga E: A preliminary study on the natural aging behavior of microplastics in indoor and outdoor environments. International Journal of Environmental Science and Technology. 2024; 21 (2): 1923-1936 Publisher Full Text 8. Thacharodi A, Hassan S, Meenatchi R, Bhat MA, et al.: Mitigating microplastic pollution: A critical review on the effects, remediation, and utilization strategies of microplastics.J Environ Manage. 2024; 351: 119988 PubMed Abstract \| Publisher Full Text 9. Thacharodi A, Meenatchi R, Hassan S, Hussain N, et al.: Microplastics in the environment: A critical overview on its fate, toxicity, implications, management, and bioremediation strategies. Journal of Environmental Management. 2024; 349. Publisher Full Text 31. Bhat, M Eraslan, F Gedik, K Gaga, et al.: Impact of Textile Product Emissions: Toxicological Considerations in Assessing Indoor Air Quality and Human Health. springer. 2021. Publisher Full Text" } ] }, { "id": "251662", "date": "27 Mar 2024", "name": "Hsuan-Cheng Lu", "expertise": [ "Reviewer Expertise microplastics", "ecotoxicology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript reviewed the research status of micro- and nanoplastics in soil and groundwater focusing on characterization methodologies, health impact, important source pathways, and available remediation options. However, the present manuscript does not advance our knowledge of any of the perspectives mentioned above because the level of details included is quite insufficient and does not meet the scientific standard for approval. There are many published review articles that elucidate the said topics in more detail. Hopefully the authors find the comments helpful. Upon reading, several major issues popped up:\nThe authors attempted to present the lack of micro and nanoplastic studies conducted in groundwater, but there is not sufficient evidence to support the context based on the current level of details. The authors should have, for example, systematically reviewed the literature and included charts to show the number of studies in different aquatic matrices instead of simply performing narrative review. Again, the level of details in each section (method, impact, role and source pathway) is not enough and has already been widely presented by a lot of published reviews over the last few years (2400 reviews found on Scopus since 2020). The authors should try harder to expand these sections. Given the large number of publications, the authors should have cited review papers to support many statements throughout the manuscript instead of citing random case studies. For example, the authors only cited a case study for each technique in the first paragraph of separation and quantification methods.\nOther minor comments:\nTitle should be revised to better reflect the context of this review. For example, the authors should add information about soil and groundwater in the title. Figure 1 and Figure 2 fundamentally provide similar information, so I suggest the authors merging them similar to the graphical abstract in the study by Wu P, et al. 2019 (Ref 1)\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? No", "responses": [ { "c_id": "11425", "date": "29 Apr 2024", "name": "Prabhakar Sharma", "role": "Author Response", "response": "Many thanks for your critical feedback. We have attempted to improve the revised version of the manuscript. As some of these comments are beyond the scope of this mini-review paper, we will work on all the suggested aspect in future comprehensive review paper." } ] }, { "id": "251664", "date": "09 Apr 2024", "name": "Claude Kiki", "expertise": [ "Reviewer Expertise Envuronmental Chemistry and Engineering" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript entitled “Micro(nano)plastics: invisible compounds with a visible impact” provides a comprehensive overview of the current understanding of micro(nano)plastics (NMPs), including their characterization methodologies, health impacts, sources, and potential remediation strategies. It is an informative piece that contributes significantly to the field. To further enhance the manuscript's clarity and depth, I recommend the following revisions for consideration.\nIn reference to Figure 1, it would be beneficial to delineate more explicitly the relationships among the depicted elements. An enhanced graphical representation could facilitate a clearer understanding of the connections and interactions between the various components related to NMPs. A revised figure that visually integrates these aspects with greater clarity would greatly benefit readers' comprehension. The sentence beginning with \"Plastics fragment into smaller...\" and ending with \"...to decompose in the environment\" could benefit from a rephrasing to enhance clarity and precision. The section addressing the identification and separation methodologies for NMPs would benefit from a more detailed exposition. It is recommended to structure this section into subsections, each dedicated to a specific method. Within each subsection, please provide a clear definition of the technique, its advantages, a summary of key findings from previous studies utilizing this method, and a discussion on its limitations. This structure will not only enrich the manuscript but also provide readers with a comprehensive understanding of the current methodological landscape. The statement regarding \"Synergistic effects of MNPs... after entering their bodies\" requires rewriting for clarity and impact. A more precise and engaging sentence could better capture the nuances of MNPs' effects on biological systems. The discussion on biodegradable and environmentally friendly remediation techniques for NMPs warrants further elaboration. It would be advantageous to detail specific methodologies, their mechanisms of action, efficacy, and potential environmental impacts. This expanded discussion could provide a critical evaluation of sustainable strategies for NMPs mitigation and offer valuable insights for future research directions.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [ { "c_id": "11424", "date": "29 Apr 2024", "name": "Prabhakar Sharma", "role": "Author Response", "response": "The manuscript entitled “Micro(nano)plastics: invisible compounds with a visible impact” provides a comprehensive overview of the current understanding of micro(nano)plastics (NMPs), including their characterization methodologies, health impacts, sources, and potential remediation strategies. It is an informative piece that contributes significantly to the field. To further enhance the manuscript's clarity and depth, I recommend the following revisions for consideration. Response: Many thanks for providing feedback to our paper. In reference to Figure 1, it would be beneficial to delineate more explicitly the relationships among the depicted elements. An enhanced graphical representation could facilitate a clearer understanding of the connections and interactions between the various components related to NMPs. A revised figure that visually integrates these aspects with greater clarity would greatly benefit readers' comprehension. Response: I couldn’t improve the suggested figure (1) yet. The sentence beginning with \"Plastics fragment into smaller...\" and ending with \"...to decompose in the environment\" could benefit from a rephrasing to enhance clarity and precision. Response: Thanks. The sentence has been rephrased. The section addressing the identification and separation methodologies for NMPs would benefit from a more detailed exposition. It is recommended to structure this section into subsections, each dedicated to a specific method. Within each subsection, please provide a clear definition of the technique, its advantages, a summary of key findings from previous studies utilizing this method, and a discussion on its limitations. This structure will not only enrich the manuscript but also provide readers with a comprehensive understanding of the current methodological landscape. Response: Many thanks for this suggestion. As this is a mini review article, we couldn’t expand this section further. The statement regarding \"Synergistic effects of MNPs... after entering their bodies\" requires rewriting for clarity and impact. A more precise and engaging sentence could better capture the nuances of MNPs' effects on biological systems. Response: This sentence has been modified. The discussion on biodegradable and environmentally friendly remediation techniques for NMPs warrants further elaboration. It would be advantageous to detail specific methodologies, their mechanisms of action, efficacy, and potential environmental impacts. This expanded discussion could provide a critical evaluation of sustainable strategies for NMPs mitigation and offer valuable insights for future research directions. Response: This section is enhanced for more clarity." } ] }, { "id": "240000", "date": "23 Apr 2024", "name": "Prabhakar Singh", "expertise": [ "Reviewer Expertise Hydrology", "watershed management", "modeling", "GIS application in drainage basin." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPlastic-related research has gained prominence, especially in realizing the presence and spread of micro(nano)plastics (MNPs) in terrestrial and aquatic environments. However, there is limited focus on the fate and remediation of MNPs in soil and groundwater, and understanding the interaction of ubiquitous organic environmental pollutants with MNPs in biological systems is insufficient. This paper highlights the need to address MNP pollution by reducing plastic consumption, enhancing waste management practices, and developing environmentally friendly alternatives. It emphasizes the urgent need for policymakers and researchers to monitor and map MNP contamination in soil and groundwater for effective environmental protection. The review paper's strength lies in acknowledging the increasing significance of plastic-related research and highlighting the well-established presence of MNPs in terrestrial and aquatic environments. The authors advocate for future research to prioritize expanding the focus on plastic-related studies, specifically addressing the current limitations in understanding the fate and remediation of MNPs in soil and groundwater. They also emphasize the need for research efforts to uncover unknown aspects of the fate and bioaccumulation of ingested MNPs within the digestive tract of animals and to bridge the knowledge gap regarding the interaction of ubiquitous organic environmental pollutants with MNPs in biological systems.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-69
https://f1000research.com/articles/13-302/v1	19 Apr 24	{ "type": "Software Tool Article", "title": "Transforming the tourism experience: Virtual Reality for customer loyalty in the tourism industry", "authors": [ "Carlos Cayahuallpa-Paquirachi", "Alex Pacheco", "Yrene Uribe-Hernandez" ], "abstract": "Background Today, the tourism sector in particular is becoming increasingly competitive, forcing companies to adopt innovative approaches to attract the attention of consumers. In this context, a virtual reality application is presented with the aim of strengthening brand loyalty through immersive experiences in tourism companies.\n\nMethods The development was divided into three phases: planning, implementation and operation, which emphasized close collaboration with stakeholders to adapt to changing requirements; implementation, which focused on a simple design with emphasis on creating a scalable and secure backend architecture; and finally, in the operation phase, two iterations were carried out. The first focused on creating an immersive virtual environment with intuitive interfaces and basic interactive elements. The second iteration enhanced these basic features and incorporated advanced features such as greater interactivity with virtual objects for a more realistic experience.\n\nResults A 66.36% increase in brand loyalty was achieved, demonstrating increased customer engagement and sustainable revenue generation. There was also a 65.48% increase in customer retention, indicating a continued willingness to purchase services from this brand. In addition, 78.15% of participants expressed a high level of satisfaction with the virtual reality experience.\n\nConclusions This research contributes to the process of inclusive and sustainable industrialization by improving infrastructure and making industries more sustainable. This will be achieved by making more efficient use of resources and promoting the adoption of technologies.", "keywords": [ "Virtual reality", "brand loyalty", "immersion", "tourism", "customers" ], "content": "Introduction\n\nThe adoption of emerging technologies in tourism not only places companies at the forefront of digital transformation, but also accelerates the move towards resilient and environmentally friendly infrastructure (Castilla et al., 2023). Virtual reality is emerging as a technology that offers the opportunity to transform the tourism industry's communication to meet the needs of tourists (Pestek & Sarvan, 2021). This technology not only enriches the traveller's experience, but also provides destinations and businesses with additional marketing tools, thus reshaping the consumer experience (Calisto & Sarkar, 2024).\n\nThe global business landscape reveals a widespread reluctance to adopt new technologies, largely due to the persistent fear of innovation caused by the economic inequality that still prevails in certain countries (Ore et al., 2021; Bernad, 2020). This situation poses significant challenges for firms in the Lima Sur region of Peru, which are struggling to differentiate themselves in a competitive environment characterized by low adoption of technological innovation. Peruvian manufacturing firms that integrate innovation and R&D activities show superior performance, highlighting the importance of innovation both in products, services and marketing to expand market share, and in processes and organization to improve productivity (Seclen-Luna et al., 2023).\n\nHowever, despite the obvious need for innovation, the scientific community lacks robust and up-to-date evidence on the effective implementation of virtual reality technologies in advertising and brand loyalty, especially in the tourism sector (Zeng et al., 2023). The lack of comprehensive studies in this area leaves a critical knowledge gap, particularly in a sector that faces unique challenges related to atypical forms of employment, low wages, high turnover and other obstacles that could hinder the adoption of advanced technologies and the continuous improvement of service quality (Castillo-Reina & Cruz, 2021).\n\nIn addition, technical limitations, bandwidth constraints, and lack of accessories also affect the quality of the virtual reality experience, raising questions about the feasibility of its implementation in tourism. Additional concerns about whether virtual reality could replace the actual travel experience add a layer of complexity to this debate and raise questions about the potential negative impact on the tourism industry. The adoption of emerging technologies in tourism is at an early stage, largely due to the perception that these technologies, such as robotics, artificial intelligence and virtual reality, are costly and complicated to use. These challenges reflect an apparent innovation gap in tourism, where the full potential of emerging technologies has not yet been realized due to economic and practical constraints (Alonso, 2019; Moscoso & Torre, 2020; Gössling et al., 2021).\n\nIn this context, the need arises for companies in the tourism sector to actively seek to transform themselves through strategic planning and the adoption of emerging technologies. Therefore, the objective of this research is to propose Virtual Reality as an integral strategy for advertising and brand loyalty in tourism companies in the district of Lunahuaná, Cañete, Peru.\n\nThe incorporation of this technology not only promotes the local tourism industry, but also stimulates innovative processes and contributes to the development of more robust and sustainable infrastructures. This not only enhances the tourism experience, but also ensures that tourism activities are carried out with respect for natural and cultural resources, preserving them for future generations.\n\n\nMethods\n\nResearch development used an agile approach to ensure collaboration, simplicity, and system flexibility (Suryantara & Andry, 2018). The development was divided into three phases: planning, implementation and operation, which emphasized close collaboration with stakeholders to adapt to changing requirements (Akhtar et al., 2022); implementation, which focused on a simple design with emphasis on creating a scalable and secure backend architecture (Fojtik, 2011); finally, in the operation phase, two iterations were carried out. The first focused on creating an immersive virtual environment with intuitive interfaces and basic interactive elements. The second iteration enhanced these basic features, incorporating advanced functions, such as greater interactivity with virtual objects for a more realistic experience (Shrivastava et al., 2021).\n\nDevelopment Technologies: A selection of advanced technologies has been used, the server uses an open-source PHP 8.0 framework, known for its robustness (Tenzin, 2022). As for the user interface, it uses an open source ES6 JavaScript framework, ensuring a smooth and customizable user experience (Shukla, 2023).\n\nStrategic integration of add-ons: To extend the capabilities of the application, key add-ons and libraries have been integrated, including:\n\n- Framevr.io (virtual world)\n\n- A-Frame (360 view of images and videos)\n\n- Googlecharts (graphics)\n\nThese libraries allow users to immerse themselves in the web application without having to download any external software.\n\nAdaptation for tourism agencies: the basic structure of the software was adapted to meet the specific needs of tourism promotion for travel agencies in the district of Lunahuaná, which has required a careful classification and organization of the services provided by the company.\n\nMinimal system requirements: The virtual reality application, accessible online, is designed to run efficiently with basic system requirements. These are:\n\n• Server:\n\no Must be compatible with and support PHP version 8.0.\n\no Must have sufficient storage space to collect data on the frequency and interest of the customer's use of the service while using the application.\n\n• Client:\n\no An up-to-date web browser with JavaScript ES6 support is required.\n\no Internet connection required to access online features.\n\no Access via a mobile device is sufficient for a good user experience, but for full immersion, the use of a virtual reality device such as Oculus Quest 2 is recommended.\n\nEnsuring that these requirements are met ensures that the application remains accessible and usable, even in travel agencies with limited technological resources.\n\nThe application has distinctive features that differentiate it from existing solutions:\n\n• Virtual Reality (VR) Exploration: Allows users to explore destinations in a fully immersive way using mobile devices or dedicated devices such as Oculus Quest.\n\n• Collaborative Virtual Reality Experiences: Allows groups of people to connect to the virtual world in real time from different locations. This allows friends and family to enjoy shared travel experiences even when they are not physically together.\n\n• Cross-Platform Compatibility: This progressive web application (PWA) works across multiple platforms and browsers, reducing the need to develop separate applications for different operating systems (Garad & Pramod, 2021).\n\nEthical approval was obtained from the Institutional Review Committee of the Research Unit of the Faculty of Engineering of the Universidad Nacional de Cañete on June 5, 2023, with the assigned number CE-UIFI-N°001-2023. Written informed consent was obtained from all participants after their agreement to participate in the study. The confidentiality of personal information and responses was guaranteed, and the data was used exclusively for research purposes.\n\n\nUse cases\n\nThe system data is loaded automatically following the installation steps detailed in the “Readme.md” file found in the repository (Cayahuallpa-Paquirachi, 2023).\n\nResults were measured and analyzed using key performance indicators (KPIs) focused on brand loyalty, customer retention and customer satisfaction.\n\nFigure 1 highlights that the adoption of the virtual reality application showed a significant 66.36% increase in brand loyalty after its implementation. This increase is based on the comparison of data obtained from June to October 2023, as presented in the “ind1.php” page. These results represent an increase in brand loyalty compared to the previous year, suggesting that the immersive experience provided by virtual reality not only captured consumers' attention, but also strengthened their connection to the brand.\n\nInput:\n\n• Enter the view “ind1.php”.\n\n• Search in the input of MONTH: “JUNE”.\n\nOutput: List of coincidences:\n\n• ID: 1\n\n• DAY: 1, MONTH: JUNE, TIME: 284 min\n\n• ID: 2\n\n• DAY: 2, MONTH: JUNE, TIME: 358 min\n\n• …\n\nFigure 2 shows that customer retention increased significantly after the implementation of virtual reality technology, with a 65.48% increase in retention after implementation. This increase is based on the comparison of data obtained from June to October 2023, as presented in the “ind2.php” page. This data is revealing, as it implies that the virtual reality application not only attracted customers, but also played a crucial role in the acquisition of their services, ensuring the survival and growth of the brand.\n\nInput:\n\n• Enter the view “ind2.php”.\n\n• Search in the input of MONTH: “AUGUST”.\n\nOutput: List of coincidences:\n\n• ID: 57\n\n• DAY: 1, MONTH: AUGUST, AMOUNT: 27\n\n• ID: 58\n\n• DAY: 2, MONTH: AUGUST, AMOUNT: 79\n\n• …\n\nFigure 3 looks at customer experience with the application, and the results of a survey of users of this technology show that 78.15% of respondents rated the implementation as “good”. This percentage not only reflects positive acceptance, but also suggests that the experience provided by the virtual reality application met or exceeded the expectations of most users. This level of satisfaction is indicative of a well-received product, which is likely to contribute to positive word-of-mouth recommendations among individuals, strengthening the brand's reputation and positioning in the industry.\n\nInput:\n\n• Enter the view “ind3.php”.\n\nOutput:\n\n• Opinions reports\n\nThese use cases demonstrate how the application builds brand loyalty and retention among users, in addition to being easy to use and meeting initial expectations.\n\n\nDiscussion\n\nThe first indicator obtained a 66.36% increase in brand loyalty, these results reflect how immersive experiences intensify consumers' emotional and cognitive connection with the brand. This result plays a crucial role in consumers' perception of and loyalty to a brand (Meißner et al., 2020). It can also positively influence the consumer's relationship with the brand (Zeng et al., 2023). In this context, it is evident that brand loyalty is intrinsically linked to the service provided to customers through its online channels (Merdiaty & Aldrin, 2022).\n\nThe second indicator shows a 65.48% improvement in customer retention, which indicates that the application not only attracts customers, but also keeps them engaged. This increase is attributed to the implementation of personalized engagement strategies, such as advanced loyalty programs and identification of customer preferences and behaviors, thus enabling more effective personalization of services and offers. This result suggests that virtual reality not only enhances the immediate experience, but also influences consumers' future intentions to share their positive experiences. This behavior of sharing positive experiences is considered a key indicator of customer retention (Lee, 2022). Previous studies have indicated that virtual reality brings significant benefits to the industry from both economic and marketing perspectives. These benefits include the enhancement of the image of tourism destinations and an increase in attractiveness to potential visitors (Ouerghemmi et al., 2023). Moreover, a comprehensive perspective is provided on how virtual reality is transforming the tourism industry, especially with regard to customer retention (Abarca et al., 2022).\n\nThe customer satisfaction rating of 78.15% represents a tangible improvement in the user experience. This high level of satisfaction was achieved through the implementation of two key initiatives. These include the optimization of user interfaces to provide more intuitive navigation, and the integration of immediate response systems to address inquiries and resolve issues efficiently. This result shows that the quality and type of experience provided by virtual reality is highly satisfactory for the users involved in such research (Orús et al., 2021). Similarly, it highlights that a positive experience with virtual reality technology has broad and lasting effects on the relationship between the customer and the company (Alcañiz et al., 2019). Furthermore, it is emphasized the importance of considering how the adoption of virtual reality transforms market dynamics and sets new standards in the customer's tourism experience (Branca et al., 2023).\n\nThe limitations of this study lie in its reliance on quantitative indicators, which do not fully capture the complexity of individual experiences. In addition, the results may have been influenced by cultural or demographic factors specific to the sample studied. In terms of future work, it would be beneficial to explore longitudinal studies that examine the persistence of virtual reality's impact on brand loyalty and customer retention over time. This could include analyzing changes in consumer perceptions as the novelty of virtual reality wears off. It would also be beneficial to incorporate qualitative approaches, such as interviews or ethnographic studies, to gain a better understanding of how consumers experience and make sense of immersive technologies.\n\n\nConclusions\n\nRemarkably, the application captured users' interest and sustained their engagement. This data not only highlights the effectiveness of the application in driving loyalty, but also suggests its potential to reshape expectations and practices in long-term customer engagement. Customer engagement reveals how an immersive experience can revolutionize the connection between customer and brand. This finding suggests that these strategies go beyond simply capturing interest and set new standards in the customer-brand dynamic. This breakthrough is notable not only for its immediate impact, but also for opening the door to future research on how technological immersion can redefine business relationships and customer loyalty. The user satisfaction rate highlights the success of virtual reality innovations that not only improve the customer experience, but also redefine expectations in the tourism sector. These results demonstrate the effectiveness of immersive experiences and their ability to drive tourism in new and engaging ways.\n\nThe application of virtual reality in tourism is characterized by its ability to transform and enrich the user experience, resulting in increased customer loyalty and retention. By providing an immersive and emotionally engaging experience, Virtual Reality is emerging as a key factor in differentiating destinations in a highly competitive market, with significant potential to enhance tourism promotion. The practical implications of virtual reality in the tourism sector are remarkable, as institutions can implement this technology to differentiate themselves in the marketplace, thereby increasing customer loyalty and retention through immersive experiences.\n\nWhile current research has observed significant improvements in brand loyalty and customer retention, there are opportunities for improvement, such as expanding the study demographic and personalizing content. This would maximize the potential of virtual reality in tourism and better tailor the user experience.", "appendix": "Data availability\n\nZenodo: Pretest and posttest - Tourism promotion variable, https://doi.org/10.5281/zenodo.10725200 (Cayahuallpa-Paquirachi & Pacheco, 2023).\n\nThis project contains the following data:\n\n- DATA Record Sheets - LunApp.xlsx\n\n- Figure 1 (Customer retention – Before and after implementing the application)\n\n- Figure 2 (Brand loyalty – Before and after implementing the application)\n\n- Figure 3 (Customer satisfaction) – Before and after implementing the application)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nSpecial thanks to the Vice-Presidency of Research of the Universidad Nacional de Cañete for providing us with the necessary resources to develop this research. To the research groups “Cañete L@B” and “Transformación Digital” of the Professional School of Systems Engineering of the Universidad Nacional de Cañete for the realization of this scientific article throughout these years of study.\n\n\nReferences\n\nAbarca Sánchez Y, Barreto Rivera U, Barreto Jara O, et al.: Fidelización y retención de clientes en una empresa líder de telecomunicaciones en Perú. Revista Venezolana de Gerencia. 2022; 27(28): 729–743. Publisher Full Text\n\nAkhtar A, Bakhtawar B, Akhtar S: Extreme Programming VS SCRUM: A Comparasion of Agile Models. International Journal of Technology, Innovation and Management (IJTIM). 2022; 2(2). Publisher Full Text\n\nAlcañiz M, Bigné E, Guixeres J: Virtual Reality in Marketing: A Framework, Review, and Research Agenda. Frontiers in Psychology. 2019; 10: 1530. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlonso Almeida MDM: Robots, inteligencia artificial y realidad virtual: Una aproximación en el sector del turismo. Cuadernos de Turismo. 2019; 44: 13–26. Publisher Full Text\n\nBernad M: Nuevas tecnologías y difusión del turismo cultural: Descubriendo a Goya con realidad aumentada. ROTUR. Revista de Ocio y Turismo. 2020; 14(1): 81–93. Publisher Full Text\n\nBranca G, Marino V, Resciniti R: How do consumers evaluate products in virtual reality? A literature review for a research agenda. Spanish Journal of Marketing - ESIC. 2023. Publisher Full Text\n\nCalisto MDL, Sarkar S: A systematic review of virtual reality in tourism and hospitality: The known and the paths to follow. International Journal of Hospitality Management. 2024; 116: 103623. Publisher Full Text\n\nCastilla R, Pacheco A, Franco J: Digital government: Mobile applications and their impact on access to public information. SoftwareX. 2023; 22: 101382. Publisher Full Text\n\nCastillo-Reina MÁ, Cruz JL: La innovación en el sector turístico: Una aproximación a los servicios y la cocreación de experiencias. Turismo y Sociedad. 2021; 30: 25–49. Publisher Full Text\n\nCayahuallpa-Paquirachi C: pKroz/LunApp: Virtual Reality PWA for tourism promotion. (1.0) [Software].2023. Publisher Full Text\n\nCayahuallpa-Paquirachi C, Pacheco A: Pretest and posttest—Tourism promotion variable.2023. Publisher Full Text\n\nFojtik R: Extreme Programming in development of specific software. Procedia Computer Science. 2011; 3: 1464–1468. Publisher Full Text\n\nGarad S, Pramod Bendale S: Progressive Web Apps: A Seamless User Interface. 2582-5208.2021.\n\nGössling S, Scott D, Hall CM: Pandemics, tourism and global change: A rapid assessment of COVID-19. Journal of Sustainable Tourism. 2021; 29(1): 1–20. Publisher Full Text\n\nLee U-K: Tourism Using Virtual Reality: Media Richness and Information System Successes. Sustainability. 2022; 14(7): 3975. Publisher Full Text\n\nMeißner M, Pfeiffer J, Peukert C, et al.: How virtual reality affects consumer choice. Journal of Business Research. 2020; 117: 219–231. Publisher Full Text\n\nMerdiaty N, Aldrin N: Effect of Brand Experience on Customer Engagement Through Quality Services of Online Sellers to Students in Bekasi. Frontiers in Psychology. 2022; 12: 801439. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoscoso Sotelo KVJ, Torre Saenz OM: Diseño de aplicación de realidad virtual para la promoción del turismo e incremento de la intención de visita de turistas a Perú. Universidad Peruana de Ciencias Aplicadas (UPC); 2020. Reference Source\n\nOre J, Pacheco A, Roque E, et al.: Augmented reality for the treatment of arachnophobia: Exposure therapy. World Journal of Engineering. 2021; 18(4): 566–572. Publisher Full Text\n\nOrús C, Ibáñez-Sánchez S, Flavián C: Enhancing the customer experience with virtual and augmented reality: The impact of content and device type. International Journal of Hospitality Management. 2021; 98: 103019. Publisher Full Text\n\nOuerghemmi C, Ertz M, Bouslama N, et al.: Impact of Virtual Reality on Tourism. Encyclopedia. 2023.\n\nPestek A, Sarvan M: Virtual reality and modern tourism. Journal of Tourism Futures. 2021; 7(2): 245–250. Publisher Full Text\n\nSeclen-Luna JP, Moya-Fernandez P, Cancino CA: Innovation and performance in Peruvian manufacturing firms: Does R&D play a role? RAUSP Management Journal. 2023; 58(2): 143–161. Publisher Full Text\n\nShrivastava A, Jaggi I, Katoch N, et al.: A Systematic Review on Extreme Programming. Journal of Physics: Conference Series. 2021; 1969(1): 012046. Publisher Full Text\n\nShukla A: Modern JavaScript Frameworks and JavaScript’s Future as a FullStack Programming Language. Journal of Artificial Intelligence & Cloud Computing. 2023; 1–5. Publisher Full Text\n\nSuryantara IGN, Andry JF: Development of Medical Record With Extreme Programming SDLC. International Journal of New Media Technology. 2018; 5(1): 47–53. Publisher Full Text\n\nTenzin S: PHP Framework for Web Application Development. IARJSET. 2022; 9(2). Publisher Full Text\n\nZeng M, Shen S, Gu J: How does the integration of cultural and tourism industries impact the value added to tourism value chain: Evidences from Jiangsu Province of China. PLoS One. 2023; 18(6): e0287610. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "282143", "date": "08 Jun 2024", "name": "Aniesa Samira Bafadhal", "expertise": [ "Reviewer Expertise virtual tourism marketing and behavior" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1) The current research article's rationale for developing the new software tool is unclear. While the paper proposes virtual reality (VR) as a pivotal strategy for advertising and fostering brand loyalty in tourism companies, the title fails to emphasize the impact of VR on advertising and brand loyalty. Furthermore, the research outlines a three-phase software development process critical for understanding how the VR application was conceptualized and refined. However, the title does not reflect this methodological depth, essential for distinguishing this software tool research from other papers. The abstract provided is generally aligned with the keywords for the article journal, which include \"virtual reality,\" \"brand loyalty,\" \"immersion,\" \"tourism,\" and \"customers.\" However, consider incorporating another keyword more explicitly into the overall research content to enhance alignment and improve clarity, such as “VR advertising” and “VR promotion.” The absence of comparative research on the same topic is notable. It is crucial to draw comparisons, identify research gaps, and address potential limitations in existing literature. Presenting counterarguments or challenges to implementing VR technology in the tourism sector would enrich the discussion and prevent the article from appearing one-sided. Moreover, the introduction heavily relies on cited sources to support its points rather than providing original insights or analyses. This approach may lead to a lack of depth or critical thinking when discussing the topic. To improve, the article could delve deeper into the current state of advertising and brand loyalty within the tourism sector, highlight existing challenges tourism companies face, and underscore the necessity for innovative solutions such as VR advertising technology. Clarifying key performance indicators such as brand loyalty, customer retention, and customer satisfaction and elucidating their interrelationship with customer experience and loyalty would ensure readers thoroughly grasp the concepts under discussion and their significance in VR technology's context in tourism advertising. Additionally, there is a lack of connection between the discussion and the need for VR advertising applications developed in the current research. Identifying existing gaps or limitations in current VR advertising applications and specifying how these new tools can address the identified challenges and enhance advertising effectiveness and brand loyalty in the tourism industry would strengthen the argument.\n2) The description of the software tool lacks essential technical details, such as features, storytelling, scenarios, prototypes, or the appearance of the VR advertising application developed by the researchers. The researchers only display the results of exposure to VR advertising on brand loyalty, customer retention, and satisfaction of tourism companies that utilize VR advertising. Including a detailed description of the software tool's features is crucial, as it gives readers insights into how the application functions and what sets it apart from other solutions. Features like interactive elements, user interfaces, navigation options, and virtual environments contribute to the VR advertising application's overall user experience and effectiveness. Storytelling and scenarios are essential to VR advertising applications, as they shape users' narrative and engagement levels. By presenting specific scenarios or use cases, researchers can demonstrate how the application immerses users in virtual environments and conveys brand messages effectively. Prototypes or visual representations of the application's appearance offer readers a tangible understanding of its design and aesthetics. Clear documentation of features and design elements enhances transparency and facilitates reproducibility, allowing other researchers or developers to replicate or build upon the software tool in their own projects. The introduction highlights the importance of VR advertising for sustainability and industrial infrastructure efficiency. Still, it has not been explained how the VR advertising researchers have developed can be a sustainable solution. The information would strengthen the methodology section by showcasing a more comprehensive approach to VR advertising application sustainability.\n3) There is an insufficient comprehensive methodological approach taken in the research and a lack of systematic development, testing, and deployment of VR for advertising and branding. Here are several key points that need to enhance the methodological research part: The research lacks thorough explanation and detail regarding several key aspects, including research type and research approach, which are not clearly outlined, leaving ambiguity about the methodology employed. There is a lack of description regarding research and experimental design, including pre-test and post-test measures to evaluate the impact of the intervention. The study population, data collection methods, types of data gathered, and survey or internet observation techniques are not sufficiently explained, leading to uncertainty about the research's validity and generalizability. Furthermore, the adaptation of the software for tourism agencies is mentioned but lacks detail on how the specific needs of these agencies were identified and addressed. It would enhance the methodology's credibility by providing insights into the research or analysis conducted to understand these requirements and how they were incorporated into the software design. The methodology does not mention specific testing methodologies or quality assurance practices implemented during development. Including information on testing strategies, such as unit testing, integration testing, and user acceptance testing, would demonstrate how the software's reliability and functionality were ensured. While the methodology mentions close collaboration with stakeholders, it does not elaborate on the extent or methods of stakeholder involvement. Including details on stakeholder engagement strategies, such as regular meetings, feedback sessions, or user testing, would provide a clearer picture of how stakeholder input influenced the development process. Additionally, research settings in tourism companies in the Lunahuaná, Cañete, Peru district, and firms in the Lima Sur region of Peru are not mentioned in the methodology. It is critical to understand the context and generalizability of the study findings. It provides insight into the specific population under study and helps determine the relevance and applicability of the research to similar settings or regions. Data analysis and analytical tools lack explanation. The absence of an explanation of data analysis and analytical tools used in the study hinders transparency and reproducibility. Understanding the methods and tools employed for data analysis is essential for evaluating the rigor and validity of the study's findings. It enables researchers to assess the appropriateness of the analytical approach and the results' reliability. Moreover, the research used an agile development framework. The development was divided into three phases: planning, implementation, and operation, but each step was not described in detail. For a research journal, providing more insight into the agile methodologies employed, such as Scrum or Kanban, and how they were tailored to suit the project's needs would enhance the depth of the methodology section. The planning phase includes functional requirements, non-functional requirements, technologies used, and hardware specifications. Implementation phases include prototype development, project repository, frontend, and backend development. Finally, two iterations were carried out in the operation phase but lacked descriptions. Another insight for readers needs to explain, such as A/B testing or other methods, compares two product versions, and gathers user feedback for optimization. User feedback is incorporated to improve the system. Hosting, security, feature and measurement, and detailed documentation and flowcharts are not provided to illustrate the system development process. While the methodology mentions two iterations during the operation phase, it does not delve into how user feedback was collected or incorporated into the development process. Including information on how user feedback influenced feature enhancements and iterative improvements would add depth to the methodology section.\n4) The information provided does not adequately enable the interpretation of the expected output datasets and any results generated using the tool. In the discussion section, the position of the results of this study compared to previous research has not been explained. By discussing how the current study's findings align with or diverge from previous research, researchers provide context for interpreting their results. This contextualization helps readers understand the broader landscape of research in the field and how the current study contributes to it. Additionally, the methodology of this study lacked an explanation of the characteristics of respondents or users involved, leading to a deficiency in exploring the study results in the discussion section, particularly in relation to the characteristics of respondents at the Lima Peru tourism company. Describing the demographics, backgrounds, and characteristics of respondents offers insights into the representativeness of the study sample. Knowledge of respondent characteristics aids in interpreting study results within the specific context of the target population. Moreover, the discussions of this study do not yet provide theoretical and practical implications. By discussing theoretical implications, researchers demonstrate how their findings contribute to advancing theoretical frameworks in the field. Practical implications elucidate how the study findings can be applied in real-world settings. Based on the study results, this may include recommendations for practitioners, policymakers, or other stakeholders. Practical implications provide actionable insights that inform decision-making, strategy development, and intervention design in relevant domains.\n5) The conclusions about the tool and its performance are not adequately supported by the findings presented in the article. The abstract, introduction, and results highlight the importance of VR advertising for sustainability and industrial infrastructure efficiency. However, the discussion and conclusion of this research fail to align with it. The provided conclusion primarily focuses on the effectiveness of VR in enhancing customer engagement, which was never mentioned before. Eventually, it does not address the research's contribution to inclusive and sustainable industrialization, infrastructure improvement, or industry resource efficiency.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? No\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-302
https://f1000research.com/articles/13-300/v1	19 Apr 24	{ "type": "Study Protocol", "title": "A prospective randomized comparative study to evaluate efficacy of intrathecal dexamethasone and dexmedetomidine added as adjuvant to bupivacaine in pregnant patients posted for elective LSCS", "authors": [ "Samarpan Patel", "Aruna Chandak", "Dnyanshree Wanjari" ], "abstract": "Any individual undergoing surgery is concerned about postoperative discomfort. It modifies the body’s physiological reaction and impacts an individual’s psychological state. A physician can meet early mobilization goals by effectively managing postoperative pain and preventing related co-morbidities. Targeting different phases of the pain pathway, from perception to central modulation, is successfully accomplished through the use of different drug combinations and regional anesthetic block techniques. Local anaesthetics injected intrathecally in a single injection create a superb surgical field and can even make a patient pain-free two to three hours following surgery. By adding certain adjuncts, this period can be prolonged, and there will be long-term benefits in terms of decreasing the dosage of opioid analgesics. Because of its faster start of the action and low side effects, spinal anaesthesia is the procedure most frequently used for caesarean sections. Many intrathecal additives have been explored since it has a limited role in postoperative pain control. Adjuvants such as opioids, clonidine, adrenaline, and phenylephrine have been explored recently. These chemicals have been linked to several problems, including tachycardia, respiratory depression with opioids, hypertension with adrenaline and clonidine, and excessive sedation. In this study, our primary objective is to compare the duration of postoperative analgesia between Dexamethasone and dexmedetomidine, as Dexamethasone is an anti-inflammatory drug and dexmedetomidine is an alpha-two agonist that binds with a G protein-coupled receptor. our secondary objectives include comparing intraoperative hemodynamics, intraoperative sedation, and intraoperative shivering between Dexamethasone and dexmedetomidine. CTRI REF.NO-REF/2023/05/067283", "keywords": [ "Cesarean section", "Dexamethasone", "Dexmedetomidine", "Postoperative analgesia", "Bupivacaine", "Intraoperative haemodynamics" ], "content": "Introduction\n\nPain is defined by the International Association for the Study of Pain as an “unpleasant sensory and emotional experience associated with actual or potential tissue damage or described in terms of such damage”. Pain perception begins before birth.1\n\nThe most used type of anaesthesia for cesarean sections is spinal anaesthesia. This approach is the best choice when there are no contraindications.2 It eliminates dangers associated with general anaesthesia, including awareness of the mother, aspiration of stomach contents, respiratory issues in the newborn, and difficulties managing the airway.3,4 Hypotension is the most common side effect of spinal anaesthesia and is closely linked to morbidity and death in both the mother and the fetus. Numerous investigations have demonstrated that despite preserving a comparatively brief duration of anaesthesia and analgesia, lowering the intrathecal local anaesthetic dose can lessen the incidence of spinal-induced hypotension.4\n\nFollowing surgery, pain is unavoidable. Most essential organ functions are disrupted, and stress is caused by postoperative discomfort. These systems include the body’s metabolic, respiratory, cardiovascular, gastrointestinal, urological, and neuroendocrine. In addition to the discomfort brought on by pain, individuals recovering after surgery frequently experience difficulties breathing normally, coughing productively, and moving around enough to take care of their daily requirements or participate in rehabilitation. Feelings of hopelessness, terror, anxiety, and sadness are frequently the outcome of this. One of the scarier parts of surgery, in the eyes of the patient, is the postoperative pain. Thus, one of the primary duties of anesthesiologists is to relieve pain.\n\nMany benefits come with appropriate postoperative pain management, such as increased patient comfort, quicker mobilization, fewer heart and lung issues, a decreased risk of deep vein thrombosis, a decreased chance of developing neuropathic pain, and a decreased medical expense. Therefore, to achieve prolonged and efficient postoperative analgesia, anesthesiologists typically have a keen interest in extending the duration of local anaesthesia.5\n\nMany adjuvants, including epinephrine, phenylephrine, clonidine, and opioids, are used to lengthen the duration of spinal anaesthesia to solve the issue of the limited duration of action of local anaesthetics.4 Nevertheless, these adjuvants are linked to undesirable side effects. Many forms of regional anaesthesia have been treated with dexamethasone1,6,7 and dexmedetomidine8–12 as adjuvants without raising the risk of neurological problems.\n\nDexmedetomidine interacts with a transmembrane G protein-binding receptor and is a highly selective α2-adrenoreceptor agonist. Based on the research, it can be combined with local anaesthetics in spinal anaesthesia to accelerate the onset of the block, decrease the intensity of postoperative pain, prolong the block’s duration, and reduce the need for analgesics following surgery. By promoting vasodilatation and suppressing central thermoregulation, it reduces the frequency of shivering.13\n\nDexamethasone has been used as an intravenous drug to lessen shivering because it alters the body’s inflammatory response and lowers the gradient between central and peripheral tissue temperatures. We reasoned that dexamethasone might be used as an intrathecal adjuvant to local anaesthetics to reduce the intensity of shivering since it has been safely injected into the cerebrospinal fluid and used as an adjuvant to enhance the efficiency of regional anaesthesia.14 A 2011 study conducted in Iran looked at the effects of using 15 mg (3cc) of 0.5% hyperbaric bupivacaine in combination with 8 mg of dexamethasone for spinal anaesthesia during orthopaedic surgery. According to their observations, the duration of analgesia rose from 202±43.67 minutes (Control Group) to 401±72.44 minutes (Intervention Group).\n\nBupivacaine is a solid local anesthetic with unique features that was first discovered in 1957. It is a member of the amide group of local anesthetics. Local anesthetics are used in spinal anesthesia, regional anesthesia, epidural anesthesia, and local infiltration. Because they increase the threshold for electrical stimulation, local anesthetics frequently stop nerve cells from generating an action potential. The way anesthesia develops depends on a number of factors, including the diameter, degree of myelination, and conduction velocity of nerve fibers.\n\nOne major worry in obstetrics is the discomfort associated with caesarean procedures. Several studies have shown how important it is to provide adequate analgesia before, during, and after surgery to assist in mobilization, encourage rehabilitation, and reduce hospital stays. Our primary goal in this study is to compare how long postoperative analgesia lasts using dexamethasone versus dexmedetomidine. Comparing intraoperative sedation, intraoperative shivering, and intraoperative hemodynamics between dexamethasone and dexmedetomidine is the secondary goal.\n\nComparing the duration of analgesia caused by adding dexmedetomidine and Dexamethasone to bupivacaine during SAB (sub arachnoid block) for expectant mothers planned for elective LSCS.\n\n1) Primary objective\n\n1. Comparison of duration of analgesia between dexmedetomidine and Dexamethasone when added to bupivacaine.\n\n2) Secondary objectives\n\n1. Comparing the effect of Dexamethasone and dexmedetomidine on intraoperative haemodynamics.\n\n2. Comparison of perioperative shivering and effect on sedating the patient.\n\n\nMethods\n\nAfter receiving approval from the Datta Meghe Institute of Education & Research,Sawangi(M), Wardha, DMIMS Institutional Ethical Committee and screening Committee, the study would be carried out in the Department of Anaesthesiology, J.N.M.C. Before the procedure, written and informed consent will be taken. A departmental steering committee will monitor the study’s progress until completion.\n\nTwo arm parallel interventional trial\n\nResearch design: Comparative Prospective\n\nStudy area: Department of Anaesthesiology J.N.M.C. & A.V.B.R.H.\n\nStudy period: 2 year\n\nStudy population: Patients undergoing elective caesarean section\n\nAllocation of patient: Computer-generated randomization.\n\n\n\n1. Age between 20 to 40 years\n\n2. Pregnant ladies who have scheduled c-sections\n\n3. Pregnant for more than 37 weeks\n\n4. Body mass index 20 to 29.9 kg/meter square\n\n5. Intact amniotic membrane\n\n6. No history of bleeding tendency\n\n7. Only caesarean sections as prior uterus surgeries\n\n8. Living fetus\n\n9. ASA class I and II\n\n10. Patients giving informed consent\n\n\n\n1. Absence of legitimate, written, informed permission\n\n2. Those who have experienced bleeding disorders\n\n3. III and IV ASA\n\n4. Localized a block site infection\n\n5. Patient using anticoagulants at this time\n\n6. Patients with a history of musculoskeletal and neurological disorders\n\n7. Failed spinal\n\nFifty volunteers who match all inclusion criteria will take part in the trial.\n\nParticipants in the study will be divided into two groups at random (Table 1):\n\nGroup A: Patients will receive intrathecally 10 mg of bupivacaine and 10 mcg of dexmedetomidine.\n\nGroup B: Patients will receive intrathecally injected doses of 8 mg dexamethasone and 10 mg bupivacaine.\n\nThe calculation of sample size is based on:\n\n2α-It is the level of significance at 5% I.e 95% confidence interval = 1.96\n\n2β-The power of test = 80% = 0.84\n\nδ1-SD of timeto reach peak sensory level in group A = 0.32\n\nδ2-SD of time to reach peak sensory level in group B = 0.32\n\nΔ-Difference between two means = 6.93-6.5 = 0.43\n\nΚ-1\n\nN = 25 patients needed in each group\n\nStudy reference: Mohamed Abdul Mohasen, Abdul Naiem Ismael et al.\n\n\n\n1. All patients will have a pre-anesthesia examination the day before the procedure.\n\n2. A general examination, thorough evaluation, blood tests, and lab work will be recommended, along with basic patient information such as demographics, the history of the illness, and any present signs.\n\n3. The patients will be told of the study’s purpose, advantages, and disadvantages.\n\n4. Each patient participating in the study will provide written informed consent.\n\n5. They must abstain from food and drink for at least eight hours before the surgery.\n\n6. Participants in the study will be randomly divided into two groups.\n\nPatients in Group A (n=25) will receive intrathecally ten10 mcg of dexmedetomidine and 10 mg of bupivacaine.\n\nPatients in group B (n=25) will get intrathecally injected doses of 8 mg dexamethasone and 10 mg bupivacaine.\n\n\n\n1. Intraoperative attachments include an E.C.G, pressure monitor, and SpO2 probe.\n\n2. An IV line will be set up using an 18g IV cannula, and fluids(10- to 15 ml/kg) of Ringer lactate will be administered.\n\n3. Baseline measurements: The electrocardiogram from Lead II will be continuously displayed, and the patient’s blood pressure, heart rate, and SpO2 will also be recorded.\n\n4. Each patient will receive a prescription for premedication. Ondansetron 75–100 mcg/kg should be intravenously administered 10 minutes before the anaesthesia procedure.\n\n5. A 23/25 gauge Quinke’s needle will administer a subarachnoid block to the midline L3-4/L4-5 intervertebral space while maintaining the patient in a sitting or left lateral position. Then, the spinal needle’s introducer is grasped and carefully inserted through it until there is no longer any resistance, dural tissue is detected, and free flow of CSF is observed.\n\n6. Group A patients receive 2.1 ml of total drug volume, which consists of hyperbaric bupivacaine (2 ml) and dexmedetomidine(0.1 ml/10 mcgs) as an adjuvant.\n\n7. Patients in Group B get hyperbaric bupivacaine (2 ml) and Dexamethasone (2 ml/8 mg) administered sequentially in two different syringes for a total volume of 2 + 2 ml = 4 ml. After SAB (subarachnoid block), patients are immediately positioned to supine. First, Dexamethasone will be administered, followed by bupivacaine.\n\nThe following values will be noted.\n\n1. H.R., SBP, DBP, and SpO2 shall be recorded:\n\n- Baseline/before (drug administration)\n\n- 0, 3, 5, 10, 15 and 30 min following administration of the drug.\n\n2. Duration of analgesia will be measured with the help of VAS (visual analogue scale). It will be measured till the first rescue analgesia. In rescue analgesia first line will be iv paracetamol.\n\n3. Sedation grade using modified Richmond agitation sedation score\n\n4. Grade of shivering using Crossley and Mahajan grading of intraoperative shivering\n\n5. Negative outcomes, if any.\n\n\nStatistical analysis plan\n\nResults over the outcome variables will be tabulated & described using descriptive statistics; data over the outcome variables will be tested for normal distribution for the mean and standard deviation (SD) median statistics will positioned for finding skewed distributions and interquartile range (IQR). Frequency and percentages for binary and categorical variables will be tabulated for descriptive statistics. R-software free version will be used for all statistical analysis. The inferential statistics will be analysed as per the description given below\n\nInferential statistics will be used for comparing the two groups for measurement score resulted for their mean change in primary variable (modified Richmond agitation sedation score, Crossley and Mahajan grading of intraoperative shivering, visual analogue scale) between baseline and end.\n\nOutcome variables will be tested for intra difference in measurement at pre & post visits using paired t-test for finding the significance in mean. While for inter group difference unpaired t-test for comparison of two group.\n\nFor non-normal distribution Mathematical algorithms will be used for conversion of the data to normal distribution. If Data over primary variable still follows the non normal distribution then we will use alternate non parametric test Mann-Whitney and Wilcoxon test.\n\nCategorial data will be evaluated using chi square analysis using for finding association at 5% level of significance with P-value ≤ 0.05.\n\nEffect size over mean change difference on primary variable will be measured with corresponding 95% confidence interval (CI) & will be presented for finding the significance at 5% level.\n\nWe predict that Group B will have more prolonged and lasting analgesia than Group A during our investigation.\n\nContinuous information collection going on.\n\n\nDiscussion\n\nAs it provides adequate anaesthesia and pain relaxation while eliminating general anaesthesia complications, spinal anaesthesia is a well-established technique used in caesarean sections. In order to produce prolonged and efficient postoperative analgesia, anesthesiologists usually worry about extending the duration of local anaesthetics.12 Numerous authors have employed Dexmedetomidine and Dexamethasone as adjuvants to local anaesthetics and have shown notable outcomes.\n\nDexmedetomidine, a targeted alpha-adrenoreceptor agonist, can prolong analgesia and anaesthesia in peripheral and neuraxial anaesthesia.11,13–17 Additionally, there is no relation with respiratory depression.18 In a preclinical study or clinical practice, there was no proof that intrathecal dexmedetomidine caused neurological deficits.19\n\nDexamethasone inhibits nociceptive C-fibre neuronal discharges, which gives it anti-inflammatory and analgesic effects. When taken intrathecally, Dexamethasone may impact the synthesis of intraspinal prostaglandins. It is still unclear exactly how analgesic activity works.19 The effects of intrathecal Dexamethasone have been encouraging. Few investigations have shown that Dexamethasone administered intrathecally prolongs the time the sensory block lasts and enhances postoperative analgesia without noticeable side effects.1,19–26\n\nAccording to a study by Mohamed Abdul Mohsen Abdul Naiem Ismaiel et al., bupivacaine can be safely supplemented with Dexamethasone and dexmedetomidine. Dexamethasone prolongs the duration of postoperative analgesia, while during and following surgery, dexmedetomidine is more efficient at sedating the patient. However, according to research by Baher Said Abdelhady et al., higher analgesia and motor inhibition were observed in the dexmedetomidine category than in the dexamethasone category. In an elective caesarean operation, the average length of analgesia increased considerably with bupivacaine when Dexamethasone was added, according to a study by Muhammad Aatir Fayyaz et al. According to a study by Mahamoud Ali Ahmed El-Shourbagy et al., adding Dexamethasone to bupivacaine increases postoperative analgesia. According to a study by Ravi Gurbani, dexmedetomidine as an adjuvant extends the time that the block and postoperative analgesia last compared to Dexamethasone with little to no effect in upper limb surgery.\n\nThe JAWAHARLAL NEHRU MEDICAL COLLEGE, SAWANGI Research Project has received approval from the institutional ethics committee. The citation is D.M.I.M.S. (DU)/IEC/2022/96.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe author would like to thank the Department of Anaesthesia, J.N.M.C., A.V.B.R.H., Sawangi, Wardha, India staff for their assistance.\n\n\nReferences\n\nTkachenko R, Pyasetska N: ESRA19-0295.The efficiency of intrathecal dexamethasone for spinal anesthesia in elective caesarean section. Reg. Anesth. Pain Med. 2019; 44: A192–A193.\n\nTkachenko R, Pyasetska N: ESRA19-0295 The efficiency of intrathecal dexamethasone for spinal anesthesia in elective caesarean section. Reg. Anesth. Pain Med. 2019; 44: A192–A193.\n\nPyasetska N: The Efficacy of Intrathecal Dexamethasone to Prevent Early Complications of Spinal Anesthesia for Elective Caesarean Section. Technology Transfer: Innovative Solutions in Medicine. 2020; 10–13.\n\nXia F, Chang X, Zhang Y, et al.: The effect of intrathecal dexmedetomidine on the dose requirement of hyperbaric bupivacaine in spinal anesthesia for caesarean section: a prospective, doubleblinded, randomized study. BMC Anesthesiol. 2018; 18(1): 74. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKrishna TM, Panda N, Batra Y, et al.: Combination of low doses of intrathecal ketamine and midazolam with bupivacaine improves postoperative analgesia in orthopedic surgery. Eur. J. Anaesthesiol. 2008; 25(4): 299–306. PubMed Abstract \| Publisher Full Text\n\nKirkham KR, Jacot-Guillarmod A, Albrecht E: Optimal Dose of Perineural Dexamethasone to Prolong Analgesia After Brachial Plexus Blockade: A Systematic Review and Meta-analysis. Anesth. Analg. 2018; 126(1): 270–279. PubMed Abstract \| Publisher Full Text\n\nMarhofer P, Columb M, Hopkins PM: Perineural dexamethasone: the dilemma of systematic reviews and meta-analyses. Br. J. Anaesth. 2018; 120(2): 201–203. PubMed Abstract \| Publisher Full Text\n\nYanshuai M, Shuang Q: Effects of dexmedetomidine in reducing postcesarean adverse reactions. Exp. Ther. Med. 2017; 14(3): 2036–2039.\n\nWu HH, Wang HT, Jin JJ, et al.: Does dexmedetomidine as a neuraxial adjuvant facilitate better anesthesia and analgesia? A systematic review and meta-analysis. PLoS One. 2014; 9: e93114. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSafari F, Aminnejad R, Mohajerani SA, et al.: Intrathecal Dexmedetomidine and Fentanyl as Adjuvant to Bupivacaine on Duration of Spinal Block in Addicted Patients. Anesth. Pain Med. 2016; 6(1): e26714. PubMed Abstract \| Publisher Full Text\n\nParamasivan A, Lopez-Olivo MA, Foong TW, et al.: Intrathecal dexmedetomidine and postoperative pain: A systematic review and meta-analysis of randomized controlled trials. Eur. J. Pain. 2020; 24(7): 1215–1227. PubMed Abstract \| Publisher Full Text\n\nKrishna TM, Panda N, Batra Y, et al.: Combination of low doses of intrathecal ketamine and midazolam with bupivacaine improves postoperative analgesia in orthopedic surgery. Eur. J. Anaesthesiol. 2008; 25(4): 299–306. PubMed Abstract \| Publisher Full Text\n\nXia F, Chang X, Zhang Y, et al.: The effect of intrathecal dexmedetomidine on the dose requirement of hyperbaric bupivacaine in spinal anesthesia for caesarean section: a prospective, double-blinded, randomized study. BMC Anesthesiol. 2018; 18(1): 74. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYanshuai M, Shuang Q: Effects of dexmedetomidine in reducing postcesarean adverse reactions. Exp. Ther. Med. 2017; 14(3): 2036–2039.\n\nWu HH, Wang HT, Jin JJ, et al.: Does dexmedetomidine as a neuraxial adjuvant facilitate better anesthesia and analgesia? A systematic review and meta-analysis. PLoS One. 2014; 9: e93114. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSafari F, Aminnejad R, Mohajerani SA, et al.: Intrathecal Dexmedetomidine and Fentanyl as Adjuvant to Bupivacaine on Duration of Spinal Block in Addicted Patients. Anesth. Pain Med. 2016; 6(1): e26714. PubMed Abstract \| Publisher Full Text\n\nZhang Y, Shan Z, Kuang L, et al.: The effect of different doses of intrathecal dexmedetomidine on spinal anesthesia: A meta-analysis. Int. J. Clin. Exp. Med. 2019; 9(10): 18860–18886.\n\nHassan A, Abd-Allah Al-Kumite A, El-Deen A, et al.: Clinical Comparative Study Between Intrathecal Dexmedetomidine and Dexamethasone on Prolonging the Duration of Intrathecal Blockade in Lower Limb Orthopedic Surgery. Al-Azhar Med. J. 2021; 50(2): 1467–1478. Publisher Full Text\n\nGupta M, Gupta P, Singh DK: Effect of 3 different doses of intrathecal dexmedetomidine(2.5microg, 5microg, and 10 microg) on subarachnoid block characteristics: a prospective randomized double-blind dose-response trial. Pain Physician. 2016; 19: E411–E420. PubMed Abstract\n\nMoeen SM, Moeen AM: Intrathecal dexamethasone vs. meperidine for prevention of shivering during transurethral prostatectomy: a randomized controlled trial. Acta Anaesthesiol. Scand. 2017; 61(7): 749–757. PubMed Abstract \| Publisher Full Text\n\nNaziri F, Rabiee SM, Banihashem N, et al.: Comparative study of intrathecal dexamethasone with epinephrine as adjuvants to lidocaine n cesarean section. Zahedan. J. Res. Med. Sci. 2013; 15: 23–26.\n\nSakić L, Tonković D, Godan BJ, et al.: The influence of dexamethasone administration in spinal anesthesia for femur fracture on postoperative cognitive dysfunction. Period. Biol. 2015; 117(2): 281–285.\n\nSakić L, Tonković D, Šakić K: Dexamethasone- Intrathecal Minimizer of Simple Haemathologic Stress Biomarkers in Hip Fracture. Acta Clin. Croat. 2019; 58(Supplement 1): 9–16.\n\nBani-Hashem N, Hassan-Nasab B, Pour EA, et al.: Addition of intrathecal dexamethasone to bupivacaine for spinal anesthesia in orthopedic surgery. Saudi J. Anaesth. 2011; 5: 382–386. PubMed Abstract \| Publisher Full Text\n\nFayyaz MA, Khan AA, Ali RL: Comparison between effect of bupivacaine and bupivacaine with dexamethasone on duration of analgesia in spinal anesthesia for elective caesarean section. Pak. J. Med. Health Sci. 2015; 9: 979–982.\n\nDutta S, Gupta LK, Sharma V: Evaluation of Efficacy of Dexamethasone as an Adjuvant to Bupivacaine for Spinal Anesthesia in Abdominal Surgery: An institutional Study. Int. J. Med. Res. Prof. 2017; 3(2): 419–422." }	[ { "id": "306865", "date": "16 Aug 2024", "name": "Israel Kolawole", "expertise": [], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a good study with practical relevance to the practice of anaesthesia. The manuscript is well written with good grammatical style. The IASP definition of pain provided is outdated. It should be updated to the 2021 definition. The results were presented, and the discussion was exhaustive, coherent and focused; supported by relevant citations. I recommend approval of the manuscript for indexing\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "316139", "date": "03 Sep 2024", "name": "Michael Hofkamp", "expertise": [ "Reviewer Expertise Obstetric anethesia" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a prospective randomized controlled trial to compare postoperative pain control following spinal anesthesia for cesarean delivery between patients who received bupivacaine and dexamethasone and patients who received bupivacaine and dexmedetomidine.\nThe primary aim of the study is to compare postoperative analgesia between the combination of bupivacaine and dexamethasone and the combination of bupivacaine and dexmedetomidine. The variable that will measure analgesia efficacy is the time to first rescue analgesic and intravenous paracetamol will be the first rescue analgesic medication. It is not clear what event will prompt the first rescue analgesic. Is it a specific VAS score? Is it patient request?\nThe authors do not make a hypothesis of which combination will be better. It is not clear to me how they arrived at their sample size. Was there a previous study that informed their power analysis? If so, please cite.\nThe results of this study will not be generalizable to contemporary obstetric anesthesia practice because this study omits the use of a short acting opioid such as fentanyl and a longer acting opioid such as morphine.\nFurthermore, there are no results reported in this version of the manuscript and I consider this manuscript to be incomplete.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] } ]	1	https://f1000research.com/articles/13-300
https://f1000research.com/articles/12-1322/v1	12 Oct 23	{ "type": "Systematic Review", "title": "Acrylamide in starchy foods subjected to deep-frying, 20 years after its discovery (2002-2022): a patent review", "authors": [ "William Yesid Díaz-Ávila", "Sylvia María Villarreal-Archila", "Francisco Javier Castellanos-Galeano", "William Yesid Díaz-Ávila", "Sylvia María Villarreal-Archila" ], "abstract": "On the occasion of the 20th anniversary of the discovery of acrylamide in food, an analysis of patents related to the mitigation of this compound in food products obtained through immersion frying was carried out. For this purpose, a comprehensive search, compilation, and information analysis were conducted using free online databases such as Google Patents, Patenscope, and Lens. The search yielded a total of 79 patents within the considered time period (2002-2022). The countries with the highest number of granted patents were the United States, the European Union, and South Korea. The patents were classified into four main approaches: raw material modification (49%), application of pre-treatments (27%), process modification (16%), and measurement techniques (8%). Among the results, Frito-Lay, an American company, stands out as the food industry company with the highest number of granted patents, totaling 15. Based on this review, it is concluded that while a significant number of patents have been granted in recent years, there is still a lag in developing countries. Furthermore, more studies are needed to determine acrylamide in starchy food matrices subjected to immersion frying different from potatoes.", "keywords": [ "Asparaginase", "Maillard reaction", "Neoforms", "Snacks", "Starch" ], "content": "Introduction\n\nOne of the dehydration processes that has become culturally and economically important is immersion frying.1 In this process, food is immersed in hot oil, usually above the boiling point of water.2 Its use is widespread in domestic and industrial settings due to its ease of operation, which gives the fried product unique characteristics of flavor, odor, color, and texture, making it very attractive to consumers. These changes are due to various phenomena: at the physical level, moisture loss and oil gain occur; at the rheological level, starch gelatinization occurs; at the chemical level, protein denaturation and non-enzymatic browning reactions, such as the Maillard reaction, occur.3\n\nThis chain of reactions generates compounds responsible for fried products' characteristic aroma and color. However, multiple investigations have shown that toxic compounds can also be generated during this process, which depends on the nature of the raw material.4,5 For example, high levels of heterocyclic amines and polycyclic aromatic hydrocarbons can be found in protein-rich foods such as beef, pork, and chicken. In the case of foods rich in carbohydrates or starchy matrices, significant levels of furans, hydroxymethylfurfural, and acrylamide have been detected.6\n\nAcrylamide is a white, odorless, crystalline substance highly soluble in water (2155 g/L at 30°C). It has a molecular weight of 71.08 g/mol, a melting point of 84.5°C, and a boiling point of 125°C at 25 mmHg.7 This compound has been listed as potentially carcinogenic since 2002, when Swedish scientists discovered its presence in foods with high carbohydrate content and significant protein concentration, especially in roasting, baking, and frying processes where temperatures exceed 120°C.8 Elevated levels of acrylamide have been found in potato chips, with values ranging from 330 to 2300 μg/kg, in corn flakes between 120 and 180 μg/kg, and in breakfast cereals, from almost undetectable levels to 1400 μg/kg.9\n\nThe formation or synthesis of acrylamide in foods subjected to immersion frying might occur in different ways and by different means. The first is related to the interaction between a free amino acid, particularly asparagine, and a reducing sugar, such as glucose or fructose.10 The second way in which this formation can occur corresponds to the interaction of the same amino acid with carbonyl group donor compounds other than reducing sugars, such as sugar fragments and lipids.11 Finally, it can also occur due to acrolein, which originates from the thermooxidation of oils used in immersion frying.12,13 These synthesis pathways require high temperatures and long processing times.14\n\nResearch studies have identified that one of the parameters that can qualitatively indicate the presence of acrylamide in starchy matrices is related to the development of color and crust on the surface.15 For example, in bread and French fries, an inverse correlation has been observed between product brightness and acrylamide level, indicating that as frying or baking time increases, the product tends to become more opaque and, therefore, the acrylamide level increases. As for crust formation, a direct relationship has been observed, showing that as the frying stage progresses, the product loses moisture and the proteins on the surface denature, which increases the thickness of the crust and the level of acrylamide.16\n\nQuantitative measurements of acrylamide in fried foods have been determined using techniques such as liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)17 and gas chromatography coupled to mass spectrometry (GC-MS).18 The extraction, identification, and quantification methods of food acrylamide levels have been developed and validated, although these methods are specific for each product type.19 However, the high cost of the necessary equipment, materials, and reagents,20 and the need for established protocols in factories dedicated to manufacturing these products have led to poor control in the measurement of this compound.\n\nIn countries, especially developing countries, there is a gap in the knowledge and application of measures for detecting and reducing acrylamide in starch matrices. However, regulations and guidelines have been implemented in developed countries to address this problem. The European Food Safety Authority (EFSA) established EU Regulation 2017/2158, which provides recommendations and regulations to mitigate acrylamide levels in foods such as coffee, potato chips, breakfast cereals, cookies, bakery products, and baby food.21 Other countries have adopted the Codex Alimentarius Code on “practices for the reduction of acrylamide in food (CAC/RCP 67-2009),” which guides preventing and reducing acrylamide formation in potato and cereal products.22 In the United States, the Food and Drug Administration (FDA) presented guidance in 2016 that describes strategies to reduce acrylamide formation, which is monitored by the Center for Food Safety and Applied Nutrition (CFSAN).23\n\nIn the last 20 years, several ways to mitigate acrylamide in the food industry have been proposed. One of them consists of using raw materials with low acrylamide precursor content, such as reducing sugars and asparagine. Regarding process control, temperatures below 120 °C and short exposure times are recommended. In addition, feedstock pretreatments have been developed to reduce acrylamide precursor levels.24,25 These forms of mitigation have led to the filing of inventions using patents for intellectual protection. Consequently, a review of patents related to the identification, quantification, and regulation of acrylamide in starchy matrices subjected to immersion frying is presented below, which may be of interest to determine the main innovations in this field and to assess their applicability in factories with capital limitations to invest in the management of this toxic compound.\n\n\nMethods\n\nFor the development of this phase, a search was performed in three worldwide patent collection databases: Google Patents, Patenscope and Lens Org. A search equation was designed using keywords, synonyms, and Boolean connectors such as “OR”, “AND”, and “AND NOT”.\n\nThe primary technology investigated focused on immersion frying processes, so the term “frying” with related English words (“fried” or “fryer”) was entered into the databases using the “OR” connector. Then, the term “acrylamide” was added to search for studies on acrylamide monitoring and reduction, delimiting the search string with the “AND\" connector.\n\nSubsequently, the search was refined to include only studies related to snacks. We also excluded raw materials not classified as starchy matrices, such as meat and fish words, using the Boolean negation “AND NOT” in Patenscope or the symbol “-” in Google Patents and Lens Org.\n\nThe results of the searches were recorded in a logbook, and the information was filtered, eliminating duplicate patent documents, and discarding those irrelevant to the work's objective, as well as patents in the process of being granted or abandoned.\n\nAt this stage, the classification of patents was considered based on the country of origin where they have been granted, the year of concession, the most prominent applicant companies, and the different approaches that have been given to the area of acrylamide reduction and mitigation in the immersion frying process of starchy matrices.\n\nThe documents were analyzed after collecting and organizing the information in an Excel database. Visualization diagrams were used to identify the main trends in monitoring and reducing acrylamide, the most common mitigation technologies and approaches, and the most active research areas. The number of granted patents was also determined based on inventors and major factories dedicated to producing starchy matrix snacks. Additionally, an analysis was conducted to determine which patent offices have granted the most patents in this field.\n\nFinally, a critical review of the patent documents and associated annexes was performed, which provided detailed information on the inventions, methods, and technologies used to detect and reduce acrylamide in fried starchy matrix foods. This analysis provided a deeper understanding of specific advancements and proposed solutions in the field of immersion frying and starchy matrix snacks.\n\n\nResults and discussion\n\nThe preliminary patent search allowed for the identification of the leading technologies applied by the industry related to monitoring and reducing acrylamide in starchy matrices subjected to the immersion frying process. The search equations were implemented in different databases, and the results are summarized in the logbook designed in Table 1.\n\nPatenscope stood out as the database with the highest number of patents in this initial phase, with 282 documents. However, upon analyzing each document, it was observed that it includes the visualization of all patent families. The latter indicates that it refers to the same patent filed in different countries and years. On the other hand, Google Patents yielded 107 documents, and it was possible to refine the search by focusing on granted patents. Lens, meanwhile, provides additional information by allowing tracking of patents, such as the number of simple and extended families, and it displays the origin of the patent, marking the one designated as the priority. The number of obtained patents was refined by cross-referencing the information obtained from each of these search engines (see Figure 1). Patent documents unrelated to the study topic were excluded from the analysis.\n\nIt is important to note that patents were found whose claims and procedures did not address the immersion frying operation specifically, but rather the treatment of the raw material in these patents can be considered a preliminary stage to food frying. For example, in the patent developed by Haynes, Levine,26 a method for developing stabilized wheat flour is proposed. During the milling process, amino acids can be released, which react with reducing sugars in the raw material and generate acrylamide due to the generated abrasion and heat. In this patent, the inventors suggest adding a portion of the coarse fraction of the grain to the fine fraction of the endosperm to avoid the presence of grits. With this method, it is possible to retain high levels of antioxidants and vitamins while substantially reducing acrylamide formation. This flour can be used to produce turnovers or breaded foods subjected to immersion frying.\n\nIn 2002, Swedish researchers discovered that a potentially carcinogenic neurotoxic compound called acrylamide was formed during the thermal processing of food, mainly due to the interaction between reducing sugars and amino acids. Since then, numerous studies have been conducted to understand the effect of this compound on the body. Animal studies have shown that acrylamide causes DNA mutations, particularly in mice. However, definitive conclusions regarding its effects on humans have not been reached, and no minimum toxicity threshold has been established. It has been determined that the infant population is most exposed to acrylamide. For this reason, in countries belonging to the European Community, food factories have been requested to follow a series of recommendations and methodologies for monitoring and mitigating acrylamide in products such as potato snacks, coffee, cookies, and infant food.\n\nThe cartogram in Figure 2 details the leading patent offices that have granted patents on the control and mitigation of acrylamide. These include the United States (25.32%), the European Community (European Patent Office, Spain, and Austria) (21.52%), South Korea (18.99%), China (13.92%), and Australia (7.59%).\n\nThe wide range of fried products and their easy accessibility in fast-food restaurants have increased their global consumption worldwide. According to a recent survey, it is estimated that there will be a $208 billion increase in food sales in the United States across supermarkets, restaurants, fast-food establishments, and other retail food outlets by 2020.27\n\nIn a globalized environment where competitiveness and business growth are based on entering new markets, companies must comply with the regulations issued by each target country for their diversification. That is why in countries such as China, South Korea, and Australia, among others, factories dedicated to snack production have shown interest in developing technologies to ensure that the fried products they market meet the highest quality standards, including compliance with the acrylamide levels established by European regulations.\n\nFigure 3 shows the number of patents issued yearly, revealing a growing trend in intellectual property protection for technologies and procedures to control and mitigate acrylamide in fried foods. Although the high level of acrylamide was discovered in 2002, the first patent related to this topic was granted in 2004. The European food and beverage industry, in collaboration with the European Commission, national authorities, and the scientific community at large, has invested significant resources in researching the carcinogenicity of acrylamide, aiming to understand its formation better and develop tools and techniques for its mitigation.\n\nDue to the lack of a single solution to reduce acrylamide levels in the wide variety of foods where it has been found, the food industry has created documents with technical guidelines and steps to follow, applicable in commercial settings. One of these initiatives is the “Acrylamide Toolbox” document, first published in 2005 and developed by the association FoodDrinkEurope, which compiles the most comprehensive knowledge on the formation and potential mitigation of acrylamide in various foods.28\n\nAnother key date in this timeline was the formulation of European Union Regulation EU 2017/2158.21 An increase in the granting of patents can be observed from 2016 onwards. This increase can be attributed to the companies' interest in complying with the regulation that came into effect. The introduction of science and technology became fundamental pillars in this transformation process as companies sought to align with the established requirements.\n\nThe International Patent Classification (IPC), later reformed as IPCR, is based on the international multilateral treaty known as the Strasbourg Agreement, administered by the World Intellectual Property Organization (WIPO). Currently, 64 countries are party to this agreement. However, more than 100 industrial property offices, four regional offices, and the WIPO International Bureau use the IPCR under the Patent Cooperation Treaty (PCT) (OEPM, 2023). The IPCR classifies technology into eight sections that contain approximately 80,000 subdivisions. Each subdivision is represented by a symbol composed of Arabic numerals and letters of the Latin alphabet.29 In this review, an analysis of patents was conducted, and a word cloud was generated, as summarized in Figure 4, with the main classification codes according to the IPCR, grouping patents according to the type of product and technology being implemented.\n\nWhen examining the different classifications established in IPCR,30 it can be observed that most of the patents shown in Figure 4 belong to the group of food or food products and their treatment (A23). Specific patents related to types of foods and processes can be observed within this subdivision. For the group of roasted or fried products, such as snacks or potato chips (A23L19/18), 78 patents have been assigned. For treatments involving removing unwanted matter, such as deodorization or detoxification (A23L5/20), 51 patents have been included. Additionally, 50 patents have been assigned to general methods of cooking foods, such as roasting or frying (A23L5/10). Furthermore, 41 patents on food products with potatoes as raw materials (A23L19/12) have been identified. In addition to these categories, a group of patents classified under group C, corresponding to the field of chemistry and metallurgy, can be observed. In this case, 18 patents related to the use of enzymes, such as asparaginase (C12N9/82), have been included.\n\nThe formation of acrylamide in starchy matrices is greatly influenced by the levels of its precursors, such as reducing sugars and asparagine. These precursors vary widely among plant varieties due to specific characteristics of each variety that regulate their biosynthesis, as well as factors such as soil, composition, climate, fertilizers, and storage conditions. Other factors that affect acrylamide formation are related to the recipe used (dilution and piece size, acidity), processing strategies (addition of exogenous additives, temperature, and humidity, pre-treatment), and preparation for consumption (baking, frying).31\n\nBased on these factors, various mitigation and inhibition strategies have been proposed to reduce acrylamide in model systems and real foods. According to the compilation of patents, four main thematic areas have been identified in which acrylamide monitoring and mitigation measures can be classified: raw material modification, pre-treatment application, process modification, and measurement techniques. Figure 5 presents the percentage distribution of the acrylamide monitoring and mitigation fields.\n\nRaw material modification\n\nIt is evident that the highest percentage of patents related to acrylamide mitigation focuses on raw material modification (49%). Among the measures applied in this area, reducing precursors such as asparagine9,32–42 and reducing sugars10,43,44 are prominent. Inventors such as Budolfsen, Jensen25 have proposed the simultaneous addition of asparaginases and enzymes capable of reacting with reducing sugars, such as oxidoreductases. These enzymes can be oxidases or dehydrogenases that react with glucose and maltose as substrates. The oxidase can be a glucose oxidase, a pyranose oxidase, a hexose oxidase, a galactose oxidase (EC 1.1.3.9), or a carbohydrate oxidase that exhibits higher activity on maltose than glucose. The concentrations and preparation of these enzymes to add them to the raw material are detailed in the claims of these patents.\n\nFrom another perspective, inventors like Bhaskar and Topor45 have considered the effect that enzyme application can have on consumer acceptance. To address this, they proposed the usage of raw materials with low native reducing sugar content (approximately 0.5%) and the application of a pre-treatment, such as blanching, to leach out these sugars. Subsequently, they add dextrose in an amount not exceeding 1%. This additive is low in reducing sugars and facilitates the Maillard reaction to achieve desired characteristics in the fried product with reduced acrylamide levels. Previously, Kim, Park46 and Oku, Kubota47 also utilized other sugar sources, such as trehalose, which maintains sensory characteristics of fried products with a significant decrease in formed acrylamide. During the development of a patented method to prevent acrylamide formation, Plank, Lewandowski48 found that adding cyclodextrins (alpha, beta, and/or gamma and/or combinations thereof) to a food product or intermediate food can capture the amino acid asparagine through hydrophobic binding of the cyclodextrin, thereby preventing its reaction with a reducing end. Alternatively, cyclodextrin can sequester glucose or other small reducing sugars, avoiding interaction with free asparagine. The result is a reduction in acrylamide levels in the product.\n\nAmong other notable measures in raw material modification, the addition of natural antioxidants,2,6,49–55 cationic salts,56–58 vitamins,59,60 organic acids,8 amino acids,4,61 and thiol sources such as N-acetyl-cysteine, dithiothreitol, casein, and combinations thereof62 are highlighted. Vegetable oils are used as a heating medium in immersion frying processes. However, they are also considered part of the raw materials for fried products, as a portion of the oil is incorporated during the process. It is important for the oil to meet stability requirements and have adequate heat transfer properties, considering that its stability plays a significant role in acrylamide generation. Cao, Green63 patented the use of oils with a high oleic acid content by genetically modifying safflower oilseed. The resulting oil exhibits good thermal resistance and provides high heat transfer rates, allowing for the production of crispy products with a satisfactory level of safety.\n\nPre-treatment application\n\nThe second line of importance corresponds to applying pre-treatments in starchy foods subjected to immersion frying, accounting for 27% of the results (Figure 5). These pre-treatments include drying,64–66 blanching,67,68 electric pulses,69 electroporation,70 and others.3,71–78 For example, inventors like Kim, Jeong79 have patented the impregnation of amino acids such as arginine, valine, proline, sodium chloride, citric acid, and vitamin C, along with prior blanching and pre-frying treatments, for the production of potato snacks. On the other hand, Boudreaux, Desai80 focus on a method to leach acrylamide precursors using an extract deficient in the precursors, proposing the leaching of asparagine and untreated potato starch with a potato extract lacking asparagine. Additionally, Barry, Burnham81 and Sahagian82 suggest that blanching can enhance the action of enzymes and the impregnation of salts and amino acids that compete with asparagine in the process of reducing acrylamide precursors. Moreover, Somsen and De Waele24 point out that during blanching, in addition to leaching reducing sugars present in the raw materials, vitamins and minerals can also be lost, affecting the nutritional value, color, and flavor of the final fried products. Therefore, they propose performing consecutive washes with the blanching water and adding enzymes such as mannitol dehydrogenase and/or glucose-fructose oxidoreductase. This technique is known as “active blanching” and allows for removing acrylamide precursors and restoring minerals and vitamins lost during heating.\n\nProcess modification\n\nMachinery and processing techniques are integral components in snack production, whether in domestic kitchens, commercial establishments, artisanal industries, or large-scale production units. These systems can vary in their level of sophistication, ranging from simple manual methods to automated plants capable of producing from a few kilograms to several tons of products per day.83\n\nRegarding modifications in the immersion frying process (16%), patents have been developed as a protective measure. One of these modifications is vacuum frying,84,85 in which the system's pressure is adjusted, typically to pressures below atmospheric pressure. This results in a decrease in the boiling temperature of the water contained in the food, reducing the immersion time of the food in the oil, and decreasing the formation of acrylamide compared to frying under ambient conditions. However, it is noted that this technology may harm other quality attributes, such as the color and texture of the fried products.\n\nTo address this issue, Liu, Zhang86 patented the use of a complementary color fixative in the vacuum frying process. This color fixative consists of a vacuum impregnator that coats the surface of the raw materials with Tartary buckwheat, gum Arabic, and L-tryptophan. The latter allows for the attainment of desirable sensory characteristics of fried products with reduced acrylamide levels. On the other hand, system pressures above atmospheric pressure have also been implemented. Johnson, Khan87 designed an immersion frying apparatus that operates at pressures higher than atmospheric pressure, achieving low-oil-content potato snacks with a crispy texture. Their experiments obtained acrylamide levels below industry-acceptable standards and suggested that variations and modifications to the invention could be made without departing from its scope.\n\nIn addition to modifications in frying processes, patents have been developed that focus on improving the equipment used in the process,1,88–93 aiming to increase thermal efficiency and ensure high standards of quality and safety in fried products. Among these inventions, the continuous frying system designed by Song, Kim14 stands out, which utilizes a heating system and automatically controlled conveyor belts to regulate oil immersion temperatures and times, resulting in products with low acrylamide levels.\n\nAnother difficulty raised in immersion frying equipment is related to removing impurities generated during operation, which, due to reheating processes, can result in the formation of a significant amount of acrylamide that later migrates to the food. Kakita, Kojima94 proposed a solution to this problem, especially in continuous frying equipment. They patented an adhesive cleaner that allows for the removal of particulate matter embedded in the conveyor belts. These patents include detailed plans and specifications of each of the components that make up the system, and their protection allows for replication only with the authorization of the inventors.\n\nMeasurements techniques\n\nMeasurement techniques for acrylamide have played a crucial role in implementing effective mitigation measures in industries, accounting for 8% of the patents found. Some approaches have utilized traditional direct measurement methods for acrylamide,95 while other researchers have patented faster methodologies for real-time measurements.96,97 Furthermore, measurements of other quality parameters have been linked to the acrylamide content in fried products. In the patent by Cantley, Desai,98 intervention in the peeling and selection process of potato snacks based on coloration is proposed. This invention aims to achieve a crispy product through immersion frying, with an oil temperature between 146°C and 152°C, low moisture content (1.4%-2.0%), and removal of skins between 85% and 95%. The measurement of the color of the fried product is associated with the acrylamide content, which should be below 1000 ppb. This method has also been used to measure other quality characteristics of fried products, such as oil content.99 Among the techniques developed for indirectly monitoring acrylamide, the patent developed by Hao, Liang,100 stands out. They patented a method for measuring acidity in correlation with the level of polar compounds (PC) in the oils used in the immersion frying processes. There is a relationship between the formation of secondary compounds from lipid thermooxidation and acrylamide generation. Although it is not a direct method for detecting the level of acrylamide in fried foods, this technique can determine the point at which the oil is still considered suitable for use (PC≤27%), ensuring that the heating medium will not contribute to the formation of the toxic compound in the product.\n\nThe industry seeks to adapt promptly to changes in consumer preferences, which involves developing products that demonstrate innovation and meet consumer expectations regarding functional or healthy snacks that offer greater nutritional value without compromising the characteristic taste and convenience.101 In this context, the granting of patents related to controlling risks associated with immersion frying, particularly the regulation, and mitigation of acrylamide, can indicate these companies' commitment to producing nutritious and safe snacks. In Figure 6, patent applicants have been grouped into six categories based on their corporate identity and company description, who have filed patents related to the control and mitigation of acrylamide in the last 20 years.\n\nFirstly, the food company sector (53%) is the most relevant group. Among these companies, Frito-Lay has associated 15 patents in the past 20 years, attributed to its parent company in the United States (Frito-Lay North America Inc.) and its subsidiary in Europe (Frito-Lay Trading Co GmbH). This company is part of the PepsiCo business group and produces some of the most popular and high-quality snacks in the United States and Canada, including Lay's and Ruffles potato chips, Doritos tortilla chips, Cheetos cheese-flavored snacks, Tostitos tortilla chips, Santitas tortilla chips, Sun Chips multigrain chips, and Fritos corn chips. Another relevant company is Procter & Gamble (P&G), with three patents. However, after selling Pringles to the Kellogg Company, P&G discontinued its product line, which included food and beverages. In Europe, snack factories such as Intersnack and Lorenz Snack-World from Germany are notable, as well as Molino Nicoli, an Italian producer offering gluten-free, allergen-free, non-genetically modified organisms (GMO), and organic snacks, breakfast cereals, and cereal bars. Leng-D'OR, a Spanish multinational dedicated to producing pellet-type snacks, is also prominent. In Asia, companies like Hoori Co., Ltd., specializing in manufacturing spiral-shaped potato snacks (\"twist\"), Nongshim, the largest producer of instant noodles and snacks in South Korea, Yamazaki Baking, the second-largest baking corporation in the world, and Xi'an Angel Food Co Ltd, a Chinese company that produces and distributes cakes, bread, mooncakes, among others, are noteworthy.\n\nSecondly, factories and laboratories that produce chemicals or food ingredients (18%) are notable. Novozymes, a global biotechnology company based in Bagsværd, Denmark, stands out with four patents filed. Their main focus is on the use of enzymes and genetic improvement of enzymes, serving as suppliers to food factories. Zeracryl is a small Norwegian company that has developed a method to reduce the formation of the carcinogenic compound acrylamide during the industrial production of potato chips, either by using lactic acid bacteria or directly utilizing the metabolite. Emsland Group is an international German company that manufactures innovative products based on plant-based raw materials for the processing industry. They also offer a wide range of dried potato products under the brand “Mecklenburger Küche” for food retailers. Hayashibara Biochemical Laboratories Co Ltd develops, manufactures, and sells food ingredients, pharmaceuticals, cosmetics, dietary supplements, functional colorants, enzymes, and phospholipids.\n\nIn this analysis, nine individual inventors (11%) were also identified, who filed their patents as natural persons. Among them, inventors like Grune and Talarico,97 designed a device and method for the rapid and reliable detection and determination of acrylamide concentration in food, as well as its prevention. Upon reviewing the impact of this patent, it was found that it has been cited 24 times in the design of other patents, demonstrating its technological relevance. Jeong59 established a method for cooking potatoes with uniform holes to improve heat transfer to the interior and prevent the formation of harmful compounds. On the other hand, Lyutikov78 designed a method for obtaining crispy cookies through the process of immersion frying, mixing different types of flour to achieve better organoleptic characteristics of the product. These inventions and others in the same group of patents2,51,54,66,84,90 are mainly equipment and methodologies designed at a pilot scale in some cases scalable to an industrial level and do not require a large number of resources for their production.\n\nAccording to Figure 6, universities and research institutes also play an important role in controlling and mitigating acrylamide in food (8%). In this aspect, the collaboration between universities and the food industry is highlighted, where the Industrial-Academic Cooperation Foundation of Konkuk University and the University-Industry Cooperation Foundation of Dankook University are key pillars for industrial development in their respective countries. The latter is reflected in patenting acrylamide mitigation mechanisms applicable to fried products. Additionally, the Institute of Food Science and Technology of the Chinese Academy of Agricultural Sciences (CAAS) and the Agrarian Technological Institute of Castilla and León (Itacyl) are notable organizations in comprehensive agronomic research, responsible for conducting basic and applied research activities, as well as developing new technologies with impacts in agriculture.\n\nIn addition to universities and research institutes, some government-associated organizations (4%) and companies dedicated to manufacturing equipment and utensils (4%) have also been involved in designing inventions for acrylamide control. The Commonwealth Scientific and Industrial Research Organisation (CSIRO) of Australia has obtained a patent related to the control of oleic acids in oils, which helps extend their shelf life and prevent the formation of harmful compounds during frying processes.63 Other government entities, such as the Korea Food Research Institute (KFRI), the Shanghai Chongming District Food and Drug Safety Committee Office, and the Korea Food Industry Cluster Promotion Agency, have also obtained patents related to acrylamide control. Regarding companies dedicated to manufacturing equipment and utensils, companies such as Nitoms, Semyung Total Co., Ltd., Lishui Yifanjia Mould Technology Co Ltd, and Chongqing Chengyue Food Co have obtained patents for designing more efficient equipment for producing safe fried products. Furthermore, the participation of inventors associated with the business environment in protecting their inventions is noteworthy (Figure 7). Among the key inventors are Jamshid Ashourian, president and founder of Jimmyash Llc, and Michael Grant Topor, who have obtained 14 patents each. Colin J. Burnham, who has collaborated with the snack factory Fritolay, has patented 11 inventions. Dr. Thomas Eidenberger from the University of Applied Sciences Upper Austria, Joseph Ponnattu, Laurie Keeler, Jingang Shi, Weiyao Shi, and Xin Shi have each distinguished themselves with ten patents in the last 20 years.\n\n\nConclusions\n\nThe study of patented technologies, treatments, and procedures for controlling and regulating acrylamide over the last 20 years has revealed that countries with established regulations in acrylamide generation in fried products have a higher number of granted patents. Additionally, there is a lag in the food industry of developing countries, where a lack of innovation is evident due to the scarce or nonexistent number of patents in the field of acrylamide mitigation.\n\nThe publication of EU Regulation 2017/2158 is considered an important date, as it has led to an increase in the trend of the number of granted patents during the study period. The classification conducted according to IPCR revealed that most patents (78) were related to fried products or snacks, demonstrating the effectiveness of the search equation used in different databases. The analysis of the various stages in which intervention can be made in the immersion frying process allowed for the identification that inventors have primarily focused their efforts on intervention in starchy raw materials, either through the addition of enzymes, antioxidants, or other compounds (49%), or through the implementation of pre-treatments such as drying, blanching, and electric pulses, among others (27%).\n\nVacuum frying, initially considered an alternative to atmospheric frying to obtain low-oil-content products, has also proven to be a viable technology for producing snacks with low acrylamide content. Fried product manufacturers have focused on automating their processes, patenting increasingly sophisticated equipment that allows for controlling variables such as temperature, pressure, and immersion time of the food in the oil. While academia has developed reliable measurement techniques, such as gas chromatography coupled with mass spectrometry, large companies have shown interest in developing faster measurement methods, either through direct measurement, the use of biosensors, or the evaluation of quality parameters that correlate with acrylamide levels, such as surface color. Among the leading factories that have protected inventions related to acrylamide control, Frito-Lay stands out, contributing to its global consolidation by complying with regulatory requirements in each country where it operates and meeting consumer demands. In general, it is concluded that although snack food factories have taken measures for acrylamide control and reduction, further advancements in this field are still required. Despite the numerous studies related to potatoes, it is necessary to determine the effectiveness of these measures in other starchy matrices.\n\nOn the other hand, integrating the analysis of patent applications is recommended, as they mark future trends in acrylamide mitigation measures. An increase in the number of applications can indicate a strengthening of technological development driven by market-oriented approaches based on new technologies. Lastly, a decrease in the number of applications may signal a shift in research and development priorities or resource limitations, such as the availability of development personnel and the costs associated with acquiring intellectual property. By predicting and understanding the background of these trends, it is possible to envision future products, technological plans, and business strategies in the field of acrylamide control and mitigation.", "appendix": "Data availability\n\nResearchgate: Acrylamide Patent Analysis Database, https://doi.org/10.13140/RG.2.2.25415.47521. 102\n\nThis project contains the following underlying data:\n\n• Acrylamide Patent Analysis Database.xlsx (Article analysis database: Acrylamide in starchy foods subjected to deep-frying, 20 years after its discovery (2002-2022): A patent review).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nResearchGate: PRISMA checklist for “Acrylamide in starchy foods subjected to deep-frying, 20 years after its discovery (2002-2022): A patent review”, https://doi.org/10.13140/RG.2.2.33541.93927. 103\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nMachida N, Shigeru Y, Takaaki H: Fly processing equipment. Patent no. 6999008. Japan.2022; p. 1–12.\n\nPark H-j: Method for producing vacuum-fried snack with improved quality and reduced oil content. Patent no. 102071258. South Korea.2020; p. 1–9.\n\nLawton SJ, Levine L, Godfroid RA, et al.: Cooking foods. Patent no. 3573467. European Patent Office.2020; p. 1–34.\n\nKim J-H, Park S-H, Kang W-S, et al.: Snack having lower acrylamide and method for preparation thereof. Patent no. 100525178. South Korea.2005; p. 1–10.\n\nElder VA, Fulcher JG, Leung HK-H, et al.: Method for reducing acrylamide formation. Patent no. 2618225. Canada.2011; p. 1–93.\n\nSakaue K, Morimoto T, Senda A, et al.: Acrylamide production inhibitor. Patent no. 4142456. Japan.2008; p. 1–14.\n\nAnand A, Kota SK, Verma R: Method for recovering and treating water from a deep fryer bowl. Patent no. 2759402. Spain.2021; p. 1–19.\n\nBaardseth P, Blom H, Enersen G, et al.: Reduction of acrylamide formation. Patent no. 3641561. European Patent Office.2022; p. 1–52.\n\nElder VA, Fulcher JG, Leung HK-H, et al.: Method for reducing acrylamide formation. Patent no. 2010100599. Australia.2010; p. 1–101.\n\nKim M-S, Lee Y-S, Lee J-J, et al.: Method for manufacturing of reduced acrylamide starchy processed foods. Patent no. 101772282. South Korea.2017; p. 1–14.\n\nBachir N, Haddarah A, Sepulcre F, et al.: Formation, Mitigation, and Detection of Acrylamide in Foods. Food Anal. Methods. 2022; 15: 1736–1747. Publisher Full Text\n\nQuan W, Li Y, Jiao Y, et al.: Simultaneous generation of acrylamide, β-carboline heterocyclic amines and advanced glycation ends products in an aqueous Maillard reaction model system. Food Chem. 2020; 332: 127387. PubMed Abstract \| Publisher Full Text\n\nUdomkun P, Innawong B, Masso C, et al.: Effects of pressure and temperature on the physico-chemical properties and acrylamide formation of starchy banana chips during the post-frying centrifuge step. Food Measure. 2021; 15: 5637–5647. Publisher Full Text\n\nSong H-H, Kim D, Dodan H-G, et al.: Apparatus for producing potato snack and method thereof. Patent no. 102105249. South Korea.2020; p. 1–13.\n\nMahendran R, Palanivel J, Varadarajan E: Influence of Processing Parameters and PYTHON Based Image Analysis for Quantification of Carcinogenic Acrylamide in Potato Chips. Chemistry Africa. 2021; 4: 669–675. Publisher Full Text\n\nKumari A, Bhattacharya B, Agarwal T, et al.: Integrated approach towards acrylamide reduction in potato-based snacks: A critical review. Food Res. Int. 2022; 156: 111172. Publisher Full Text\n\nGoerke K, Ruenz M, Lampen A, et al.: Biomonitoring of nutritional acrylamide intake by consumers without dietary preferences as compared to vegans. Arch. Toxicol. 2019; 93: 987–996. PubMed Abstract \| Publisher Full Text\n\nKamankesh M, Nematollahi A, Mohammadi A, et al.: Investigation of Composition, Temperature, and Heating Time in the Formation of Acrylamide in Snack: Central Composite Design Optimization and Microextraction Coupled with Gas Chromatography-Mass Spectrometry. Food Anal. Methods. 2021; 14: 44–53. Publisher Full Text\n\nYuan Y, Chen F: Acrylamide.Wang S, editor. Chemical Hazards in Thermally-Processed Foods. Singapore: Springer Singapore; 2019; p. 47–85.\n\nWongthanyakram J, Kheamphet P, Masawat P: Fluorescence Determination of Acrylamide in Snack, Seasoning, and Refreshment Food Samples with an iOS Gadget–Based Digital Imaging Colorimeter. Food Anal. Methods. 2020; 13: 2290–2300. Publisher Full Text\n\nEFSA: Commission Regulation (EU) 2017/2158: Mitigation measures and benchmark levels for the reduction of the presence of acrylamide in food. France2017. 21. Reference Source\n\nFAO/WHO: Code of practice for the reduction of acrylamide in foods. Netherlands.2009. [Accessed 2023, March]. Reference Source\n\nFDA: Guidance for industry acrylamide in foods. USA2016. [Accessed March, 2023]. Reference Source\n\nSomsen DJ, De Waele ET: Selective withdrawal of reducing sugars and/or asparagine during blanching. Patent no. 1713351. European Patent Office.2009; p. 1–22.\n\nBudolfsen G, Jensen MT, Heldt-Hansen HP, et al.: Method of preparing a heat-treated product. Patent no. 8859023. USA.2014; p. 1–25.\n\nHaynes L, Levine H, Slade L, et al.: Production of stabilized whole grain wheat flour and products thereof. Patent no. 8133527. USA.2012; p. 1–42.\n\nPankaj SK, Keener KM: A review and research trends in alternate frying technologies. Curr. Opin. Food Sci. 2017; 16: 74–79. Publisher Full Text\n\nFoodDrinkEurope: Acrylamide toolbox. Bruselas: BEL; 2019. [Accessed March, 2023]. Reference Source\n\nOMPI: Reseña del Arreglo de Estrasburgo relativo a la Clasificación Internacional de Patentes (1971). Strasbourg, France2016. [Accessed March, 2023]. Reference Source\n\nOMPI: IPC Publication (International Patent Classification). Strasbourg, France2023. [Accessed March, 2023]. Reference Source\n\nOrsák M, Kotíková Z, Podhorecká K, et al.: Acrylamide formation in red-, purple- and yellow-fleshed potatoes by frying and baking. J. Food Compos. Anal. 2022; 110: 104529. Publisher Full Text\n\nMatsui T, Friis EP, Yamagishi A: Asparaginases. Patent no. 7871806. USA.2011; p. 1–37.\n\nHendriksen HV, Ernst S, Barfoed M: Stabilization of asparaginase. Patent no. 102256497. China.2014; p. 1–24.\n\nMatsui T, Tomiki A, Svendsen A, et al.: Thermostable asparaginase variants and polynucleotides encoding same. Patent no. 10472617. USA.2019; p. 1–54.\n\nBindzus W, Lagrange J: Method for reducing acrylamide. Patent no. 2009301043. Australia.2015; p. 1–19.\n\nAnderson KS, Boudreaux ER, Emerson DB, et al.: Method and system for the direct injection of asparaginase into a food process. Patent no. 9095145. USA.2015; p. 1–14.\n\nGreiner-Stoeffele T, Struhalla M: Heat stable asparaginase for reducing acrylamide in food stuffs or stimulants. Patent no. 9723854. USA.2017; p. 1–22.\n\nTurgeon ZJ, Swanson JM, Dahabieh MS, et al.: Development of an asparagine-reducing yeast by adaptive evolution and uses thereof to reduce acrylamide formation. Patent no. 11051535. USA.2021; p. 1–45.\n\nBerends P, Rabe S, Berger RG, et al.: Basidiomycetes asparaginase. Patent no. 2593473. European Patent Office.2016; p. 1–36.\n\nZyzak DV, Sanders RA, Stojanovic M, et al.: Method for reducing acrylamide in foods, foods having reduced levels of acrylamide and article of commerce. Patent no. 7867529. USA.2011; p. 1–18.\n\nElder VA, Koh CJ, Henson JK: Method for increasing asparaginase activity in a solution. Patent no. 2187764. European Patent Office.2011; p. 1–28.\n\nCorrigan PJ: Methods for reducing asparagine in a dough food component. Patent no. 1968389. European Patent Office.2018; p. 1–24.\n\nHowie JK, Lin P, Zyzak DV, et al.: Method for reducing acrylamide in foods comprising reducing the level of reducing sugars. Patent no. 1641353. European Patent Office.2009; p. 1–16.\n\nMathis L, Voytas DF, Zhang F, et al.: Potatoes with reduced cold-induced sweetening. Patent no. 2895909. Canada.2021; p. 1–35.\n\nBhaskar AR, Topor MG: Method for making a low-acrylamide content snack with desired organoleptical properties. Patent no. 9215886. USA.2015; p. 1–10.\n\nKim J-H, Park S-H, Kim H-J, et al.: Manufacturing method for snack reduced the content of acrylamides. Patent no. 100830680. South Korea.2008; p. 1–12.\n\nOku K, Kubota M, Fukuda S, et al.: Method of inhibiting acrylamide formation and use thereof. Patent no. 1568283. European Patent Office.2009; p. 1–35.\n\nPlank DW, Lewandowski DJ, Novak DJ: Method for preventing acrylamide formation in food products and food intermediates. Patent no. 7335386. USA.2008; p. 1–10.\n\nBykov DE, Makarova NV, Aleksashina SA: Berries and vegetable chips production method with increased antioxidant action. Patent no. 2738968. Russia.2020; p. 1–9.\n\nZhao H: Tea stuffing fried dough twist based on molecular embedding technology and making method thereof. Patent no. 109430348. China.2021; p. 1–10.\n\nPark J-S: A process for the preparation of Deep-fried Glass Noodles in Seaweed of potato and the Deep-fried Glass Noodles in Seaweed of potato prepared therefrom. Patent No. 101754320. South Korea.2017; p. 1–7.\n\nYoo Y-G, Yoo S-J: Method for reducing acrylamide formation in thermally processed foods. Patent no. 101775011. South Korea.2017; p. 1–5.\n\nKimura S, Tomita A, Himata K: Method for reduction of acrylamide content in heat treated processed food. Patent no. 2586320. European Patent Office.2016; p. 1–10.\n\nZhang Y, Wu X, Zhang Y, et al.: Method for using bamboo leaf extract as acrylamide inhibitor for heat processing food. Patent no. 8206766. USA.2012; p. 1–19.\n\nOrtiz DE, Zimmerman SP, Pinkston JD: Acrylamide control in cooked food products. Patent no. 10721949. USA.2020; p. 1–19.\n\nAlbero JC: Procedure to reduce the formation of acrilamide in foods obtained from vegetable pellets. Patent no. 2376117. Spain.2013; p. 1–15\n\nBrouwer JT, Boerboom F, Bontenbal EW: Food product comprising a mixture of calcium salts or a calcium double salt. Patent no. 1993379. European Patent Office.2010; p. 1–12.\n\nElder VA, Fulcher JG, Leung HK-H, et al.: Procedure to reduce the formation of acrylamide in thermically processed foods. Patent no. 2298721. Spain.2008; p. 1–13.\n\nJeong D-S: Processed potatoes and a manufacturing method thereof, and a recipe using the said potatoes for baked potatoes tasting french fries. Patent no. 101466126. South Korea.2014; p. 1–8.\n\nJung E-S: Method for manufacture of honeycomb-type potato and honeycomb-type potato thereby. Patent no. 101610909. South Korea.2016; p. 1–11.\n\nPlank DW, Novak DJ: Method for reducing acrylamide levels in food products and food products produced thereby. Patent no. 7264838. USA.2007; p. 1–8.\n\nElder VA: Method for enhancing acrylamide decomposition. Patent no. 2588004. Canada.2011; p. 1–73.\n\nCao S, Green A, Liu Q, et al.: High oleic acid oils. Patent no. 2013252489. Australia.2018; p. 1–352.\n\nHuang Z, Duan C, Guo X: Potato chip preparation method and potato chips. Patent no. 109588659. China.2022; p. 1–13.\n\nNicoli G, Nicoli S: Cereal based chip shaped snack. Patent no. 2010220277. Australia.2013; p. 1–17.\n\nSchwarzhans P: Method for producing a fat-free or low-fat snack products. Patent no. 412051. Austria.2004; p. 1–7.\n\nAshourian J, Keeler LJ, Smith DA: Methods of making snack food products and products made thereby. Patent no. 10542769. USA.2020; p. 1–24.\n\nWoll KL, Vette M: Food product made from plant parts containing starch, and method for the production of said food product. Patent no. 2888608. Canada.2021; p. 1–37.\n\nBhaskar AR, Ruegg RJ, Sullivan LS: Atmospherically fried crisps, equipment and method for making same. Patent no. 3417721. European Patent Office.2021; p. 1–16.\n\nUlrich B, Haferkamp R, Kern M: Removal of acrylamide and/or melanoidin-forming cell content. Patent no. 8206767. USA.2012; p. 1–12.\n\nChou H-T: Dough preparation method and potato chip preparation method. Patent no. 602513. Taiwan.2017; p. 1–22.\n\nBowes JR, Bailey RA, Herbert O: Method of making snack foods. Patent no. 2658983. Russia.2018; p. 1–12.\n\nOnishi A, Miyazaki Y, Tanaka M: Non-fried potato chips and method for manufacturing same. Patent no. 516209. Taiwan.2016; p. 1–17.\n\nSevenou OD: Reduced acrylamide snack product and method for the manufacture thereof. Patent no. 2520178. European Patent Office.2017; p. 1–11.\n\nRico D, Martín AB, Albertos I: Manufacturing procedure for a fruit and vegetable snack. Patent no. 2547262. Spain.2016; p. 1–8.\n\nSong Y-O, Hong S-H, Kim M-J, et al.: Method for preparing dried laver-bugak. Patent no. 101610723. South Korea.2016; p. 1–14.\n\nChoi H-D, Park Y-G, Choi I-W, et al.: Vacuum fried sweet potato snack and method thereof. Patent no. 101294312. South Korea.2013; p. 1–11.\n\nLyutikov AA: Method for producing of hardtacks. Patent no. 2260953. Russia.2005; p. 1–9.\n\nKim C-J, Jeong J-Y, Choi J-H, et al.: Method for manufacturing of reduced-acrylamide foods. Patent no. 101137982. South Korea.2012; p. 1–10.\n\nBoudreaux E, Desai PM, Elder VA, et al.: Method for reducing acrylamide formation in thermally processed foods. Patent no. 2124622. European Patent Office.2018; p. 1–39.\n\nBarry DL, Burnham CJ, Desai PM, et al.: Method for reducing acrylamide formation in thermally processed foods. Patent no. 8124160. USA.2012; p. 1–26.\n\nSahagian M: For composition and the method for surface modification of root vegetable products. Patent no. 101448412. China.2016; p. 1–18.\n\nBhattacharya S: Chapter 12 - Processes and machinery.Bhattacharya S, editor. Snack Foods. Mysore, IND: Academic Press; 2023; p. 321–382. Publisher Full Text\n\nShin H-S: Vaccum frying apparatus. Patent no. 101952885. South Korea.2019; p. 1–11.\n\nRüdiger J, Bernd W, Knut F, et al.: Method for the production of potato chips. Patent no. 2063720. European Patent Office.2010; p. 1–16.\n\nLiu W, Zhang H, Zhang N, et al.: Color fixative and application thereof in color potato chips. Patent no. 109770165. China.2022; p. 1–5.\n\nJohnson KR, Khan AN, Vandecasteele N: Frying method and apparatus. Patent no. 2014262263. Australia.2016; p. 1–19.\n\nZhang J: Convenient and environment-friendly processing equipment for crispy chips. Patent no. 212650364. China.2021; p. 1–7.\n\nZhong X: Special deoiling device of fruit vegetables do. Patent no. 211510474. China.2020; p. 1–10.\n\nTang Z: Energy-saving time-saving oil pot. Patent no. 210642174. China.2020; p. 1–15.\n\nLiu H: A kind of fried food processing device. Patent no. 209314712. China.2019; p. 1–7.\n\nBailey RA, Lawton SJ, Worth PD: Frying method and apparatus. Patent no. 10512362. USA.2019; p. 1–9.\n\nLee H-K: A cooking device. Patent no. 101773119. South Korea.2017; p. 1–17.\n\nKakita T, Kojima T, Suyama Y, et al.: Adhesive cleaner. Patent no. 102385102. South Korea.2022; p. 1–31.\n\nEdgington A, Williams L: Sample preparation method for analysis of acrylamide. Patent no. 9995663. USA.2018; p. 1–13.\n\nBourg-Jr WM: Method for real time measurement of acrylamide in a food product. Patent no. 8158175. USA.2012; p. 1–18.\n\nGrune GL, Talarico T: Devices and methods for the rapid, reliable detection and determination of acrylamide concentration in food substances and prevention of acrylamide formation in the same. Patent no. 8129133. USA.2012; p. 1–9.\n\nCantley CS, Desai PM, Michel E, et al.: Method for reducing acrylamide formation in thermally processed foods. Patent no. 2009257364. Australia.2012; p. 1–59.\n\nLiu Y, Ji X: Chips oil content detecting and screening device. Patent no. 203786022. China.2014; p. 1–5.\n\nHao D, Liang Y, Wu J, et al.: Whether reach the method in frying service life by acid value determination result judgement edible oil. Patent no. 107515284. China.2019; p. 1–14.\n\nChacón-Orduz G, Muñoz-Rincón A, Quiñonez-Mosquera GA: Descripción del mercado de los snacks saludables en Villavicencio, Meta. Revista Libre Empresa. 2017; 14: 33–45. Publisher Full Text\n\nDíaz-Ávila WY, Villarreal-Archila SM, Castellanos-Galeano FJ: Acrylamide Patent Analysis Database.xlsx. Dataset. ResearchGate. 2023.\n\nDíaz-Ávila WY, Villarreal-Archila SM, Castellanos-Galeano FJ: PRISMA checklist for Acrylamide in starchy foods subjected to deep-frying, 20 years after its discovery (2002-2022). A patent review. ResearchGate. PRISMA checklist.2023." }	[ { "id": "221641", "date": "18 Dec 2023", "name": "Traiphop Phahom", "expertise": [ "Reviewer Expertise Food processing and analysis." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript is well constructed. The content is academically sound and interesting for the production of deep-fried foods.\nHowever, there are some points that need to be considered. 1. The writing is required to be clear and concise because there are a number of compound and complex sentences used in this manuscript, some of which make the sentences unclear and less concise. 2. Misspellings are found in the manuscript so, the authors are required to check them. 3. Some references are required for the topic \"Applications and inventors\" (paragraphs 2,3,5 and 6). 4. The authors did not mention GC-MS analysis in the result section, but it appears in the conclusion part. Therefore, the authors are required to review and revise.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [ { "c_id": "11380", "date": "19 Jun 2024", "name": "William Yesid Díaz-Ávila", "role": "Author Response", "response": "Dear Ph.D. Traiphop Phahom, We appreciate your detailed comments and observations on our manuscript. Below, we address each of them: 1. The writing is required to be clear and concise because there are a number of compound and complex sentences used in this manuscript, some of which make the sentences unclear and less concise. Response: Regarding clarity and conciseness in writing, we have conducted a thorough review of the document to address this aspect. However, to further improve, we would appreciate it if you could point out the specific sections and paragraphs that you find confusing. We are fully prepared to make any necessary adjustments to enhance the readability of the manuscript. 2. Misspellings are found in the manuscript so, the authors are required to check them. Response: Concerning spelling errors, we have carried out a meticulous review of the document, focusing on correcting any potential mistakes. However, if you could indicate the specific paragraphs where you found such errors, it would assist us in ensuring their complete correction. 3. Some references are required for the topic \"Applications and inventors\" (paragraphs 2,3,5 and 6). Response: We have incorporated the relevant citations and bibliographic references into the mentioned paragraphs related to the topic \"Applications and inventors.\" We appreciate your observation, and we have taken the necessary steps to comply with this requirement. 4. The authors did not mention GC-MS analysis in the result section, but it appears in the conclusion part. Therefore, the authors are required to review and revise. Response: Regarding the omission of mentioning GC-MS analysis in the results section, we understand the importance of this consistency and have thoroughly reviewed both the conclusions and the results section. We have made the necessary modifications to ensure coherence and accuracy in presenting the measurement techniques. We deeply appreciate your comments and suggestions as they allow us to improve the quality and accuracy of our work. We remain available for any further observations or suggestions you may have. Sincerely, William Yesid Díaz Ávila" } ] }, { "id": "234854", "date": "14 Feb 2024", "name": "Owen M. McDougal", "expertise": [ "Reviewer Expertise Food chemistry - analysis of fried potato product for reducing sugars", "amino acids", "and acrylamide" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript is a good summary of the patents related to starchy foods, mainly potato products exposed to immersion frying. The content is well described and organized in terms of patents and the advancement of knowledge related to acrylamide in the past 20 years. Some notes:\nSome citations don’t match the references. Keywords include “neoforms”, which was not described or mentioned within the manuscript. The introduction mentions that toxic compounds can be generated during immersion frying, however, the authors only mention the dependency on the nature of the raw material when several other factors can generate the formation of acrylamide. There is no specific mention of the acrylamide limits determined by the EFSA, Codex Alimentarius, or FDA that can be used as a baseline for the patents mentioned in the results section. There is a sentence in the results section that mentions a prediction of the estimated increase in food sales that is outdated. Also, the manuscript mentions developing countries, so an amount that describes the consumption in those developing countries and that can be tied to the need for acrylamide monitoring would be helpful. In the classification section, a brief description of the classification group A21D8 would be useful. In the pre-treatment application and process modification section, there is a description for the application of vacuum frying, but not for drying, blanching, electric pulses, or electroporation related to the patents mentioned.\nThe measurement techniques section is very brief and is missing detection methods like Computer-based visualization, spectrophotometry, atomic absorption, fluorescence, NIR, Raman spectroscopy, to mention a few.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [ { "c_id": "11381", "date": "19 Jun 2024", "name": "William Yesid Díaz-Ávila", "role": "Author Response", "response": "Dear Dr. McDougal, I am pleased to greet you. Below, I respond to each of your observations: Some citations don’t match the references. Response: We have reviewed the document and verified the citations with the respective references. However, we have been unable to identify the mentioned errors. We would appreciate it if you could specifically indicate in which sections and paragraphs of the document you found such errors. 2. Keywords include “neoforms”, which was not described or mentioned within the manuscript. Response: We have changed the keyword \"neoforms\" to \"pre-treatment\", which is more frequent in the document. 3. The introduction mentions that toxic compounds can be generated during immersion frying, however, the authors only mention the dependency on the nature of the raw material when several other factors can generate the formation of acrylamide. Response: We have included in paragraph 2 of the introduction other factors that may influence the elevation of acrylamide levels in processed foods. 4. There is no specific mention of the acrylamide limits determined by the EFSA, Codex Alimentarius, or FDA that can be used as a baseline for the patents mentioned in the results section. Response: In the introduction, in paragraph 4, we have included some reference levels presented by the EFSA and FDA. 5. There is a sentence in the results section that mentions a prediction of the estimated increase in food sales that is outdated. Also, the manuscript mentions developing countries, so an amount that describes the consumption in those developing countries and that can be tied to the need for acrylamide monitoring would be helpful. Response: In the \"Country and year of grant\" section, we have modified paragraph 3 to include more updated figures on consumption and sales of snacks in recent years. 6. In the classification section, a brief description of the classification group A21D8 would be useful. Response: We have modified the second paragraph of the \"Classification and type of technology\" section to include a more detailed description of group A21D8. 7. In the pre-treatment application and process modification section, there is a description for the application of vacuum frying, but not for drying, blanching, electric pulses, or electroporation related to the patents mentioned. Response: We have modified the \"Pre-treatment application\" section to include the effect of electric pulse and drying pre-treatments on the reduction of acrylamide levels in fried products. Regarding blanching, a brief description had already been provided in that section previously. 8. The measurement techniques section is very brief and is missing detection methods like Computer-based visualization, spectrophotometry, atomic absorption, fluorescence, NIR, Raman spectroscopy, to mention a few. Response: We have expanded the section by providing a little more detail on patents related to acrylamide measurement techniques addressed in the database according to the search equation used. However, it is beyond the scope of this review to explain other methodologies different from those found in the related patents. This could be interesting in another review where a comparison could be made between measurement techniques validated in academia and those already implemented in the industry. We appreciate your collaboration and valuable contributions to improving our work. Sincerely, William Yesid Díaz Ávila" } ] }, { "id": "234853", "date": "14 Feb 2024", "name": "Maria Alessia Schouten", "expertise": [ "Reviewer Expertise Food technology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe aim of the introduction is to familiarise the reader with the challenges posed by the formation in starchy matrices during immersion frying. The introduction sets the stage for the subsequent examination of patents related to the identification, quantification and regulation of acrylamide and shows that the focus is on innovation and its applicability in factories with limited capital. The introduction is concise and sets the context for the examination of patents related to acrylamide in starchy matrices subjected to immersion frying. The stated aim is consistent with the subsequent sections and provides a clear and logical flow for the reader. The methods section accurately and clearly describes the systematic process of searching, collecting and analysing patent information related to acrylamide reduction in dip frying of starchy matrices. The methodology described is in line with best practice in patent searches and ensures a comprehensive and rigorous approach to data collection and analysis. The results and discussion illustrate the multi-faceted approach being taken globally to tackle acrylamide in fried starchy foods. The patents cover different stages of the food production process, which emphasises the importance of a comprehensive strategy. The collaboration between industry, research organisations and regulatory authorities underlines the commitment to food safety and quality. The findings provide valuable insights into the evolving landscape of acrylamide mitigation and offer a comprehensive understanding of technological advances and regulatory actions in the food industry over the past two decades. In summary, the conclusion provides a comprehensive review of the current state of acrylamide control technologies and draws attention to regulatory influences, global trends, industry practices and the potential for future innovation. It serves as a valuable resource for policymakers, industry professionals and researchers seeking to navigate the complex landscape of food safety and technology.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [ { "c_id": "11382", "date": "19 Jun 2024", "name": "William Yesid Díaz-Ávila", "role": "Author Response", "response": "Dear Maria Alessia Schouten We sincerely appreciate your detailed and constructive feedback on our work. We are pleased to hear that the introduction provides a solid foundation for understanding the challenges related to acrylamide formation in starchy matrices during immersion frying, and clearly outlines the focus of our study on innovation and its applicability in resource-limited industrial settings. Regarding the methods section, we are pleased that you found our description of the systematic process of searching, collecting, and analyzing patent information related to acrylamide reduction in fried starchy matrices to be accurate and clear, and in line with best practices in patent searches. We also appreciate your positive comments on the results and discussion. We agree that the results illustrate the multifaceted approach taken globally to address acrylamide in fried starchy foods, and highlight the importance of a comprehensive strategy covering different stages of the food production process. We also agree that the collaboration between industry, research organizations, and regulatory authorities demonstrates a strong commitment to food safety and quality. Finally, with regards to the conclusion, we value your recognition that it provides a comprehensive review of current acrylamide control technologies and highlights regulatory influence, global trends, industry practices, and the potential for future innovation. We agree that our conclusion can serve as a valuable resource for policymakers, industry professionals, and researchers interested in food safety and technology. We sincerely appreciate your comments and suggestions, which will undoubtedly enhance the quality and relevance of our work. We are committed to addressing all concerns raised and revising the manuscript in accordance with your recommendations. Best regards, William Yesid Díaz Ávila" } ] } ]	1	https://f1000research.com/articles/12-1322
https://f1000research.com/articles/13-297/v1	18 Apr 24	{ "type": "Research Article", "title": "Determinants of immediate postpartum long acting reversible contraceptive utilization among women who gave birth in public health facilities in northwest Ethiopia: unmatched case-control study design", "authors": [ "Getachew Asmare Adella", "Getiye Kibret Abtew", "Mihiret Tesfaw Gellaw", "Gizachew Ambaw Kassie", "Molalegn Mesele Gesese", "Endeshaw Chekol Abebe", "Misganaw Asmamaw Mengstie", "Mohammed Abdu Seid", "Sefineh Fenta Feleke", "Tadesse Asmamaw Dejenie", "Berihun Bantie", "Yenealem Solomon", "Melkamu Aderajew Zemene", "Anteneh Mengist Dessie", "Denekew Tenaw Anley", "Wubet Alebachew Bayih", "Natnael Amare Tesfa", "Natnael Atnafu Gebeyehu", "Getiye Kibret Abtew", "Mihiret Tesfaw Gellaw", "Gizachew Ambaw Kassie", "Molalegn Mesele Gesese", "Endeshaw Chekol Abebe", "Misganaw Asmamaw Mengstie", "Mohammed Abdu Seid", "Sefineh Fenta Feleke", "Tadesse Asmamaw Dejenie", "Berihun Bantie", "Yenealem Solomon", "Melkamu Aderajew Zemene", "Anteneh Mengist Dessie", "Denekew Tenaw Anley", "Wubet Alebachew Bayih", "Natnael Amare Tesfa", "Natnael Atnafu Gebeyehu" ], "abstract": "Background The aftermath of childbirth plays a vital role in addressing unmet family planning requirements and is instrumental in mitigating the risks associated with pregnancies that are closely spaced. Recognizing factors that indicate immediate postpartum utilization of long-acting reversible contraceptives is essential for crafting focused initiatives. This helps meet unaddressed family planning needs and contributes to the reduction of maternal and child mortality rates in the country. Therefore, this research aimed to pinpoint factors influencing the utilization of long-acting reversible contraceptives immediately after childbirth among women delivering in public health facilities in northwest Ethiopia.\n\nMethods A facility-based unmatched case-control study was carried out, involving 342 postpartum women (comprising 108 cases and 216 controls) who delivered in public health facilities in northwest Ethiopia. Data collection involved employing a structured interviewer-administered questionnaire, and binary logistic regression analysis was conducted. The statistically significant association between independent factors and the outcome variable was assessed using the adjusted odds ratio with a 95% confidence interval, considering a p-value less than 0.05.\n\nResult The educational status of women at secondary level and above (AOR=2.314, 95% CI=1.645-5.043), adherence to ANC follow-up (AOR=2.930, 95% CI=1.829-4.769), lack of desire to have a child (AOR=1.421, 95% CI=1.026-2.006), receiving counseling (AOR=3.029, 95% CI=2.085-5.988), and possessing knowledge (AOR=1.642, 95% CI=1.086-3.186) were identified as significantly correlated with immediate postpartum LARC utilization at p <0.05.\n\nConclusion In this investigation, the utilization of immediate postpartum long-acting reversible contraceptives (LARC) was significantly linked to women’s educational attainment, attendance at antenatal care (ANC), their desire for additional children, counseling, and knowledge about immediate postpartum LARC. To promote family planning in the postnatal phase, it is recommended to prioritize maternal education, offer comprehensive counseling and health education, and enhance adherence to targeted ANC services.", "keywords": [ "Long-acting reversible contraceptive", "postpartum", "immediate", "factors", "Ethiopia" ], "content": "Introduction\n\nMaternal health remains a prominent global concern due to the fact that pregnancy and childbirth are the leading causes of morbidity, mortality, and impairment among women of reproductive age.1 Worldwide, there were 121 million unintended pregnancies, with an annual rate of 64 per 1000 women.2 This prevalence is more pronounced in Sub-Saharan Africa (99 per 1000 pregnancies) and notably in Ethiopia (100 per 1000).3 The World Health Organization (WHO) recommends a minimum interpregnancy interval of two years.4 Brief intervals between births heighten the risk of health problems for both the mother and child, including preterm birth, low birth weight, small for gestational age, an elevated likelihood of chronic malnutrition, stunted growth, and child mortality.5,6 If a pregnancy occurs within six months of a preceding delivery, the risk of low birth weight and prematurity doubles, while children born within 24 months of a previous birth are 60% more likely to experience infant mortality compared to those born more than 24 months apart.7\n\nThe period following childbirth is pivotal for addressing unfulfilled family planning requirements and minimizing the likelihood of pregnancies occurring in quick succession.8 Fertility can resume as early as 45 days after birth for non-breastfeeding women,9,10 and it may occur before the return of menstruation in those who do not exclusively breastfeed.11 Employing family planning during the postpartum phase enables women to space their births by a minimum of 24 months, leading to a 30% reduction in maternal mortality and a 10% decrease in child mortality.12\n\nCounseling and provision of long-acting reversible contraception (LARC), encompassing intrauterine devices (IUDs) and subdermal implants, possess several attractive qualities, such as a high retention rate and enhanced protection against unintended pregnancy.13,14\n\nIn Sub-Saharan Africa, there is a persistent low utilization of postpartum contraception.15 DHS data from 21 low- and middle-income countries, gathered between 2005 and 2012, revealed that a substantial majority (95%) of women within 0-12 months postpartum expressed a desire to avoid pregnancy in the next 24 months, yet less than one-third (31%) were actively using any contraceptive method. Additionally, around half (61%) of postpartum women faced challenges in accessing family planning services.8,16 Despite this, there exists a notable unmet need for family planning during the postpartum period, ranging from 32 to 62% in low and middle-income countries.9,17,18\n\nDue to the limited acceptance of postpartum family planning (PPFP), the key factors influencing PPFP acceptance include the level of education, perinatal family planning, counseling, resumption of menstruation, breastfeeding status, return of sexual activity, concerns about side effects, and a perceived low risk of pregnancy.19\n\nNumerous investigations have revealed that socio-demographic factors, including women’s age, marital status, educational attainment, place of residence, and religious affiliation, influence the acceptance of long-acting reversible contraception (LARC) in diverse contexts.20–23 Additional studies have indicated that factors such as secondary and higher education, communication with the husband, return of menstruation, antenatal care (ANC) follow-up, awareness of modern family planning methods, and receiving family planning counseling during ANC are predictors of postpartum contraceptive utilization.24\n\nCountless investigations have additionally discovered reproductive health factors like fertility intention, parity, and desire for FP as influencers of LARC method uptake and contraceptive use in general. In plenty of other study results, the reproductive health contributing factors with LARC use were identified as parity, desired family size, women who gave birth prematurely, previous history of abortion, women who had ever experienced an unwanted pregnancy, and women who had visited a clinic in the previous year for FP services.25–29\n\nUp to now, research in Ethiopia has primarily examined the prevalence of postpartum family planning utilization, particularly intrauterine contraceptive devices (IUCD). The factors influencing immediate postpartum family planning utilization, specifically long-acting reversible contraceptives, remain inadequately understood across Ethiopia. The identification of predictors for immediate postpartum use of long-acting reversible contraceptives is crucial for the development of more targeted programs, addressing unmet family planning needs, and mitigating maternal and child mortality in the country. Consequently, the objective of this study aims to ascertain the determinants of immediate postpartum utilization of long-acting reversible contraceptives among women delivering in public health facilities in northwest Ethiopia.\n\n\nMethods\n\nThe research was carried out in the Kelela district of northwest Ethiopia between May 15 and July 10, 2022. Situated 565 km away from Addis Ababa, the capital city of Ethiopia, the district is home to a projected total population of 169,187 in 2022, with 82,902 (49%) being females. The reproductive age group comprises 19,067 women, and an estimated 823 women are expected to give birth each month. Within the district, there is one public hospital, 9 health centers, and 33 health posts. According to the Kelela district health office annual report for 2022, there are 10 public health facilities offering immediate postpartum long-acting contraceptive services.\n\nA facility-based unmatched case-control study design was conducted.\n\nSource population\n\nAll women in the postpartum period who delivered in the public health facilities of the Kelela district throughout the study duration.\n\nStudy population\n\nFor Cases: All women in the postpartum phase who gave birth in designated public facilities during the study timeframe and opted for a long-acting reversible contraceptive device within the initial 48 hours following vaginal delivery or after the expulsion of the placenta before uterine closure in the case of intra-cesarean deliveries.\n\nFor controls: All women in the postpartum period who delivered in the identical public health facilities but refrained from utilizing the postpartum long-acting reversible contraceptive device.\n\nInclusion criteria\n\nWomen in the postpartum phase who delivered through any method in the chosen public facilities were encompassed.\n\nExclusion criteria\n\nExclusion criteria for the study comprised women who delivered through any mode in designated public facilities but did not meet the World Health Organization’s medical eligibility criteria for the postpartum long-acting reversible contraceptive device during the investigation period.30\n\nThe sample size was calculated using the two population proportion formula in Epi Info software Version 7. The calculation took into account the following assumptions: 95% confidence interval, 80% power, a 1:2 ratio of cases to controls, counselled by a healthcare provider as the exposure variable, 26.4% of PPIUCD users and 43.2% of nonusers with exposure,31 and a 10% nonresponse rate as compensation for both groups. As a result, 342 postpartum women were included in the study (114 cases and 228 controls). Ten public health facilities in the study area provide immediate postpartum long-acting reversible contraception (LARC) services, with approximately six of them chosen using simple random sampling methods. The average monthly case flow was calculated using the number of immediate postpartum LARC utilisations per three months obtained from each selected public health facility’s quarterly report. Cases were identified by asking whether they used IUCD or implants after delivery and crosschecking their charts, and they were selected consecutively. Once cases were identified consecutively, two controls were chosen using simple random methods to increase the power of the study.\n\nTo gather data, a structured interviewer-administered questionnaire was utilized, adapted and refined from various literature sources.31–38 Prior to distribution, a panel of experts in the field assessed its content validity. Additionally, a 5% sample size test was conducted in the Legambo district, and modifications were made based on expert feedback and pretest results. The questionnaire’s reliability was assessed through a reliability analysis, revealing a Cronbach’s Alpha exceeding 0.7, indicating internal consistency in the responses. To ensure uniformity, it was initially crafted in English, translated into a local language, and then back-translated into English.\n\nThe survey consisted of sections covering socio-demographic details, obstetric and reproductive care elements, knowledge, attitudes, and family planning topics. Six diploma midwives were designated as data collectors, and two BSc midwives were appointed as supervisors. A two-day training session was conducted for both data collectors and supervisors to instruct them on questionnaire administration and collection procedures. Prior to data entry, a thorough check for completeness was carried out on the questionnaire.\n\nLong-acting reversible contraceptives are contraceptive options with durations of effectiveness spanning from 3 to 12 years (including intrauterine devices and implants), and fertility typically resumes shortly after their removal.\n\nImmediate postpartum long-acting reversible contraceptive (LARC) utilization refers to the practical application of long-acting reversible contraceptive devices (such as IUCD and implants) within the initial 48 hours after childbirth and before the discharge to home, irrespective of the mode of delivery.\n\nWomen who received counseling on immediate postpartum long-acting reversible contraception (LARC) are those mothers who were informed by healthcare providers about the advantages, potential side effects, or recommended duration of using immediate postpartum LARC during antenatal care (ANC), the latent phase of labor, and/or the immediate postnatal period.\n\nKnowledge of immediate postpartum long-acting reversible contraception (LARC) was determined by adding the responses to all seven knowledge-related questions regarding immediate postpartum LARC. Each correct answer was assigned a score of “1,” while an incorrect answer received a score of “0.” Consequently, participants who achieved a score equal to or higher than the mean value of the cumulative knowledge assessment questions were categorized as having good knowledge, whereas those who scored below the mean were considered to have poor knowledge.\n\nThe attitude-related inquiries were evaluated using a Likert scale consisting of nine items, graded on a 5-point scale from strongly disagree to strongly agree, with scores ranging from 1 to 5. Individuals who obtained scores equal to or higher than the mean value of the total attitude-related questions were categorized as having a positive attitude, while those with scores below the mean were deemed to have a negative attitude.\n\nThe information was encoded and inputted into Epi-Data version 3.1, followed by exportation to SPSS version 25.0 for analysis. Descriptive statistics, such as frequency, mean, percentages, and standard deviations, were computed, and the findings were presented in tables. A binary logistic regression was carried out. Variables with a P-value of 0.2 were taken into account for multivariable logistic regression to manage potential confounding effects. The backward likelihood ratio method was used for multivariable logistic regression to control potential confounders. To assess multicollinearity, a correlation analysis between independent variables was conducted. Ultimately, the adjusted odds ratio with a 95% confidence interval was determined to evaluate the strength of the association, and a p-value less than 0.05 was utilized to ascertain the existence of a significant relationship between factors and outcome variables.\n\nEthical approval was obtained from the Institutional Review Board of Wolaita Sodo University with approval number and date RCSPG-179/14, May 15/2022 respectively. Additionally, a permission letter was granted by the Kelela district health office. Prior to the interview, participants were presented with the consent form, and written consent was obtained from each individual. Participants were assured that they had the option to skip any questions they were not comfortable answering, either partially or entirely, and that they could discontinue the interview at any point. The confidentiality of individual information was safeguarded by refraining from recording any identifying details.\n\n\nResults\n\nThis research involved 324 women who had recently given birth, comprising 108 individuals with specific conditions and 216 without. The overall response rate was 94.7%. The reason for non-responding was, no time, not interested. The average age of the participants was 27.69 years, with a standard deviation of 6.25. About 66(61.1%) of cased women and 149(69.0%) of controlled women lived in the rural area and 73(66.7%) of cased women and 148(68.5%) of controlled women were Muslim religious followers. About 101(93.5%) cased women and 194(89.8%) controlled women were married. Regarding the educational status of women, 62(28.7%) and 28(13.0%) of controlled women were unable to read and write and above the secondary level of education respectively. Also, 22(20.4%) and 32(29.6%) of husband-cased women were unable to read and write and were above the secondary level of education respectively (Table 1).\n\nAbout 43(39.8%) of cased women and 114(52.8%) of controlled women had more than five family sizes.in addition, 68(63.0%) of cased women and 108(50.0%) controlled women had more than five live child. From live children, 28(26.9%) in the case group and 61(28.2%) in the control group were only females. Regarding birth interval, 27(25.0%) were in the case group and 54(25.0%) in the control group spaced more than 36 months. About 85(78.1%) of cased women and 175(81.0%) of controlled women had the plan to have a child. From those, 70(64.8%) of cased women and 135(62.5%) of controlled women prefer to have a male child. About 56(51.9%) of cased women and 115(53.2%) of controlled women husbands were the sole decision maker to have the child in the future. About 101(93.5%) cased women and 200(92.6%) controlled women had ANC follow-up, of those, 40(37.0%) of cased women and 68(31.5%) of controlled women had more than four visits. Seventy-eight (72.2%) of cased women and 144(66.7%) of controlled women were counseled about immediate postpartum LARC (Table 2).\n\nA majority of participants in both the case and control groups exhibited insufficient knowledge and a pessimistic attitude regarding immediate postpartum Long-Acting Reversible Contraception (LARC), as depicted in Figure 1.\n\nEighty-five (78.7%) of cased women and 167(77.3%) of controlled women ever used family planning before the last pregnancy. The injectable contraceptive emerged as the most frequently utilized birth control method in both the case and control groups, as indicated in Table 3. Currently, only 108(33.3%) of women used immediate postpartum LARC (Figure 2). The most common reason for not using immediate postpartum LARC had no information, husband refusal, and desire to have a child, 38.9%, 20.8%, and 18.1% respectively (Figure 3).\n\nEvery sociodemographic, obstetric, and reproductive-related factor, along with knowledge about and attitude towards immediate postpartum Long-Acting Reversible Contraception (LARC), were included in the bivariable logistic regression. All variables met the assumptions of binary logistic regression, and those with a p-value ≤ 0.25 were incorporated into the multivariable logistic regression model. Ultimately, it was determined that women’s educational status, attendance at antenatal care (ANC), desire for childbirth, counseling on immediate postpartum LARC, and knowledge about immediate postpartum LARC were significantly linked to the use of immediate postpartum LARC at a significance level of p < 0.05.\n\nWomen with a secondary education or higher demonstrated 2.314 times greater likelihood of using immediate postpartum Long-Acting Reversible Contraception (LARC) compared to those who were unable to read and write (Adjusted Odds Ratio = 2.314, 95% Confidence Interval = 1.645-5.043).\n\nWomen possessing adequate knowledge about immediate postpartum Long-Acting Reversible Contraception (LARC) exhibited a 1.642 times higher likelihood of using it compared to those with insufficient knowledge (Adjusted Odds Ratio = 1.642, 95% Confidence Interval = 1.086-3.186).\n\nWomen who received counseling had a 3.029 times greater likelihood of using immediate postpartum Long-Acting Reversible Contraception (LARC) compared to those who did not receive counseling (Adjusted Odds Ratio = 3.029, 95% Confidence Interval = 2.085-5.988).\n\nWomen who attended antenatal care (ANC) for the current delivery had a 2.930 times higher likelihood of using immediate postpartum Long-Acting Reversible Contraception (LARC) compared to those who did not have ANC follow-up (Adjusted Odds Ratio = 2.930, 95% Confidence Interval = 1.829-4.769).\n\nWomen who expressed no desire to have a child exhibited a 1.421 times higher likelihood of using immediate postpartum Long-Acting Reversible Contraception (LARC) compared to those who had a desire to have a child (Adjusted Odds Ratio = 1.421, 95% Confidence Interval = 1.026-2.006) (Table 4).\n\n\nDiscussion\n\nThis research aimed to uncover the factors influencing the use of immediate postpartum Long-Acting Reversible Contraception (LARC) in postpartum women in northwest Ethiopia. The results indicated that factors such as a lack of desire to have a child, attainment of a secondary education or higher, attendance at antenatal care (ANC) follow-up, receiving counseling about immediate postpartum LARC, and possessing good knowledge about immediate postpartum LARC were identified as key determinants influencing the utilization of immediate postpartum LARC.\n\nWomen with a secondary education or higher were 2.314 times more likely to use immediate postpartum Long-Acting Reversible Contraception (LARC) compared to those who were unable to read and write. This finding aligns with studies conducted in the west Gojjam zone, south Gondar zone, Bale zone, Hawassa, Ethiopia, Uganda, India, low-income countries, and low and middle-income countries.24,31–33,36,39–44 One plausible explanation is that an increase in women’s educational attainment tends to positively influence healthcare-seeking behavior. Additionally, heightened education levels enable women to comprehend the advantages and drawbacks of contraceptives, providing them with accurate information about fertility and contraception. Empowering maternal education, therefore, plays a crucial role in enabling informed decision-making regarding fertility and contributes to improved maternal and child health.\n\nThe likelihood of using immediate postpartum Long-Acting Reversible Contraception (LARC) was 1.642 times higher among women with good knowledge about immediate postpartum LARC compared to those with poor knowledge. This observation aligns with studies conducted in Bahir Dar, West Arsi, Addis Ababa, Ethiopia, India, and low-income countries.24,32,37,45–47\n\nAdditionally, the odds of utilizing immediate postpartum LARC were 3.029 times higher among women who received counseling compared to those who did not. This finding is consistent with studies conducted in the Sidama zone, West Gojjam zone, Hawassa, South Gondar zone, Bahir Dar, Addis Ababa, Ethiopia, and low and middle-income countries.24,31–33,36,43,46,48,49 According to the World Health Organization (WHO), postpartum family planning counseling is ideally initiated during antenatal care (ANC), offering an opportune time to counsel women. However, counseling during early labor and immediately postpartum is also deemed acceptable. Another potential rationale is that counseling enables women to receive accurate information about immediate postpartum LARC, potentially altering their attitudes and behaviors by dispelling rumors and misconceptions that could impede the acceptance of immediate postpartum LARC.\n\nThe likelihood of utilizing immediate postpartum Long-Acting Reversible Contraception (LARC) was 2.930 times higher among women who attended antenatal care (ANC) for the current delivery compared to those who did not. This finding is consistent with research conducted in the south Gondar zone, Bale zone, Bahir Dar, Ethiopia, low and middle-income countries, USAID findings from 17 countries, and USAID DHS Comparative Reports, India, and Egypt.24,31,32,43,44,49–54 The observed association could be attributed to the recommendation of focused antenatal care, which includes counseling about contraceptive methods during ANC follow-up. The increased frequency of ANC follow-ups, typically three times, may provide pregnant women with opportunities for discussions about immediate postpartum LARC and other contraceptive methods. Healthcare providers, during these interactions, often clarify misconceptions about immediate postpartum LARC. Therefore, delivering effective contraceptive counseling during ANC visits has the potential to address any misperceptions and motivate women to accept the use of immediate postpartum LARC.\n\nThe likelihood of utilizing immediate postpartum Long-Acting Reversible Contraception (LARC) was 1.421 times higher among women who expressed no desire to have a child compared to those who desired childbirth. This finding aligns with studies conducted in Hawassa City and the Sidama zone.36,48 The overarching objective of family planning programs is to assist women who wish to delay or avoid childbearing in achieving these stated fertility goals. This approach offers the additional advantage of affording mothers sufficient time to recover from the physical stress of one pregnancy before embarking on the next, allowing for adequate lactation periods. Consequently, promoting healthy timing and spacing of pregnancies presents an opportunity to positively impact maternal health and newborn outcomes.\n\nThe cross-sectional nature of the study inherently constrains the ability to establish the causal relationship between dependent and independent variables. Additionally, due to its quantitative approach, the study does not delve into participants’ profound emotions regarding acceptability, reasons for refusal, or beliefs about immediate postpartum Long-Acting Reversible Contraception (LARC), as would be possible in a qualitative approach. Moreover, the research was exclusively carried out in public hospitals, limiting the applicability of the findings to women who gave birth at home, in health centers, or private health institutions.\n\n\nConclusion\n\nIn this study, we identified factors that significantly influence the utilization of immediate postpartum Long-Acting Reversible Contraception (LARC). Educational attainment, attendance at antenatal care (ANC), desire for additional children, counseling, and knowledge about immediate postpartum LARC were found to be significantly linked to the use of this contraceptive method. The research aimed to pinpoint the determinants of immediate postpartum LARC among postpartum women in northwest Ethiopia. The results indicated that factors such as a lack of desire for additional children, a secondary education or higher, ANC follow-up, counseling on immediate postpartum LARC, and possessing good knowledge about it were key determinants influencing its utilization.\n\nHence, it is crucial to prioritize the empowerment of maternal education, provide comprehensive counseling on immediate postpartum Long-Acting Reversible Contraception (LARC) during any interaction, and reinforce adherence to focused antenatal care (ANC) attendance. These efforts are essential in encouraging women to adopt contraception during the postnatal period, contributing to overall improvements in maternal and child health. Additionally, emphasizing health education and communication becomes paramount for enhancing women’s understanding of immediate postpartum LARC utilization.\n\nEthical approval was obtained from the Institutional Review Board of Wolaita Sodo University with approval number and date RCSPG-179/14, May 15/2022 respectively. Additionally, a permission letter was granted by the Kelela district health office. Prior to the interview, participants were presented with the consent form, and written consent was obtained from each individual.\n\n\nAuthors’ contribution\n\nEach author significantly contributed to the conception and design, data acquisition, or analysis and interpretation of the data. They participated in drafting the article or made substantial revisions to ensure intellectual integrity. All authors consented to submitting the work to the present journal, provided final approval for the version intended for publication, and committed to being accountable for all aspects of the study.", "appendix": "Data availability\n\nFigshare: Determinants of Immediate Postpartum Long Acting Reversible Contraceptive Utilization among Women Who Gave Birth in Public Health Facilities in Northwest Ethiopia: Unmatched Case-control Study Design. https://doi.org/10.6084/m9.figshare.25050845.v1. 55\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFishare: Online resource for STROBE Checklist for case control study. https://doi.org/10.6084/m9.figshare.25478374.v1. 56\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe express our sincere gratitude to the College of Health Science and Medicine at Woliata Sodo University for granting us ethical clearance. Additionally, we extend our heartfelt thanks to the study participants for their cooperation during the data collection process.\n\n\nReferences\n\nKassebaum NJ, Bertozzi-Villa A, Coggeshall MS, et al.: Global, regional, and national levels and causes of maternal mortality during 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet. 2014; 384(9947): 980–1004. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAskew I, Weinberger M, Dasgupta A, et al.: Harmonizing Methods for Estimating the Impact of Contraceptive Use on Unintended Pregnancy, Abortion, and Maternal Health. Glob. Health Sci. Pract. 2017; 5(4): 658–667. Publisher Full Text\n\nSingh S, Sedgh G: Unintended Pregnancy: Worldwide Levels, Trends, and Outcomes. Stud. Fam. Plan. 2010; 45(3).\n\nWHO: Report of a WHO technical consultation on birth spacing. Geneva: WHO; 2005. Reference Source\n\nDaVanzo J, Hale L, Razzaque A, et al.: Effects of interpregnancy interval and outcome of the preceding pregnancy on pregnancy outcomes in Matlab, Bangladesh. BJOG. 2007; 114(9): 1079–1087. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWinfrey W, Rakesh K: Use of family planning in the postpartum period. ICF International; 2014. Reference Source\n\nCleland J, Conde-Agudelo A, Peterson H, et al.: Contraception and health. Lancet. 2012; 380(9837): 149–156. Publisher Full Text\n\nGaffield ME, Egan S, Temmerman M: It’s about time: WHO and partners release programming strategies for postpartum family planning. Glob. Health Sci. Pract. 2014; 2(1): 4–9. PubMed Abstract \| Publisher Full Text\n\nPearson E, Senderowicz L, Pradhan E, et al.: Effect of a postpartum family planning intervention on postpartum intrauterine device counseling and choice: evidence from a cluster-randomized trial in Tanzania. BMC Womens Health. 2020; 20(1): 1–13. Publisher Full Text\n\nCwiak C, Cordes S: Postpartum intrauterine device placement: a patient-friendly option. Contracept. Reprod. Med. 2018; 3(1): 3–7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBano Z, Memon S, Khan FA, et al.: Comparative analysis of postpartum IUCD versus interval IUCD insertion: a study conducted in a tertiary care hospital in Karachi, Pakistan. Int. J. Res. Med. Sci. 2020; 8(6): 2213. Publisher Full Text\n\nHounton S, Winfrey W, Barros AJD, et al.: Patterns and trends of postpartum family planning in Ethiopia, Malawi, and Nigeria: evidence of missed opportunities for integration. Glob. Health Action. 2015; 8(1): 29738. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKanakuze CA, Kaye DK, Musabirema P, et al.: Factors associated with the uptake of immediate postpartum intrauterine contraceptive devices (PPIUCD) in Rwanda: a mixed methods study. BMC Pregnancy Childbirth. 2020; 5: 1–12.\n\nBlumenthal P, Voedisch A, Gemzell-Danielsson K: Strategies to prevent unintended pregnancy: Increasing use of long-acting reversible contraception. Hum. Reprod. Update. 2011; 17: 121–137. Publisher Full Text\n\nEliason S, Baiden F, Quansah-Asare G, et al.: Factors influencing the intention of women in rural Ghana to adopt postpartum family planning. Reprod. Health. 2013; 10(1): 34. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoore Z, Pfitzer A, Gubin R, et al.: Missed opportunities for family planning: an analysis of pregnancy risk and contraceptive method use among postpartum women in 21 low- and middle-income countries. Contraception. 2015; 92(1): 31–39. PubMed Abstract \| Publisher Full Text\n\nFikadu Geda Y, Siyoum M, Tirfie WA: Pregnancy History and Associated Factors among Hawassa University Regular Undergraduate Female Students. Southern Ethiopia: 2020; 2020.\n\nGeda Y: Determinants of teenage pregnancy in Ethiopia: a case–control study, 2019. Curr. Med. Issues. 2019; 17(4): 112. Publisher Full Text\n\nDemie TG, Demissew T, Huluka TK, et al.: Postpartum family planning utilization among postpartum women in public health institutions of Debre Berhan town, Ethiopia. J. Women’s Health Care. 2018; 07(2). Publisher Full Text\n\nKavanaugh ML, Jerman J, Hubacher D, et al.: Characteristics of women in the United States who use long-acting reversible contraceptive methods. Obstet. Gynecol. 2011; 117: 1349–1357. Publisher Full Text\n\nSaleem S, Bobak M: Women’s autonomy, education, and contraception use in Pakistan: A national study. Reprod. Health. 2005; 2: 1. Publisher Full Text\n\nCurtis SL, Neitzel K: Contraceptive Knowledge Use and Sources. Calverton, MD, USA: Macro International; 1996.\n\nYeatman SE, Trinitapoli J: Beyond denomination: The relationship between religion and family planning in rural Malawi. Demographic Res. 2008; 19: 1851.\n\nYemane TT, Bogale GG, Egata G, et al.: Postpartum family planning use and its determinants among women of the reproductive age group in low-income countries of Sub-Saharan Africa: a systematic review and meta-analysis. Int. J. Reprod. Med. 2021 Aug 20; 2021: 1–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMelka AS, Tekelab T, Wirtu D: Determinants of long-acting and permanent contraceptive methods utilization among married women of reproductive age groups in western Ethiopia: A cross-sectional study. Pan Afr. Med. J. 2015; 21: 246.\n\nAnguzu R, Sempeera H, Sekandi JN: High parity predicts the use of long-acting reversible contraceptives in the extended postpartum period among women in rural Uganda. Contracept. Reprod. Med. 2018; 3: 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDempsey AR, Billingsley CC, Savage AH, et al.: Predictors of long-acting reversible contraception use among unmarried young adults. Am. J. Obstet. Gynecol. 2012; 206: 526.e1–526.e5. PubMed Abstract \| Publisher Full Text\n\nEeckhaut MC, Sweeney MM, Gipson JD: Who Is Using Long-Acting Reversible Contraceptive Methods? Findings from Nine Low-Fertility Countries. Perspect. Sex. Reprod. Health. 2014; 46: 149–155. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBharadwaj P, Akintomide H, Brima N, et al.: Determinants of long-acting reversible contraceptive (LARC) use by adolescent girls and young women. Eur. J. Contracept. Reprod. Health Care. 2012; 17: 298–306. PubMed Abstract \| Publisher Full Text\n\nOrganization WHO: WHO Medical Eligibility Criteria Wheel for Contraceptive Use. Geneva, Switzerland: WHO; 2015.\n\nAssefaw M, Azanew G, Engida A, et al.: Determinants of postpartum intrauterine contraceptive device uptake among women delivering in public hospitals of South Gondar zone, Northwest Ethiopia, 2019: an unmatched case-control study. Obstet. Gynecol. Int. 2021 Feb 22; 2021: 1–1, 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKassa BG, Ayele AD, Belay HG, et al.: Postpartum intrauterine contraceptive device use and its associated factors in Ethiopia: systematic review and meta-analysis. Reprod. Health. 2021 Dec; 18: 1–2. Publisher Full Text\n\nMelkie A, Addisu D, Mekie M, et al.: Utilization of the immediate postpartum intrauterine contraceptive device and associated factors among mothers who gave birth at selected hospitals in west Gojjam zone, Ethiopia, multi-level facility-based study, 2019. Heliyon. 2021 Jan 1; 7(1): e06034. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeleko A, Azale T, Sisay M: Utilization of long-acting reversible contraceptive methods and its associated factors among women of reproductive age groups in Mizan-Aman Town, Bench Maji Zone. J. Women’s Health Issues Care. 2017; 6(6): 2. Publisher Full Text\n\nGebremichael H, Haile F, Dessie A, et al.: Acceptance of long-acting contraceptive methods and associated factors among women in Mekelle city, Northern Ethiopia. Sci. J. Public Health. 2014; 2(4): 239–245.\n\nDeneke YS, Jisso M, Fantahun S, et al.: Acceptance, Utilization and Factors Associated With Immediate Postpartum Intrauterine Contraceptive Devise Among Mothers Delivered in Public Health Facilities of Hawassa City, Sidama Regional State, Ethiopia.\n\nFekadu H, Kumera A, Yesuf EA, et al.: Prevalence and determinant factors of long-acting contraceptive utilization among married women of reproductive age in Adaba Town, West Arsi Zone, Oromia, Ethiopia. J. Women’s Health Care. 2017; 6(1): 0420–2167.\n\nOntiri S, Ndirangu G, Kabue M, et al.: Long-acting reversible contraception uptake and associated factors among women of reproductive age in rural Kenya. Int. J. Environ. Res. Public Health. 2019 May; 16(9): 1543. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOmona K, Namuli W: Factors influencing utilization of intra-uterine device among postpartum mothers at Gombe Hospital, Butambala district, Uganda. Cogent medicine. 2020 Jan 1; 7(1): 1846264. Publisher Full Text\n\nJairaj S, Dayyala S: A cross-sectional study on acceptability and safety of IUCD among postpartum mothers at tertiary care hospital, Telangana. J. Clin. Diagn. Res. 2016 Jan; 10(1): LC01–LC04. PubMed Abstract \| Publisher Full Text\n\nPriya S, Tuteja A, Mittal P, et al.: Exploring reasons behind Low acceptance for PPIUCD in postnatal women. New Indian J. Surg. 2011; 2: 246I.\n\nHounton S, Winfrey W, Barros AJ, et al.: Patterns and trends of postpartum family planning in Ethiopia, Malawi, and Nigeria: evidence of missed opportunities for integration. Glob. Health Action. 2015 Dec 1; 8(1): 29738. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDev R, Kohler P, Feder M, et al.: A systematic review and meta-analysis of postpartum contraceptive use among women in low-and middle-income countries. Reprod. Health. 2019 Dec; 16: 1–7. Publisher Full Text\n\nGonie A, Worku C, Assefa T, et al.: Acceptability and factors associated with post-partum IUCD use among women who gave birth at Bale zone health facilities, Southeast-Ethiopia. Contracept. Reprod. Med. 2018 Dec; 3(1): 1–8. Publisher Full Text\n\nYadav S, Joshi R, Solanki M: Knowledge attitude practice and acceptance of postpartum intrauterine devices among postpartum women in a tertiary care center. Int. J. Reprod. Contracept. Obstet. Gynecol. 2017 Apr 1; 6(4): 1507–1511. Publisher Full Text\n\nGeda YF, Nejaga SM, Belete MA, et al.: Immediate postpartum intrauterine contraceptive device utilization and influencing factors in Addis Ababa public hospitals: a cross-sectional study. Contracept. Reprod. Med. 2021 Dec; 6: 1. Publisher Full Text\n\nTesfa E, Gedamu H: Factors associated with utilization of long-term family planning methods among women of reproductive age attending Bahir Dar health facilities, Northwest Ethiopia. BMC Res. Notes. 2018 Dec; 11(1): 1–7. Publisher Full Text\n\nTefera LB, Abera M, Fikru C, et al.: Utilization of Immediate Post-Partum Intra Uterine Contraceptive Device and Associated Factors: A Facility based Cross-Sectional Study among Mothers Delivered at Public Health Facilities of Sidama Zone, South Ethiopia. J. Preg. Child Health. 2017; 4: 326. 1000326 Page 2 of 8 J Preg Child Health, an open access journal ISSN: 2376-127X Volume 4• Issue 3• 1000326. one quarter. 2017;121(39.0):16-24. Publisher Full Text\n\nTafere TE, Afework MF, Yalew AW: Counseling on family planning during ANC service increases the likelihood of postpartum family planning use in Bahir Dar City Administration, Northwest Ethiopia: a prospective follow-up study. Contracept. Reprod. Med. 2018 Dec; 3: 1–9. Publisher Full Text\n\nWinfrey W, Rakesh K: Use of family planning in the postpartum period. ICF International; 2014.\n\nBorda M, Winfrey W: Postpartum fertility and contraception: an analysis of findings from 17 countries. Baltimore: Jhpiego; 2010 Mar.\n\nPradhan S, Kshatri JS, Sen R, et al.: Determinants of uptake of post-partum intra-uterine contraceptive device among women delivering in a tertiary hospital, Odisha, India. Int. J. Reprod. Contracept. Obstet. Gynecol. 2017; 6(20): 1770–2320.\n\nKant S, Archana S, Singh AK, et al.: Acceptance rate, probability of follow-up, and expulsion of postpartum intrauterine contraceptive device offered at two primary health centers, North India. J. Family Med. Prim. Care. 2016 Oct; 5(4): 770–776. PubMed Abstract \| Publisher Full Text\n\nMohamed SA, Kamel MA, Shaaban OM, et al.: Acceptability for the use of postpartum intrauterine contraceptive devices: Assiut experience. Med. Princ. Pract. 2003; 12(3): 170–175. PubMed Abstract \| Publisher Full Text\n\nAsmare G, Abtew GK, Gellaw MT, et al.: Determinants of Immediate Postpartum Long Acting Reversible Contraceptive Utilization among Women Who Gave Birth in Public Health Facilities in Northwest Ethiopia: Unmatched Case-control Study Design. Dataset. figshare. 2024. Publisher Full Text\n\nAsmare G: STROBE_checklist_case-control [1].doc. figshare. 2024. Publisher Full Text" }	[ { "id": "298148", "date": "30 Jul 2024", "name": "Anne Khasakhala", "expertise": [ "Reviewer Expertise Demography and Population studies", "reproductive health including FP issues", "Gender among others. I am well vast in statistical analysis of large data sets such as DHS", "Census" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for giving me the opportunity to review this interesting article. I have gone through the document section by section and the following are my comments: Introduction The article provides a comprehensive background on the importance of maternal health and family planning by using relevant statistics to underscore the importance and urgency of issue and clearly articulates the gap in existing research and the study's objective. However, the introduction could be more concise to enhance readability (consider focusing on key points and eliminating redundancy). The following are some suggestions:\nTo avoid redundancies and enhance readability, the authors could highlight the global concern for maternal Health; the magnitude of unintended pregnancies both globally, Sub-Saharan and in Ethiopia; discuss the WHO Recommendations, specifically on birth intervals with emphasis on health risks of short birth intervals (less than two years); why postpartum FP is important for the health of the mother and child; highlight the benefits of Long-Acting Reversible Contraceptives (LARCs); Low Utilization of Postpartum Contraception in Sub-Saharan Africa and highlight some of the facilitating factors that influence utilization PPFP and the gap in Research in Ethiopia.\nPlease ensure the information in your introduction is up-to-date and references relate to recent studies, when looking for recent references, the authors might search academic databases like PubMed, Google Scholar, or other similar data bases.\nMore detailed information on why immediate postpartum LARC utilization specifically (as opposed to other types of contraception) is critical could be included such as it ensures reliable prevention of unintended pregnancies during the critical postpartum period. It is beneficial for postpartum women who may be managing the demands of a new baby. It can facilitate immediate protection for postpartum women, whose fertility can return as early as 45 days after childbirth if not exclusively breastfeeding further, have minimal to no impact on lactation, making them suitable for breastfeeding mothers. Minimizes the risk of repeat unintended pregnancies. LARCs are in that they can help bridge this gap by offering a long-term solution that requires fewer healthcare visits for maintenance and hence addressing the unmet need for family planning in the postpartum period. It also has positive impact on maternal and child health in that it helps to ensure adequate birth spacing between pregnancies. Immediate initiation of LARCs can be integrated into routine postpartum care, ensuring that women leave the hospital with an effective contraceptive method in place.\nMethods Study Setting: There is detailed description of the study setting, ensuring clarity about where the research took place. However, the rational for the choice of the study setting could enrich this section.\n\nStudy Design The choice of an unmatched case-control design is appropriate for identifying factors associated with LARC utilization. However, justification for choosing an unmatched rather than a matched design could be provided.\nPopulation There is clear definitions and sources of information on the population. However, it is crucial to explain why specific inclusion and exclusion criteria were set. Inclusion and Exclusion Criteria The inclusion criteria were broad, encompassing all postpartum women in the selected facilities, while the exclusion criteria were based on WHO medical eligibility for LARC. This specific criteria ensures the relevance and safety of participants included in the study. However, the authors could consider potential biases introduced by these criteria. Sample Size Determination There is a detailed explanation of the sample size calculation process. However, a brief rationale for the chosen assumptions could be included for transparency. Data Collection Tools, Measurements, and Quality Control Procedures The authors have carried out a thorough validation and reliability assessment of the data collection tools. However, the process of adapting and refining the questionnaire from literature sources could be described in more detail. Data Processing and Analysis The article includes a comprehensive description of data processing and analysis methods. However, a more detailed explanation of how multicollinearity was assessed could be included. Ethical Approval and Consent to Participate Ethical approval was obtained, and informed consent was acquired from participants, ensuring ethical standards were met. No improvements needed here as the section is clear and complete.\nResults The study achieved a high response rate of 94.7%, ensuring the results are representative and minimizing the potential for non-response bias. The study collected extensive socio-demographic, obstetric, and reproductive data, providing a holistic view of the factors influencing immediate postpartum LARC utilization. The use of multivariable logistic regression allowed for the identification of significant predictors of immediate postpartum LARC utilization, accounting for potential confounding factors. The study's focus on immediate postpartum LARC utilization addresses a critical period for contraceptive counselling and decision-making, with implications for improving maternal and child health outcomes in the study area. The study’s findings are consistent with existing literature, reinforcing the importance of education, ANC attendance, counselling, and knowledge in promoting contraceptive use.\nStudy Limitations: The cross-sectional nature of the study limits the ability to establish causal relationships between the identified factors and LARC utilization. Longitudinal studies would provide stronger evidence of causality. Incorporating qualitative methods would have provided deeper insights into participants’ beliefs, attitudes, and reasons for refusing LARC, enriching the understanding of barriers and facilitators to its use. The study was conducted in public hospitals, which may limit the generalizability of the findings to women who gave birth at home, in health centers, or private institutions (Selectivity Bias). Expanding the study to include these groups would enhance generalizability. Despite identifying knowledge and attitudes as significant predictors, the study found that a majority of participants had insufficient knowledge and pessimistic attitudes towards LARC this call for a recommendation on future interventions should focus on improving these areas. The study’s findings are specific to northwest Ethiopia, and cultural factors may influence the applicability of the results to other regions. Comparative studies across different cultural contexts would be beneficial. The study highlights the role of husbands in decision-making about contraception. Further exploration of male involvement and targeted interventions to address this influence would be beneficial.\nRecommendations for Future Research Conduct longitudinal studies to establish causal relationships between identified predictors and LARC utilization. Use a mixed methods approach to combine quantitative data with qualitative insights, this will provide a more comprehensive understanding of barriers and facilitators. Expand the sample to include women from various birthing locations, including home births, health centers, and private institutions, to improve generalizability.: Implement and evaluate interventions aimed at improving knowledge and attitudes towards LARC, and assess their impact on utilization rates. Investigate the role of male partners in contraceptive decision-making and develop strategies to engage men in family planning discussions.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-297
https://f1000research.com/articles/10-371/v1	11 May 21	{ "type": "Research Article", "title": "Atopic biomarker changes after exposure to Porphyromonas gingivalis lipopolysaccharide: a small experimental study in Wistar rats", "authors": [ "Sindy Cornelia Nelwan", "Ricardo Adrian Nugraha", "Anang Endaryanto", "Asti Meizarini", "Udijanto Tedjosasongko", "Seno Pradopo", "Haryono Utomo", "Nunthawan Nowwarote", "Ricardo Adrian Nugraha", "Anang Endaryanto", "Asti Meizarini", "Udijanto Tedjosasongko", "Seno Pradopo", "Haryono Utomo", "Nunthawan Nowwarote" ], "abstract": "Background: IgE and IgG4 are implicated in atopic development and clinically utilized as major biomarkers. Atopic responses following certain pathogens, such as Porphyromonas gingivalis (Pg), are currently an area of interest for further research. The aim of this study is to measure the level of IgE, IgG4, and IgG4/IgE ratio periodically after exposure of periodontal pathogen Pg lipopolysaccharide (LPS).\nMethods: We used 16 Wistar rats (Rattus norvegicus) randomly subdivided into four groups: Group 1, injected with placebo; Group 2, injected with LPS Pg 0.3 µg/mL; Group 3, injected with LPS Pg 1 µg/mL; and Group 4, injected with LPS Pg 3 µg/mL. Sera from all groups were taken from retro-orbital plexus before and after exposure.\nResults: Levels of IgE and IgG4 increased significantly following exposure of LPS Pg at day-4 and day-11. Greater increase of IgE rather than IgG4 contributed to rapid decline of IgG4/IgE ratio, detected in the peripheral blood at day-4 and day-11.\nConclusion: Modulation of atopic responses following exposure to LPS Pg is reflected by a decrease in IgG4/IgE ratio that accompanies an increase of IgE. Therefore, Pg, a keystone pathogen during periodontal disease, may have a tendency to disrupt atopic biomarkers.", "keywords": [ "allergic diseases", "atopic inflammatory pathway", "immunoglobulin", "periodontal pathogen", "Porphyromonas gingivalis LPS" ], "content": "Editorial note\n\nEditorial Note (20th October 2023): The F1000 Editorial Team has not yet received a new version of this article, as detailed in the Editorial Notes published on 16th June and 4th August 2023. The F1000 Editorial Team will no longer be requesting a new version from the authors. Readers should be aware that there is key information missing from the article regarding adverse events, anaesthetic and euthanasia procedures, and ethical approval; this information had been previously given to and verified by the F1000 Editorial Team, but the authors have not yet updated their article. Peer review activity remains suspended until the authors publish a new version of this article.\n\nEditorial Note (4th August 2023): The F1000 Editorial Team has not yet received a new version of this article, as detailed in the Editorial Note published on 16th June 2023. The F1000 Editorial Team is actively contacting the authors to request the new version of the article. Peer review activity remains suspended until the authors publish a new version of this article.\n\nEditorial Note (16th June 2023): Since publication, it has been brought to the attention of the Editorial Team that the article was missing key information regarding adverse events, anaesthetic and euthanasia procedures, and ethical approval. The Editorial Team requested further detail and an explanation from the authors in March 2023. The authors provided an adequate response and were requested by the Editorial Team to create a new version of the article to include the additional details. Peer review activity has been suspended until the authors publish a new version of this article.\n\n\nIntroduction\n\nThe oral cavity is the habitat of numerous bacteria, including Porphyromonas gingivalis (Pg). Pg is a gram negative, facultative anaerobic pathogen, which is responsible in causing gingivitis or periodontitis.1 In low-income countries, gingivitis and periodontitis can affect up to 90% of the adult population.2 Rather than alveolar bone and ligament destruction, Pg is believed to be involved with the development of atopic responses in a susceptible host.3 Following Pg infection, hosts’ adaptive immune response (both cell-mediated and humoral-mediated) could induce a systemic inflammatory reaction, not only just local destruction of tooth-supporting tissues.4–5 Although periodontal pathogens, such as Pg, play a major role in the initiation of local and systemic inflammatory reaction,6 the host aberrant immune responses require further study. Since humoral immune responses are stimulated following Pg infection, there might be a link to the occurrence of atopy.\n\nDespite long-standing research about hygiene hypothesis for several decades, there is an unequivocally accepted fact that the prevalence of atopy increases more among children who have periodontal pathogen colonization or infection.7 While endorsing these hygiene hypothesis approaches, there is an alternative hypothesis in which exposure to some periodontal pathogens will exclusively trigger an “immunoglobulin-E skew” rather than reducing it.8 Within the context of the hygiene hypothesis, the most essential microbial exposures needed to be studied is the biomolecular relationship between host antibody and regulatory T-cell with lipopolysaccharide (LPS), an endotoxin released by Pg to affect host immune reaction.\n\nHygiene hypothesis principles might not be able to answer all phenomenon of increasing incidence of atopy among children with poor oral hygiene.9 Some studies report a positive association between the colonization/infection of Pg with the development of allergic diseases,10–15 whereas some studies report no association.16–21 Due to lack of conclusive evidence about the association between Pg and allergic diseases,22 we try to measure the level of atopic biomarkers following Pg infection.\n\nTo the best of our knowledge, measuring IgG4 and IgE antibody may have a closer association to atopic profiles, since IgG4 and IgE are released after activation of mature B cells following the modulation of IL-4 and IL-5 released by Th-2 cells during type I hypersensitivity.23 By looking at the alteration of IgG4 and IgE antibodies level after exposure to these selected components of Pg in a rat model, we hope to understand more deeply the biological mechanism of B-cell production antibodies pattern and humoral immune responses before the clinical manifestation of atopy. We chose a rat model since they are inbred so they are almost identical genetically and their genetic, biological and behavior characteristics closely resemble those of humans.\n\n\nMethods\n\nThis article was reported in line with the ARRIVE guidelines. Animal experimental study was conducted under the approval of the Institutional Animal Research Ethics Committee of Universitas Airlangga (UNAIR), Surabaya, Indonesia (animal approval no:50/KKEPK.FKG/IV/2015) under the name of Sindy Cornelia Nelwan as the Principal Investigator. The study was carried out in strict accordance to internationally accepted standards of the Guide for the Care and Use of Laboratory Animals of the National Institute of Health. All efforts were made to ameliorate any suffering of animals through using anaesthetic to euthanize the rats at the end of the experimental procedure.\n\nSample size\n\nN = (Zα/2)2 s2/d2, where s is the standard deviation obtained from previous study or pilot study, and d is the accuracy of estimate or how close to the true mean. Zα/2 is normal deviate for two- tailed alternative hypothesis at a level of significance. Suppose sample size calculated by software is 3 animals per group and researcher is expecting 10% attrition then his final sample size will be 4 animals per group or 16 animals in total.\n\nRats\n\nThe present study used 16 male Wistar rats (Rattus novergicus) between eight and ten weeks of age (average body weight 120-150 grams). The rats were housed in microisolator cages and maintained in a constant room temperature ranging from 22°C to 25°C, with a 12-h light/12-h dark cycle, under artificially controlled ventilation, with a relative humidity ranging from 50% to 60%. The rats were fed a standard balanced rodent diet (NUTRILAB CR-1®) and water were provided ad libitum.\n\nInclusion criteria was male Wistar rats, age 8-10 weeks, with body weight 120-150 grams. Female Wistar rats, diseased, sick, and lazy male Wistar rats were strictly excluded.\n\nThe present study design was a pre-test post-test-controlled unblinded group design using quantitative method. The 16 male Wistar rats were randomized using randomized block sampling and classified into four groups. Each group consisted of 4 matched Wistar rats (age, weight, IgE and IgG4 baseline characteristic). Group 1 were given placebo (0.9% normal saline solution). Group 2 were given lipopolysaccharide (LPS) of Porphyromonas gingivalis (Pg) (American Type Culture Collection, Rockville, Md.) at dose 0.3 μg/mL. Group 3 were given LPS Pg at dose 1 μg/mL. Group 4 were given LPS Pg at dose 3 μg/mL.\n\nThe rats received LPS by an intra-sulcular injection. Intra-sulcular injection has an advantage due to the its direct delivery of LPS to oral cavity in which the tip of needle is injected slowly at the crestal bone. Longitudinal quantitative measurement was performed; IgE level, IgG4 level, and IgG4/IgE ratio in both groups on day-0 (before treatment), day-4, and day-11. An average of 0.2 ml peripheral blood sera was obtained by Pasteur pipette from retro-orbital plexus, using a lateral approach on each of these days from each rat. The potential expected adverse events were anaphylactic shock, allergic reaction, bleeding and infection. However, to the best our knowledge, there were no expected nor unexpected adverse events in the experimental procedures. Following the end of the experiments, all efforts were made to ameliorate any suffering of animals through injection of sodium pentobarbital anesthetic to euthanize the rats at the end of the experimental procedure.\n\nSample of the sera were collected and stored at −70°C (−94°F) at Institute of Tropical Diseases Universitas Airlangga (UNAIR). All sera were assessed by direct-sandwich enzyme-linked immunosorbent assay (ELISA) with mouse IgE antibody (MAB9935) and IgG4 antibody (MAB9895) under the manufacturer's (R&D System Europe Ltd, Abingdon, UK) protocol. Briefly, the sera were examined using microtiter plates using 25 ml of 3,3’,5,5’-tetramethylbenzidine to 1 ml of phosphate-citrate buffer plus perborate in a mildly acidic buffer (adjust pH 5.7). Levels of IgG4 were detected using monoclonal antibody anti-IgG4, transferring it to microtiter plates, adding the supplied conjugate, adding blocking solution, diluting plasma sample (1:100,000), and washing between the steps. Level of IgE was detected using monoclonal antibody anti-IgE, following similar steps until diluting the plasma sample (1:200). A minimum value of 0.01 pg/mL for IgE and 0.01 ng/mL for IgG4 were assigned for below the limit of detection. We used 3,3’,5,5’-tetramethylbenzidine as chromogenic substrate, which allows direct visualization of signal development through spectrophotometer.\n\nAll measurements were performed at least three times. Results were presented as means ± standard errors (SEM). The assumption of the normality for the complete data was assessed by Shapiro-Wilk test. Test of homogeneity of variances was assessed by Levene Statistics. Statistical significance was examined by one-way ANOVA and repeated measure ANOVA using SPSS version 17.0 for Microsoft (IBM corp, Chicago, USA).\n\n\nResults\n\nTable 1 show the baseline characteristics of the 16 Wistar rats (Rattus norvegicus). No significant differences were found for mean age (p = 0.774), body weight (p = 0.700), baseline IgE (p = 0.071), baseline IgG4 (p = 0.770), and baseline IgG4/IgE ratio (p = 0.053) among the four groups.\n\n* Data are presented as mean ± standard error of the mean (SEM).\n\n One-way ANOVA for categorical variables; significant at p < 0.05.\n\n* IgE, immune globulin E; IgG4, immune globulin G4; IgG4/IgE, ratio between average IgG4 levels divided by average IgE levels.\n\nPrior to experiments (day-0), there was no difference of serum IgE level between the four groups (p > 0.05). On day-4, there was a significance difference of serum IgE level between all groups (p = 0.006). At day-4, the highest average IgE level could be found in Group 3 treated with LPS Pg 1 μg/ml (17.00 ± 1.69 pg/ml) and the lowest average IgE level could be found in Group 1 (control) (5.31 ± 0.76 pg/ml). On day-11, there was also a significance difference of serum IgE level between both groups (p = 0.047). At day-11 the highest average IgE level could be found in Group 2 treated with LPS Pg 0.3 μg/ml (180.34 ± 10.42 pg/ml) and the lowest average IgE level could be found in Group 1 (5.06 ± 1.86 pg/ml) (Table 2).\n\n* Measured by one-way ANOVA (df1 = 3, df2 = 12, f table 3.490; significant at p < 0.05).\n\nPrior to experiments (day-0), there was no difference of serum IgG4 level between the four groups (p > 0.05). On day-4, there was a significance difference of serum IgG4 level between all groups (p = 0.008). At day-4, the highest average IgG4 level could be found in Group 4 (LPS Pg 3 μg/ml; 23.86 ± 1.59 ng/ml) and the lowest average IgG4 level could be found in Group 1 (8.34 ± 0.58 ng/ml). On day-11, there was a greater difference of serum IgG4 level between all groups (p = 0.005). At day-10, the highest average IgG4 level could be found in Group 4 (LPS Pg 3 μg/ml; 63.74 ± 4.74 ng/ml) and the lowest average IgG4 level could be found in Group 1 (13.91 ± 0.99 ng/ml) (Table 3).\n\n* Measured by one-way ANOVA (df1 = 3, df2 = 12, f table 3.490; significant at p < 0.05).\n\nThe average IgG4/IgE ratio for the control group at day-0, day-4, and day-11 was 1.87 × 103, 1.72 × 103, and 3.62 × 103. In Group 2 (low-dose LPS group; 0.3 μg/ml), the average IgG4/IgE ratio was 2.20 × 103, 1.27 × 103, and 0.22 × 103, respectively. In Group 3 (medium-dose LPS group; 1 μg/ml), the average IgG4/IgE ratio was 1.19 × 103, 0.69 × 103, and 0.56 × 103, respectively. In Group 4 (high-dose LPS group; 3 μg/ml), the average IgG4/IgE ratio was 1.59 × 103, 1.64 × 103, and 0.65 × 103, respectively. All groups exhibited significant differences of IgG4/IgE ratios, except at day-0. The highest IgG4/IgE ratio at day-4 and day-11 could be found in Group 1. The lowest IgG4/IgE ratio at day-4 could be found in Group 3, whilst the lowest ratio at day-11 could be found in Group 2 (Table 4).\n\n* Measured by one-way ANOVA (df1 = 3, df2 = 12, f table 3.490; significant at p < 0.05).\n\nGroup 2 (0.3 μg/ml LPS Pg)\n\nLevel of IgE were increased dramatically from day-0 to day-11 after experiments (5.36 ± 0.19 pg/ml to 180.34 ± 10.42 pg/ml; p = 0.011). Level of IgG4 also increases significantly from day-0 to day-11 after experiments (11.76 ± 0.85 ng/ml to 39.85 ± 2.14 ng/ml; p = 0.006). On the other hand, IgG4/IgE ratio were decreased following experiments (2.20 ± 0.13 × 103 to 0.22 ± 0.01 × 103; p = 0.014) (Table 5).\n\n* Measured by repeated measure ANOVA.\n\n** df times = 2, df error = 14, f table 3.739; significant at p < 0.05.\n\nGroup 3 (1 μg/ml LPS Pg)\n\nLevel of IgE were raised dramatically from day-0 to day-11 after experiments (10.27 ± 0.70 pg/ml to 112.90 ± 3.87 pg/ml; p = 0.003). Level of IgG4 also increased significantly from day-0 to day-11 after experiments (11.91 ± 1.66 ng/ml to 63.6 ± 10.76 ng/ml; p = 0.027). On the other hand, IgG4/IgE ratio declined following experiments (1.19 ± 0.20 × 103 to 0.56 ± 0.09 × 103; p = 0.362) (Table 6).\n\n* Measured by repeated measure ANOVA.\n\n** df times = 2, df error = 14, f table 3.739; significant at p < 0.05.\n\nGroup 4 (3 μg/ml LPS Pg)\n\nLevel of IgE were raised dramatically from day-0 to day-11 after experiments (6.69 ± 0.61 pg/ml to 102.01 ± 11.04 pg/ml; p = 0.009). Level of IgG4 were also increase significantly from day-0 to day-11 after experiments (10.14 ± 1.44 ng/ml to 63.74 ± 4.74 ng/ml; p = 0.029). On the other hand, IgG4/IgE ratio declined following experiments (1.59 ± 0.34 × 103 to 0.65 ± 0.08 × 103; p = 0.113) (Table 7).\n\n* Measured by repeated measure ANOVA.\n\n** df times = 2, df error = 14, f table 3.739; significant at p < 0.05.\n\n\nDiscussion\n\nSeveral mechanisms have been suggested to alter atopic inflammatory responses following LPS Pg infection. One of the mechanisms proven in this study is an elevation of IgE antibody and reduction of IgG4/IgE ratio.24 As far as we have known, Th-1 and Th-2 cells are not two different CD4+ T-cell subsets, but it represents polarized forms of the highly heterogenous CD4+ Th cell–mediated immune response. Host genetic and microenvironmental factors could have contributed with series of modulatory factors including:1 the ligation of T-cell receptor (TCR);2 the activation of costimulatory molecules and its particular components;3 the predominance of an inflammatory cytokine in the local environment; and4 the number of postactivation cell divisions following exposure to antigens. Down-regulation of the Th-1 cell is associated with depression of cell-mediated immune response and stimulation of humoral immune response, thus pathogens are able to evade immune clearance.25\n\nPorphyromonas gingivalis possess very sophisticated defense mechanisms against host immune responses. These pathogens produce capsules containing long chain LPS which is designed effectively to counter membrane attack complex. These long chain LPS can also downgrade cell-mediated immunity by shifting Th-1 into Th-2 which less dangerous to pathogens.26 LPS may have an essential role in switching cell-mediated to humoral-mediated immune responses.27 LPS Pg antigen is processed and presented on its surface with MHC-II molecule. Recent studies suggest an activation of alternative complement pathway, disruption of classical complement pathway, modulation of antigen presenting cells, and downregulation of anti-inflammatory cytokines are responsible for the Th2-skewed immune response following exposure to LPS Pg. Predominance shifting from Th-1 into Th-2 occurs in several extra-lymphoid tissues; the ideal site for Porphyromonas gingivalis is the oral cavity.28\n\nInterleukin-4 (IL-4), which is produced by naive T cells, acts as autocrine manner known to be responsible for the differentiation and activation of Th-2 phenotype.29 Guo et al (2014) shows upon the occurrence and development of allergic diseases, there is a complex pathobiology which results in an imbalance of Th-1/Th-2.30 In an atopic disease such as bronchial asthma or urticaria, naive T cell can differentiate into Th-2 under IL-4–induced STAT6 and GATA-3 transcription factors.30 Th-2 predominant immune response will automatically stimulate plasma cell to release IgE and IgG4.31 Upon re-exposure of antigen or allergen, binding of the allergen to IgE orchestrates the adaptive immune system to initiate rapid sensitization. Frequent sensitization is a major risk factor for the development of allergic diseases such as urticaria, bronchial asthma, hay fever or atopic dermatitis/eczema.32\n\nOur previous study used whole-cell body of Porphyromonas gingivalis to study different molecular responses in Wistar rats. Our first project studied the association between periodontal pathogen and host innate immunity. Exposure to Porphyromonas gingivalis had been shown to stimulate level of TLR2 and depress level of TLR4.33 Our findings might indicate that several bacterial properties can turn-off host innate immunity and host inflammatory response. Our second project studied the association between periodontal pathogen and host adaptive immunity. We summarized that high dose CFU of Pg stimulates fold increase of Th-2 cytokines (IL-4, IL-5 and IL-13) and decrease of Th-1 cytokines (IFN-γ and IL-17).34 These were the cornerstone to continue our project in studying LPS as the most important component of these bacteria.\n\nAt this moment, both total IgE or specific IgE antibodies have little diagnostic value in the occurrence of allergic manifestation. Even total or specific IgE is increasing, yet the manifestation of allergy doesn’t usually develop, since IgG4 level also increases as a counter-regulator.35 It means that even human or rat become susceptible to atopic allergy due to the increasing level of IgE, body mechanism is able to provide protection, with increased IgG4 as a counter response to prevent manifestation of allergic diseases and immediate hypersensitivity. Thus, exposure of LPS Pg will develop chance of atopic and hypersensitivity markers, but manifestation of allergic reaction is a complex pattern.36 IgG4/IgE ratio has closer accuracy to detect any alteration of atopic inflammatory pathway. Increase level of IgE, which isn’t accompanied by IgG4, can be seen in patients with urticaria or atopic dermatitis.37 IgE-switched B cells are much more likely to differentiate into plasma cells, whereas IgG4-switched B cells are less likely to differentiate.38 This reason would explain why IgE antibody is the most dominant antibody in the development of atopic inflammatory pathway, whereas IgG4 antibodies become prominent later during chronic non-atopic stimulation.39 According to this reason, IgG4/IgE ratio may predict atopic responses more accurately than total or specific IgE level.\n\nSeveral limitations should be highlighted. First, this study had limitations with regard to very small number of samples which can increase the likelihood of error and imprecision. Second, results from animal models often do not translate into replications in humans.40 IgE antibody responses in Wistar rats are typically transient, whereas the atopic IgE response in human persists for many years.41 Other crucial difference is IgG4/IgE ratio, which is usually much higher in the Wistar rats than humans.42–43 These factors may have an impact on the interpretation of our results. Thus, the findings should be interpreted within the context of this study and its limitations. The strengths of the study were its high statistical power and the homogeneity of each group to enable comparison between groups and periods.\n\n\nConclusion\n\nSeveral experiments in rats indicate that exposure to LPS Pg may have a tendency to increase levels of IgE and IgG4. On the contrary, declining IgG4/IgE ratio following exposure to LPS Pg suggests the potential role of LPS Pg for isotype switching from IgG4 to IgE. The results of the present study favor indirect isotype switching route for most IgE as secondary responses from LPS Pg infection that leads to systemic atopic inflammatory pathway.\n\n\nData availability\n\nFigshare: Raw Data - Atopic Biomarker Changes after Exposure to Porphyromonas gingivalis Lipopolysaccharide: A Small Experimental Study in Wistar Rat, https://doi.org/10.6084/m9.figshare.14350271.v1.44\n\nThis project contains the following underlying data:\n\n- Data fixed LPS grup A.sav (Group 1 results)\n\n- Data fixed LPS grup B1.sav (Group 2 results)\n\n- Data fixed LPS grup B2.sav (Group 3 results)\n\n- Data fixed LPS grup B3.sav (Group 4 results)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Competing interests\n\n\n\nNo competing interests were disclosed.\n\n\nGrant information\n\nThe author(s) declared that no grants were involved in supporting this work.\n\n\nAcknowledgments\n\nThis project is fully supported by Agung Sosiawan as Dean of Universitas Airlangga College of Dentistry and Coen Pramono as Director of Airlangga Oral and Dental Hospital. We would like to acknowledge Harjanto from Physiology Department and Indrawati Retno from Biochemistry Department for providing material and reagent generation. We also thank all lecturers and research assistants from Universitas Airlangga, who are willing to help in the technical aspect.\n\nA previous version of this article is available on bioRXiv: https://doi.org/10.1101/2021.01.14.426656.\n\n\nReferences\n\nHerrero ER, Fernandes S, Verspecht T, et al.: Dysbiotic Biofilms Deregulate the Periodontal Inflammatory Response. J Dent Res. 2018; 97(5): 547–55. PubMed Abstract \| Publisher Full Text\n\nMazurek-Mochol M, Majorczyk E, Banach J, et al.: The influence of KIR gene presence/absence polymorphisms on the development of periodontal disease in smokers and non-smokers. Cent Eur J Immunol. 2017; 42(4): 347–53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSperr M, Kundi M, Tursic V, et al.: Prevalence of Comorbidities in Periodontitis Patients Compared to the General Austrian Population. J Periodontol. 2018; 89(1): 19–27. PubMed Abstract \| Publisher Full Text\n\nTarannum F, Faizuddin M: Effect of gene polymorphisms on periodontal diseases. Indian. J Hum Genet. 2012; 18(1): 9–19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPathan MM, Bhat KG, Joshi VM: Comparative evaluation of the efficacy of a herbal mouthwash and chlorhexidine mouthwash on select periodontal pathogens: An in vitro and ex vivo study. J Indian Soc Periodontol. 2017; 21(4): 270–275. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRafiei M, Kiani F, Sayehmiri F, et al.: Study of Porphyromonas gingivalis in periodontal diseases: A systematic review and meta-analysis. Med J Islam Repub Iran. 2017; 31: 62. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDowarah R, Verma AK, Agarwal N, et al.: Selection and characterization of probiotic lactic acid bacteria and its impact on growth, nutrient digestibility, health and antioxidant status in weaned piglets. PLoS One. 2018; 13(3): e0192978. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFishbein AB, Fuleihan RL: The hygiene hypothesis revisited: does exposure to infectious agents protect us from allergy? Curr Opin Pediatr. 2012; 24(1): 98–102. PubMed Abstract \| Publisher Full Text\n\nTse K, Horner AA: Allergen tolerance versus the allergic march: the hygiene hypothesis revisited. Curr Allergy Asthma Rep. 2008; 8(6): 475–83. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang P, Duan D, Zhou X, et al.: Relationship between expression of human gingival beta-defensins and levels of periodontopathogens in subgingival plaque. J Periodontal Res. 2014; 50(1): 113–122. PubMed Abstract \| Publisher Full Text\n\nTomitaa S, Komiya-Ito A, Imamura K, et al.: Prevalence of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythia in Japanese patients with generalized chronic and aggressive periodontitis. Microb Pathog. 2013; 61-62: 11–15. PubMed Abstract \| Publisher Full Text\n\nTing Z, Hong X, Zhaohui Y: Relationships of five periodontal pathogens causing subgingival plaque in patients with chronic periodontitis under different periodontal conditions. West China J Stomatol. 2013; 5: 518–21. PubMed Abstract\n\nAmano A, Kuboniwa A, Nakagawa I, et al.: Prevalence of specific genotypes of Porphyromonas gingivalis fimA and periodontal health status. J Dent Res. 2000; 79(9): 1664–8. PubMed Abstract \| Publisher Full Text\n\nLu R, Feng L, Gao X, et al.: Relationship between volatile fatty acids and Porphyromonas gingivalis and Treponema denticola in gingival crevicular fluids of patients with aggressive periodontitis. Beijing Da Xue Xue Bao. 2013; 45(1): 12–16. PubMed Abstract\n\nScapoli L, Girardi A, Palmieri A, et al.: Microflora and periodontal disease. Dent Res J (Isfahan). 2012; 9(2): S202–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarinci F, Scapoli L, Girardi A, et al.: Oral microflora and periodontal disease: new technology for diagnosis in dentistry. Ann Stomatol. 2013; 5(2): 170–3. PubMed Abstract \| Free Full Text\n\nAvila-Campos MJ, Velasquez-Melendez G: Prevalence of putative periodontopathogens from periodontal patients and healthy subjects in São Paulo SP Brazil. Rev Inst Med trop S. Paulo. 2002; 44(1): 1–5. PubMed Abstract \| Publisher Full Text\n\nWilson M, Lopatin D, Osborne G, et al.: Prevalence of Treponema denticola and Porphyromonas gingivalis in plaque from periodontally- healthy and periodontally-diseased sites. J Med Microbiol. 1993; 38: 406–10. PubMed Abstract \| Publisher Full Text\n\nRiep B, Edesi-Neuss L, Claessen F, et al.: Are putative periodontal pathogens reliable diagnostic markers? J Clin Microbiol. 2009; 47(6): 1705–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKato A, Imai K, Ochiai K, et al.: Higher Prevalence of Epstein–Barr Virus DNA in Deeper Periodontal Pockets of Chronic Periodontitis in Japanese Patients. PLoS ONE. 2013; 8(8): e71990. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKato A, Imai K, Ochiai K, et al.: Salivary detection of periodontopathic bacteria in Fanconi’s anemia patients. Anaerobe. 2013; 24: 32–35. PubMed Abstract \| Publisher Full Text\n\nRafiei M, Kiani F, Sayehmiri F, et al.: Study of Porphyromonas gingivalis in periodontal diseases: A systematic review and meta-analysis. Med J Islam Repub Iran. 2017; 31: 62. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOkamoto S, Taniuchi S, Sudo K, et al.: Predictive value of IgE/IgG4 antibody ratio in children with egg allergy. Allergy Asthma Clin Immunol. 2012; 8: 9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPortnoy J: IgE in Clinical Allergy and Allergy Diagnosis. [accessed on 1 July 2018]. Reference Source\n\nHerman RA, Ladics GS: Allergenic sensitization versus elicitation risk criteria for novel food proteins - short communication. Regul Toxicol Pharmacol. 2018; 94: 283–5. PubMed Abstract \| Publisher Full Text\n\nMatthews CR, Joshi V, de Jager M, et al.: Host-bacterial interactions during induction and resolution of experimental gingivitis in current smokers. J Periodontol. 2013; 84(1): 32–40. PubMed Abstract \| Publisher Full Text\n\nFinlay BB, McFadden G: Anti-Immunology: Evasion of the Host Immune System by Bacterial and Viral Pathogens. Cell. 2006; 124(4): 767–782. PubMed Abstract \| Publisher Full Text\n\nSchmid-Hemple P: Immune defence, parasite evasion strategies and their relevance for ‘macroscopic phenomena’ such as virulence. Philos Trans R Soc Lond B Biol Sci. 2009; 364(1513): 85–98. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTheodorou GL, Marousi S, Ellul J, et al.: T helper 1 (Th1)/Th2 cytokine expression shift of peripheral blood CD4+ and CD8+ T cells in patients at the post-acute phase of stroke. Clin Exp Immunol. 2008; 152(3): 456–63. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuo HW, Yun CX, Hou GH, et al.: Mangiferin attenuates TH1/TH2 cytokine imbalance in an ovalbumin-induced asthmatic mouse model. PLoS One. 2014; 9: e100394. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEttinger R, Karnell JL, Henault J, et al.: Pathogenic mechanisms of IgE-mediated inflammation in self-destructive autoimmune responses. Autoimmunity. 2017; 50(1): 25–36. PubMed Abstract \| Publisher Full Text\n\nVarricchi G, Raap U, Rivellese F, et al.: Human mast cells and basophils-How are they similar how are they different? Immunol Rev. 2018; 282(1): 8–34. PubMed Abstract \| Publisher Full Text\n\nNelwan SC, Nugraha RA, Endaryanto A, et al.: Modulating toll-like receptor-mediated inflammatory responses following exposure of whole cell and lipopolysaccharide component from Porphyromonas gingivalis in wistar rat models. Eur J Dent. 2017; 11(4): 422–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNelwan SC, Nugraha RA, Endaryanto A, et al.: Converging findings from linkage between periodontal pathogen with atopic and allergic immune response. Cytokine. 2019; 113: 89–98. PubMed Abstract \| Publisher Full Text\n\nSaulite I, Hoetzenecker W, Guenova E, et al.: Skin Test Reactivity to Hymenoptera Venom after Venom Immunotherapy Correlates Inversely with the IgG/IgE Ratio. Int Arch Allergy Immunol. 2017; 174(3-4): 190–9. PubMed Abstract \| Publisher Full Text\n\nGarman L, Smith K, Muns EE, et al.: Unique Inflammatory Mediators and Specific IgE Levels Distinguish Local from Systemic Reactions after Anthrax Vaccine Adsorbed Vaccination. Clin Vaccine Immunol. 2016; 23(8): 664–71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDeo SS, Mistry KJ, Kakade AM, et al.: Role played by Th2 type cytokines in IgE mediated allergy and asthma. Lung India. 2010; 27(2): 66–71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKubo M: T follicular helper and TH2 cells in allergic responses. Allergol Int. 2017; 66(3): 377–81. PubMed Abstract \| Publisher Full Text\n\nZhang Y, Fear DJ, Willis-Owen SA, et al.: Global gene regulation during activation of immunoglobulin class switching in human B cells. Sci Rep. 2016; 6: 37988. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPlatts-Mills TA, Vaughan JW, Blumenthal K, et al.: Serum IgG and IgG4 antibodies to Fel d 1 among children exposed to 20 microg Fel d 1 at home: relevance of a nonallergic modified Th2 response. Int Arch Allergy Immunol. 2001; 124: 126–9. PubMed Abstract \| Publisher Full Text\n\nRamadani F, Bowen H, Upton N, et al.: Ontogeny of human IgE-expressing B cells and plasma cells. Allergy. 2017; 72(1): 66–76. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAalberse RC, Platts-Mills TA, Rispens T: The Developmental History of IgE and IgG4 Antibodies in Relation to Atopy, Eosinophilic Esophagitis, and the Modified TH2 Response. Curr Allergy Asthma Rep. 2016; 16(6): 45. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHatipoğlu U, Subramanian A, Campbell T, et al.: Intrasubject Variability in Total IgE Levels in Patients with Moderate to Severe Persistent Allergic Asthma Over 1 Year. J Allergy Clin Immunol Pract. 2016; 4(4): 691–6. PubMed Abstract \| Publisher Full Text\n\nNelwan SC, Nugraha RA, Endaryanto A, et al.: Raw Data - Atopic Biomarker Changes after Exposure to Porphyromonas gingivalis Lipopolysaccharide: A Small Experimental Study in Wistar Rat. figshare. Dataset. 2021. Publisher Full Text\n\n\n\n\nANOVA\n\nanalysis of variant\n\nBCR\n\nB cell receptor\n\nCD-40\n\nCluster Differentiation-40\n\nCFU\n\ncolony-forming unit\n\nCSR\n\nclass-switch recombination\n\ndf\n\ndegree of freedom\n\nELISA\n\nenzyme-linked immunosorbent assay\n\nFDA\n\nFood and Drug Administration\n\nHDM\n\nhouse dust mite\n\nIACUC\n\nInstitutional Animal Care and Use Committee\n\nIFN-γ\n\ngamma-Interferon\n\nIgE\n\nimmunoglobulin-E\n\nIgG4\n\nimmunoglobulin-G 4\n\nIL\n\ninterleukin\n\nLLPC\n\nlong-lived plasma cell\n\nLPS\n\nlipopolysaccharide\n\nmAb\n\nmonoclonal antibody\n\nMAC\n\nmembrane attack complex\n\nMHC\n\nmajor histocompatibility complex\n\nNIH\n\nNational Institutes of Health\n\nNGS\n\nnext-generation sequencing\n\nNK\n\nnatural killer cells\n\nOIT\n\noral immunotherapy\n\nPAMP\n\npathogen-associated molecular patterns\n\nPCR\n\nPolymerase Chain Reaction\n\nPg\n\nPorphyromonas gingivalis\n\nSD\n\nstandard deviation\n\nSEM\n\nstandard error of the mean\n\nSPSS\n\nStatistical Package for the Social Sciences\n\nTh-1\n\ntype-1 helper T-cells\n\nTh-2\n\ntype-2 helper T-cells\n\nTNF-α\n\nTumor Necrosis Factor-α" }	[ { "id": "92329", "date": "31 Aug 2021", "name": "Carla Alvarez", "expertise": [ "Reviewer Expertise Periodontology", "Immunology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Manuscript by Nelwan et al. presents a pilot study where they administer different concentrations of Pg LPS by Intra-sulcular injection to rats and then analyzed the IgE and IgG4 after 0, 4, and 11 days in the peripheral blood serum by ELISA. The results are that Pg injection increased both IgE and IgG4 at days 4 and 11 post-injection. IgE concentration was increased to a higher extend than IgG4.\nOverall Comments:\nEven though the study is simple in its design and results, the data analysis results layout (plots and tables) and all sections are very confusing. The study is presented as a pilot study (small experimental study), yet they provided a sufficient sample size to achieve statistical significance, which needs to include an appropriately detailed analysis.\n\nSpecific comments:\nThe introduction does not explain why the authors decided to perform this study. The sentence: ‘Since humoral immune responses are stimulated following Pg infection, there might be a link to the occurrence of atopy’ is extremely vague. There are no references to support that connection of ideas.\n\nThe link between periodontitis and atopy is not explained, and the literature does not back several statements. For instance, the sentence “Rather than alveolar bone and ligament destruction, Pg is believed to be involved with the development of atopic responses in a susceptible host” has as reference Sperr et al.: Prevalence of Comorbidities in Periodontitis Patients Compared to the General Austrian Population. J Periodontol. 2018; 89(1): 19–27. What authors believe that Pg is involved in the development of atopic responses in a host? And why? These are critical elements missing in the introduction.\n\nThe sentence “there is an unequivocally accepted fact that the prevalence of atopy increases more among children who have periodontal pathogen colonization or infection” is a bold statement with no literature backup. The paper cited is Dowarah R et al.: Selection and characterization of probiotic lactic acid bacteria and its impact on growth, nutrient digestibility, health, and antioxidant status in weaned piglets. PLoS One. 2018; 13(3): e0192978. How does that paper in piglets explain that unequivocally accepted fact in human children?\n\nA proper introduction must explain all the variables studied in the paper and present them in an organized and coherent way. The knowledge gap must be evident and support the hypothesis established by the authors and the experimental design. All this, using solid references that can accurately backup the statements as are presented.\n\nThe results should be three grouped graphs: IgE and IgG4 concentrations, then the ratio of them, that’s it. There is no need for most tables, and the graphs should show which group is significantly different from another group by using asterisks. The authors should use a posthoc analysis after ANOVA to show the individual comparisons in the graph.\n\nThe discussion is very confusing; the authors often change the topic or don’t explain the point they try to make. Also, several statements have no literature references, such as “Th-1 and Th-2 cells are not two different CD4+ T-cell subsets, but it represents polarized forms of the highly heterogenous CD4+ Th cell-mediated immune response”, is again a bold statement with no references. Please check the relevant literature.\n\nI suggest including in your discussion the following elements: What are the significant findings of the study, their meaning, and why are they important? Relate the results to those of similar studies. Clarify alternative explanations of your results. State what is the relevance of the conclusions in the clinical scenario. Suggest future studies and provide a conclusion with a take-home message. Don’t overinterpret the results, provide unwarranted speculation or explain tangential issues.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11352", "date": "30 May 2024", "name": "Ricardo Adrian Nugraha", "role": "Author Response", "response": "Even though the study is simple in its design and results, the data analysis results layout (plots and tables) and all sections are very confusing. The study is presented as a pilot study (small experimental study), yet they provided a sufficient sample size to achieve statistical significance, which needs to include an appropriately detailed analysis. Answer: thank you for your comment. We have included statement “this study had limitations with regard to very small number of samples which can increase the likelihood of error and imprecision” in the Limitation subsection, thus readers should be careful when interpreted results of our study. The introduction does not explain why the authors decided to perform this study. The sentence: ‘Since humoral immune responses are stimulated following Pg infection, there might be a link to the occurrence of atopy’ is extremely vague. There are no references to support that connection of ideas. Answer: Thank you for your suggestion. We chose to delete statement ‘Since humoral immune responses are stimulated following Pg infection, there might be a link to the occurrence of atopy’ The link between periodontitis and atopy is not explained, and the literature does not back several statements. For instance, the sentence “Rather than alveolar bone and ligament destruction, Pg is believed to be involved with the development of atopic responses in a susceptible host” has as reference Sperr et al.: Prevalence of Comorbidities in Periodontitis Patients Compared to the General Austrian Population. J Periodontol. 2018; 89(1): 19–27. What authors believe that Pg is involved in the development of atopic responses in a host? And why? These are critical elements missing in the introduction. Answer: Thank you for your very constructive feedback. We have replaced the references to support our statement. Takaoka et al (2022) reported an estimate of the RR and OR between metal allergy, periodontitis, and PPP in patients who visited a dental metal allergy clinic. It was shown that the periodontal disease risk was 2.54 times higher in patients with PPP than in PPP-negative patients. The OR for periodontal disease between patients with PPP and the PPP-negative patients in the national average was 2.63. The sentence “there is an unequivocally accepted fact that the prevalence of atopy increases more among children who have periodontal pathogen colonization or infection” is a bold statement with no literature backup. The paper cited is Dowarah R et al.: Selection and characterization of probiotic lactic acid bacteria and its impact on growth, nutrient digestibility, health, and antioxidant status in weaned piglets. PLoS One. 2018; 13(3): e0192978. How does that paper in piglets explain that unequivocally accepted fact in human children? Answer: thank you for your correction. We have replaced that references with Teles F et al (2022) who investigates the biological basis of the connections between periodontal diseases and systemic allergic conditions which generally emphasized the bacteriome. A proper introduction must explain all the variables studied in the paper and present them in an organized and coherent way. The knowledge gap must be evident and support the hypothesis established by the authors and the experimental design. All this, using solid references that can accurately backup the statements as are presented. Answer: thank you for your very well suggestion. We try to make more proper introduction according to your suggestion. The results should be three grouped graphs: IgE and IgG4 concentrations, then the ratio of them, that’s it. There is no need for most tables, and the graphs should show which group is significantly different from another group by using asterisks. The authors should use a posthoc analysis after ANOVA to show the individual comparisons in the graph. Answer: thank you for your suggestion, but we decided to show the tables for the readers to easier understanding the analysis behind each graphs. The discussion is very confusing; the authors often change the topic or don’t explain the point they try to make. Also, several statements have no literature references, such as “Th-1 and Th-2 cells are not two different CD4+ T-cell subsets, but it represents polarized forms of the highly heterogenous CD4+ Th cell-mediated immune response”, is again a bold statement with no references. Please check the relevant literature. Even though thank you for your very well suggestion. We try to make more proper discussion according to your suggestion and add the references for our statement. I suggest including in your discussion the following elements: What are the significant findings of the study, their meaning, and why are they important? Relate the results to those of similar studies. Clarify alternative explanations of your results. State what is the relevance of the conclusions in the clinical scenario. Suggest future studies and provide a conclusion with a take-home message. Don’t overinterpret the results, provide unwarranted speculation or explain tangential issues. Answer: thank you for your very well suggestion. We try to make more proper discussion according to your suggestion." } ] }, { "id": "92330", "date": "14 Sep 2021", "name": "Tomoki Maekawa", "expertise": [ "Reviewer Expertise Immunology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper reaches its conclusions based on data from a small number of analysis samples, making it difficult to evaluate. In particular, there are few prerequisite statements and reference papers on the relevance of IgG and IgG4 in periodontitis, and the purpose of the study is not clear. No rationale was given for using Pg LPS in measuring pan-IgG4 and IgE levels that makes this manuscript a simple descriptive survey.\nEnsure all the references are appropriately selected. Some of the references in this manuscript are not presented correctly. The authors should refer to the comprehensive scientific paper in such a scientific journal.\n\nThere are many papers that stated IgG rises when Pg (not only Pg but also the other LPS) is administered, so the authors need to be clear about what is new and what the purpose is.\n\nA more detailed explanation of the relationship between IgG4 and IgG and periodontal disease is needed.\n\nIn the Introduction, Ref 2 Mazurek et al. paper is too specific to cite since this paper mentioned the influence of KIR gene presence/absence polymorphisms, which the description has not related to a comprehensive explanation of periodontitis. Ref 3 is also an irrelevant paper, it is a review of comorbidities. Moreover, Refs 4, 5, 7, 8 suddenly appeared immunoglobulin-E skew and is not suitable for citing. Some of the references cannot be found in NCBI (i.e. Refs 14, 24).\n\nPlease check all references throughout the paper.\n\nMaterial and Methods are poorly written. How do the authors isolate LPS from Pg? The authors should describe the strain of Pg you selected.\n\nDiscussion, page 8, third line from the back: wrong reference papers are cited.\n\nLPS Pg should be Pg LPS.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "11351", "date": "30 May 2024", "name": "Ricardo Adrian Nugraha", "role": "Author Response", "response": "This paper reaches its conclusions based on data from a small number of analysis samples, making it difficult to evaluate. In particular, there are few prerequisite statements and reference papers on the relevance of IgG and IgG4 in periodontitis, and the purpose of the study is not clear. No rationale was given for using Pg LPS in measuring pan-IgG4 and IgE levels that makes this manuscript a simple descriptive survey. Answer: thank you for your comment. We have included statement “this study had limitations with regard to very small number of samples which can increase the likelihood of error and imprecision” in the Limitation subsection, thus readers should be careful when interpreted results of our study Ensure all the references are appropriately selected. Some of the references in this manuscript are not presented correctly. The authors should refer to the comprehensive scientific paper in such a scientific journal. Answer: thank you for your suggestion, we have re-checked and replaced several references which are inappropriate. There are many papers that stated IgG rises when Pg (not only Pg but also the other LPS) is administered, so the authors need to be clear about what is new and what the purpose is. Answer: thank you for your very constructive feedback. We understood that several conflicting literatures are existed and try to included them fairly. A more detailed explanation of the relationship between IgG4 and IgG and periodontal disease is needed. Answer: thank you for your very constructive feedback. We have added more detailed explanation regarding the relationship between IgG4 and IgG and periodontal disease In the Introduction, Ref 2 Mazurek et al. paper is too specific to cite since this paper mentioned the influence of KIR gene presence/absence polymorphisms, which the description has not related to a comprehensive explanation of periodontitis. Ref 3 is also an irrelevant paper, it is a review of comorbidities. Moreover, Refs 4, 5, 7, 8 suddenly appeared immunoglobulin-E skew and is not suitable for citing. Some of the references cannot be found in NCBI (i.e. Refs 14, 24). Answer: thank you for your suggestion, after discussion among co-authors, we have replaced several references which are too specific to support our hypothesis. Please check all references throughout the paper. Answer: thank you for your suggestion, we have re-checked and replaced several references which are inappropriate. Material and Methods are poorly written. How do the authors isolate LPS from Pg? The authors should describe the strain of Pg you selected. Answer: The Porphyromonas gingivalis strains W50 and W83 were obtained from the culture collection of Institute of Tropical Disease Universitas Airlangga. The purified LPS was solubilized in sample buffer to the desired concentration (1 mg/mL), and boiled for 5 min with denatured proteins in a hot MgCl2-Triton X-100 solution, solubilization with EDTA-Triton X-100 and precipitation with MgCl2. After that, 16 µL/well from each sample was separated on 15% SDS gel with a 4% stacking gel under reducing condition at 100 mA for 2 hr using mini-PROTEAN electrophoresis instrument (Bio-Rad Laboratories, California, USA). Silver and coomassie blue staining of the gels was performed according to the standard protocol. Staining of agarose gel with ethidium bromide was done as well in order to show if any contamination with nucleic acids persist. To do this, 10 µL/well of reconstituted LPS from Porphyromonas gingivalis and also 10 µL/well bacterial suspensions (108 CFU/ mL), as positive control, were loaded on agarose gel and stained with ethidium bromide. Discussion, page 8, third line from the back: wrong reference papers are cited. Answer: thank you for your suggestion, after discussion among co-authors, we have replaced that reference you mentioning. LPS Pg should be Pg LPS. Answer: thank you for your feedback. We have replaced LPS Pg with Pg LPS" } ] } ]	1	https://f1000research.com/articles/10-371
https://f1000research.com/articles/12-429/v1	21 Apr 23	{ "type": "Research Article", "title": "A systematic investigation of detectors for low signal-to-noise ratio EMG signals", "authors": [ "Monisha Yuvaraj", "Priyanka Raja", "Ann David", "Etienne Burdet", "Varadhan SKM", "Sivakumar Balasubramanian", "Monisha Yuvaraj", "Priyanka Raja", "Ann David", "Etienne Burdet", "Varadhan SKM" ], "abstract": "Background: Active participation of stroke survivors during robot-assisted movement therapy is essential for sensorimotor recovery. Robot-assisted therapy contingent on movement intention is an effective way to encourage patients' active engagement. For severely impaired stroke patients with no residual movements, a surface electromyogram (EMG) has been shown to be a viable option for detecting movement intention. Although numerous algorithms for EMG detection exist, the detector with the highest accuracy and lowest latency for low signal-to-noise ratio (SNR) remains unknown.\nMethods: This study, therefore, investigates the performance of 13 existing EMG detection algorithms on simulated low SNR (0dB and -3dB) EMG signals generated using three different EMG signal models: gaussian, Laplacian, and biophysical model. The detector performance was quantified using the false positive rate (FPR), false negative rate (FNR), and detection latency. Any detector that consistently showed FPR and FNR of no more than 20%, and latency of no more than 50ms, was considered an appropriate detector for use in robot-assisted therapy. Results: The results indicate that the Modified Hodges detector – a simplified version of the threshold-based Hodges detector introduced in the current study – was the most consistent detector across the different signal models and SNRs. It consistently performed for ~90% and ~40% of the tested trials for 0dB and -3dB SNR, respectively. The two statistical detectors (Gaussian and Laplacian Approximate Generalized Likelihood Ratio) and the Fuzzy Entropy detectors have a slightly lower performance than Modified Hodges.\nConclusions: Overall, the Modified Hodges, Gaussian and Laplacian Approximate Generalized Likelihood ratio, and the Fuzzy Entropy detectors were identified as the potential candidates that warrant further investigation with real surface EMG data since they had consistent detection performance on low SNR EMG data.", "keywords": [ "EMG detectors", "Low SNR EMG", "Movement intent detection", "EMG-BCI", "Robot-assisted therapy", "Neurorehabilitation" ], "content": "Introduction\n\nSubstantial recovery of sensory-motor function after a stroke is possible with high-intensity and high-dosage movement training.1 Rehabilitation robots can facilitate such high-intensity movement training while providing physical assistance to the user for completing movements consistently and precisely. About 30% of stroke survivors are severely impaired2,3 and require physical assistance to actively engage in movement training. While physical assistance from a robot can motivate such subjects to attempt and train movements, they can also provide inappropriately timed or too much assistance4,5 leading to slacking, where patients reduce their voluntary effort and exploit robotic assistance to perform the movements. Inappropriately timed robotic assistance also alters the patient’s sense of agency or subjective awareness of control. This could lead to a lack of intrinsic motivation and attention, affecting motor learning and performance.6 Positive therapeutic effects have been observed only when patients actively engage in therapy.7–10 Jo et al.11 reported no improvement in clinical scales with passive range of motion therapy. Thus, active patient participation during movement therapy is an essential ingredient for sensorimotor recovery.\n\nRobotic assistance contingent on a subject’s intention to move is an effective way to guide neuroplasticity.12 However, it can be difficult to detect the intention to move in stroke patients with no residual movement. Electroencephalogram (EEG) based brain-computer interface (BCI) has been used to detect movement intention in order to trigger robotic movement assistance and the effectiveness of EEG-BCI in robot-assisted rehabilitation has been investigated in several studies.13–19 Ramos et al. reported a 3 point improvement in the Fugl-Meyer assessment (FMA) score of the experimental group who were given robot-assisted therapy contingent on movement intention.17 There are, however, several drawbacks to EEG-BCI systems:\n\n1) They have a poor signal-to-noise ratio (SNR) with large trial-to-trial intra-subject variability.20 The use of sophisticated signal processing techniques can increase the delay in intent detection, which can result in inappropriately timed robotic assistance leading to suboptimal recovery12,21\n\n2) EEG-BCI modalities do not precisely identify which limb segment is intended to move due to its low information rate.21\n\n3) Event-related desynchronization of the EEG sensorimotor rhythm may not necessarily reflect movement intention.22\n\n4) Critical for practical use, current EEG-BCI systems are too complex and time-consuming for clinical work.23\n\nElectromyogram (EMG) could be a viable alternative to address these drawbacks of the EEG-BCI modality for robot-assisted therapy. EMG is a simple, robust, compact modality suitable for routine clinical use. In a recent study, we identified EMG as a potential alternative to EEG-BCI to detect movement intention from severely affected stroke patients without residual movement.23 About 70% (22 out of the 30) of the study participants had residual EMG in the forearm muscles that showed a consistent increase in amplitude with wrist/finger movement attempts.\n\nHowever, our study reported poor agreement between the EEG and EMG modalities for detecting movement intention. The authors suggested that this discrepancy could be because of the simple root mean square detector with temporal thresholding that was used. This detector may not optimally pick up low SNR surface EMG signals23 expected from severe patients with no residual movements.\n\nNumerous EMG detection algorithms have been proposed for the automatic detection of EMG onset.24–31 The review article by Staude et al.24 compared different EMG detector types to identify the best detectors for detecting EMG onset.24 However, this work was done on high SNR (3dB and 6dB) simulated EMG signals generated by bandpass-filtering white Gaussian noise, and it only investigated detectors reported till 2001. Other detectors have been reported in the last 20 years, and a systematic characterization of existing EMG detector types on low SNR EMG signals (generated using different signal models) is still lacking. Identifying an optimal detector is essential for further exploring the use of EMG-based movement intent detection for robot-assisted therapy in severely affected stroke subjects with no residual movements.\n\nOur goal in this study is to systematically compare the detection accuracy and latency of existing EMG detectors on low SNR EMG signals to identify the most promising detectors, while eliminating the ones with poor performance, for further investigation. To this end, we will here:\n\n• Generate simulated low SNR (0dB and -3dB) EMG data using two phenomenological (Gaussian and Laplacian) models and a biophysical model to evaluate the performance of the different detector types.\n\n• Define an appropriate cost function considering the detection accuracy and latency to evaluate the performance of the different detector types.\n\n• Compare the performance of the different detector types on simulated surface EMG signals from the three signal models for two different SNRs (0dB and -3dB) and identify the most appropriate detector type(s).\n\nWe note that the detectors studied in this work produce a binary output suitable for on-off control of robotic assistance during therapy. This is in contrast to previous studies exploring continuous control paradigms using EMG amplitude estimates on less severely affected stroke patients with some residual limb movements32,33 However, for severely affected patients with no residual movements, who may or may not have detectable EMG, an on-off control scheme might be the easiest modality for human-robot interaction. Continuous control schemes might be appropriate as patients gain better control of their muscles that are still too weak to produce residual movements.\n\n\nMethods\n\nNeurorehabilitation training consists of repeating specific movements of interest punctuated by periods of rest.17,34 A typical training session will involve several “trials” of a particular movement, each with a period of rest (rest-phase) followed by a period of movement/movement attempt (move-phase). In EMG-triggered robot-assisted therapy, robotic assistance is triggered whenever EMG is detected in real-time in the target muscle during the move phase of a trial. In this paper, EMG always refers to surface-recorded muscle activity, as this modality will most likely be employed in routine robot-assisted therapy. The rest of this section starts with the formal definition of the signal processing problem solved by an EMG detector, followed by the details of the simulated EMG signals, a description of the general structure of EMG detectors, and the approach used to compare the performance of the different detectors.\n\nLet xin,0≤n<Nt be the recorded signal from a target muscle during the ith trial; n is the sampling instant, where n=0 is the start of a trial, Nt is the number of data points from each trial. Let Nr and Nm be the number of samples in the rest- and move-phases of a trial, respectively, then Nt=Nr+Nm. The time segments 0≤n<Nr and Nr≤n<Nt correspond to the rest-phase and move-phase of the trial, respectively.\n\nProblem definition: To detect the presence of EMG in real-time in the move-phase of a trial using only the current and past EMG data xk,0≤k≤n from the start of the trial. Let yn represent the binary output of the EMG detector at the current sampling instant n,\n\nwhere, D∙ is the detector function that maps the EMG signal xkk=0n, from the start of a trial to a binary output corresponding to the presence or absence of EMG at the current time instant n; p is the set of detector parameters that control the detector’s performance. The function D∙ is often a complex mathematical operation consisting of a series of simpler operations performed on the EMG data to produce the binary output. This binary output can be used as a simple on/off control of robotic assistance by severely affected patients to relearn movement initiation.35,36\n\nThe analysis of the different EMG detectors was performed using simulated EMG data. To generate this simulated EMG, we assume that:\n\n• the measurement noise has a fixed variance throughout the experiment,\n\n• the muscle is fully relaxed in the rest-phase of any trial, i.e., there is no EMG activity from the target muscle during the rest-phase, and\n\n• the muscle is activated at a constant level for the entire duration of the move-phase.\n\nThese assumptions were made to evaluate the EMG detectors under the conditions that: (a) the EMG signal has a fixed signal-to-noise ratio (SNR) in the move-phase, and (b) all other intra- and inter-trial variabilities in the EMG signal characteristics are minimized. The detectors that perform poorly under these ideal conditions will likely perform worse with real EMG data from patients, since real EMG data from severely affected stroke patients might occur in random bursts and is likely to have time-varying amplitude.\n\nWe simulated 100 trials of EMG data with an individual trial duration of 13 seconds (8 s and 5 s for rest- and move-phases, respectively). The sampling frequency of the simulated signal was set to 1000 Hz. Three different EMG signal generation models were employed in the current analysis – two phenomenological (Gaussian and Laplacian) models and one biophysical model. The phenomenological models were based on the work of De Luca37 where a surface EMG signal from a muscle activated at a fixed level can be treated as zero-mean white noise followed by a shaping filter (electrode properties); this model is widely accepted in the literature.24,38–41 The exact probability density of the EMG signal depends on the muscle activation level, with high levels of activation following a Gaussian distribution.38,39 However, at low levels of muscle activation, EMG signals have been reported to follow a distribution that lies between a Gaussian and a Laplacian distribution.42 Therefore, to ensure that the detectors are tested with the appropriate signals, we generated data using both white Gaussian and white Laplacian signals, resulting in two phenomenological models.\n\nThe first step in this model is the generation of the zero-mean unit-variance white Gaussian and Laplacian noise en. A step change in the signal variance, within a trial, at the transition between the rest- and move-phases of a trial was obtained by multiplying en by σn:\n\nIn addition to the phenomenological models, we also wanted to test the detectors on more realistic data based on the biophysics of the EMG signal, accounting for the physiological origin of the electrical muscle activity and the recording electrode geometry. In this paper, the biophysical model proposed in Devasahayam S43 was employed to generate the simulated EMG data. Assuming a linear, isotropic volume conduction model, a simple muscle geometry with parallel muscles fibres ignoring the effects due to the finite muscle fibre length, the EMG recorded by a bipolar electrode configuration can be approximated using the following expression:\n\nThe EMG simulator developed by Devasahayam41 was employed in the current work to generate the simulated EMG signals.43 A bipolar surface electrode configuration with a 10 mm interelectrode distance was considered. The simulator takes in the muscle force level as its input and computes the corresponding firing pattern for the motor units. In the current study, the force levels from the muscle were set to 0N in the rest-phase (no muscle activation) and 10N in the move-phase (average firing rate of 16.4 Hz for the muscle). The simulator generated pure muscle activity xpuren recorded by the chosen electrode configuration. The force level for the muscle in the move-phase was chosen empirically to ensure that the temporal profile of the simulated EMG signal xpuren0≤n≤Nt visually resembled that of real surface EMG signals. A zero-mean white Gaussian noise en of fixed noise variance σ02 was added to xpuren to introduce measurement noise. The noise variance was chosen based on the signal power (σ12) of xpuren in the move-phase to obtain a signal with the desired SNR:\n\nFollowing this, the noisy signal xpuren+en is bandpass filtered (8th order non-causal FIR filter) between 10 Hz and 450 Hz cut-off frequencies:\n\nThe three rows correspond to the three different signal models: Biophysical in the top row, Gaussian in the middle, and Laplacian in the bottom row. The left most column shows the time series of the simulated 13 seconds of data with the first 8 seconds corresponding to the rest phase and the next 5 seconds to the move phase. The middle column shows the corresponding Fourier magnitude spectrum of the 5 seconds of move phase data. The right column displays the estimate of the probability density functions of the 5 seconds of move phase data from the three models.\n\nThe general structure for EMG detectors proposed by Staude et al.24 is shown in Figure 2, which consists of three steps carried out sequentially to map the given real-time EMG data into a binary output:\n\n1. Signal conditioning is the first step to improve EMG signal quality for better detection, often involving high-pass filtering for movement artefact removal. Some detectors might employ additional filtering operations, such as adaptive whitening for stable EMG amplitude estimation.44,45 The conditioned signal is represented by\n\n2. Test function computation transforms x~n into a scalar variable or feature that can distinguish the presence or absence of EMG. The test function gn is computed at the current time instant n over a causal window of size W:\n\nSome examples of test functions in the literature include the moving average of x~n, χ2 test variable,46 likelihood ratio47 etc.\n\n3. A decision rule is applied on the test function gn by comparing it to a threshold h to identify the presence/absence of an EMG signal:\n\nSome detectors employ a more sophisticated decision rule, such as double thresholding, to control the false positive rates of detection.46,48\n\nWe note that each detector has a set of parameters associated with it. The current study compares the performance of 13 detector types reported in the literature which can be implemented in real-time, listed in Table 1. Each detector type fits into the general structure shown in Figure 2. The different parameters associated with these detector types are also provided in Table 2. A detailed description of the individual detector types and the algorithms for their implementation are provided in the extended data (Table S1). All detector algorithms were obtained from the literature and implemented in MATLAB51 with appropriate modifications required for real-time detection.\n\nThe simulated EMG data from the three different signal models and the two different SNRs were used to evaluate the performance of the different detector types. Each trial of EMG signal (13 seconds long) was input to the different detectors to compute binary output indicating the presence or absence of EMG signal. The performance of a detector must consider the accuracy (false positive and false negative rate) and the detection latency. These are computed from the output yn of each trial (Figure 3), where the EMG signal from each trial was analysed in the following three steps:\n\n1. the first three seconds (0–3s) of the rest-phase data is used for estimating the threshold h for detection:\n\n2. the remaining 5 seconds of the rest-phase are used to estimate the false positive rate rFP.\n\n3. the 5 seconds of the move-phase are used to estimate the false negative rate rFN and the detection latency ∆t.\n\nThe plot shows the rectified EMG signals, its lowpass filtered output, and the binary output from the detector. The trial is 13 seconds long with first 8 seconds corresponding to the rest-phase and the next 5 seconds to the move-phase. The rest-phase is further divided into the baseline phase (yellow background) that is used for computing the threshold h, and the remaining rest-phase (red background) is used for computing rFP. The move-phase (green background) is used to compute ∆t and rFN.\n\nWe defined a performance measure to compute a single number referred to as the cost of detection that considers the false positive rate rFP, the false negative rate rFN, and the detection latency ∆t. Let c≜rFPrFNf∆tT be the cost vector associated with the output yn of the detector for a particular trial. We define the cost of detection C as the infinity norm of the cost vector c.\n\nThe false positive rate rFP is defined as the ratio of the number of 1s in the detector output yn in the rest-phase of a trial, and the false negative rate rFN is defined as the ratio of the number of 0s in yn in the move-phase.\n\nFrom Figure 3, the detection latency is defined as the time delay from the start of the move-phase to when the detector output goes to 1:\n\nLatencies between 0 to 250 ms have linearly increasing costs while the ones above 250 ms are considered as bad as 250 ms. Based on the definitions of rFP, rFN, and f∆t, C∈01. A detector with a consistently lower cost of detection C would be considered a better detector.\n\nA detector’s performance or cost is determined by the SNR of the input signal, the detector type, and its associated parameters. Thus, for a fixed SNR input signal, comparing two detector types must be done only after controlling for the influence of their corresponding detector parameters. In the current work, this was done by first choosing the optimal parameters for each detector type, before comparing different detector types. The optimal parameters for a detector type were selected by first splitting the 100 movement trials of simulated EMG data of the three models (which was generated as explained above) into training and validation datasets with 50 trials each. This was done for both SNRs (0dB and -3dB) and for all three signal models (Gaussian, Laplacian, and biophysical). The training dataset was used to identify the optimal parameter values for the different detector types, i.e. the values of the parameter combination that consistently resulted in the least cost for the detector on the training dataset. The exact procedure is given in Algorithm 1 (end of the document), while details are provided in the extended data.\n\nAfter identifying the optimal parameter combination for each detector type, the optimal parameter values were used to run the detector on the 50 trials of the validation dataset, which resulted in the validation cost set CvalD=CiDi=150 for the detector type D. The cost set from the different detector types were compared using two-way ANOVA with the detector type and signal SNR as the two factors for each of the three-signal model. The complete code for the analysis can be found here.\n\n\nResults\n\nThe entire analysis – generation of the simulated data, the various detection algorithms, optimization52 of the detector parameters, and analysis of the results – reported in this paper were implemented in MATLAB R2020 (RRID:SCR_001622) (alternative languages could also recreate this study i.e. Python [RRID:SCR_008394] or GNU Octave [RRID:SCR_014398]). A sample of the individual trials from the three EMG signal models is depicted in Figure 1. A sample output of the different processing stages of the Modified Hodges detector from a Gaussian EMG signal trial is shown in Figure 3. The Modified Hodges detector, filters (2nd order Butterworth low pass filter) the rectified raw EMG signal (blue coloured trace in Figure 3). This lowpass filtered signal is the test function of the detector (red-coloured trace in Figure 3). The threshold h for this trial is shown by the green-coloured horizontal line in Figure 3. The output of the detector (black coloured trace in Figure 3) is 1 whenever the test function crosses the threshold, it is 0 otherwise. The figure also shows the values of rFP, rFN, ∆t, and f∆t for the trial.\n\nThe 13 detector types were compared after choosing the optimal parameter set for each detector type using the training dataset of 50 trials for each of the six combinations of the three signal models and two SNRs.53 This procedure is depicted in Figure 4 for the Modified Hodges detector for the 0 dB SNR Gaussian signal model, which shows the outcomes from the different steps in the optimization process described in Algorithm 1. Figure 4(a) shows the histograms of the cost C for the different parameter combinations, in light blue traces. These histograms are estimated from the cost values Cii=150 obtained from the 50 trials in the training dataset for the different combinations of the detector parameters. The scatter plot of the median cmed and inter-quartile range ciqr of these histograms are shown in Figure 4(b). The choice of the best parameter for the detector was determined to be the one with the least Euclidean norm cmed2+ciqr2 which is shown as the red circle in Figure 4(b); its corresponding histogram is shown in the thick red trace in Figure 4(a). Figure 4(c) shows the marginal histograms of the individual contributors rFPrFPf∆t to the cost C for the optimal parameter combination for the Modified Hodges detector. The values of the optimal parameters for the different detector types are listed in Table 2.\n\n(a) Estimated probability density function of cost for the different combinations of parameters (in light blue traces). The red trace corresponds to the cost of the optimum parameter combination. (b) Scatter plot of median vs IQR for the cost of different parameter combinations. (c) Estimated histograms of latency, false positive rate, false negative rate and cost of the optimum parameter.\n\nThe performance of the different “optimal” detector types, i.e., detectors using the optimal parameter values, were compared using the 50 trials from the validation datasets. The boxplot of the performance of these different detector types for the three different signal models – Gaussian, Laplacian, and biophysical – are shown in Figure 5(a), (b), (c), respectively; each of these subplots displays the performance for the 0dB and -3dB SNRs in red and blue boxplots, respectively. Note that the order of the depiction of the different detectors is in terms of the increasing average cost across the three signal models and two SNRs; the detectors on the left are better than the ones on the right in an average sense. A two-way ANOVA on the effect of the detector type and SNR on performance revealed a significant difference between the detector types (p < 0.001) and SNRs (p < 0.001) for all three signal models. The test revealed a significant interaction between the factors for all three models (biophysical: p < 0.0001; Gaussian: p < 0.0001; Laplacian: p < 0.0001). These statistical results confirm the results shown in the boxplots in Figure 5, where the performance is different among the detector types, with consistently poorer performance for -3dB compared to 0dB. The costs for both 0dB and -3dB appear to be lower for the biophysical model compared to the Gaussian and Laplacian models.\n\nAll detectors shown in this plot use the optimal detector parameter sets optimized on the training dataset. (a) Cost of detection for the Gaussian signal model, (b) Laplacian signal model and (c) Biophysical signal model. The red and blue colored boxplots are of 0dB and -3 dB SNR, respectively. The red dashed line is the acceptable cost Caccept=0.2.\n\nMost detector types perform similarly except for the Sample entropy, Continuous wavelet transform (CWT), and Singular spectrum analysis (SSA) detector types which perform worse across the different signal models and SNRs. Among the other detector types – the Modified Hodges, the approximate generalise likelihood ratio test- Gaussian (AGLR-G), and the approximate generalise likelihood ratio test- Laplacian (AGLR-L) detectors – have almost similar costs for the different signal models and SNRs. The other detector types – Root mean square (RMS), Hodges, Bonato, Lidierth, Modified Lidierth, Teager Kaiser Energy Operator (TKEO), and Fuzzy entropy – have slightly higher costs for one or more specific signal models and SNRs. We note that the Fuzzy entropy detector performs very well on the biophysical signal model for both SNRs with an acceptable cost for more than 95% of the validation trials.\n\nThe choice of appropriate detector type(s) for use in robot-assisted therapy requires the specification of an acceptable cost of detection Caccept. To this end, we specify the upper limits for the false positive rate, false negative rate, and the latency of detection as Caccept=0.2, which corresponds to a detector with the following cost components:\n\nWe believe that these upper limits are a reasonable compromise among the three competing factors determining the cost. Any detector type with costs consistently lower than Caccept would be deemed an appropriate detector for use in robot-assisted therapy. To determine the detector types with consistently lower costs than Caccept, we computed the proportion (racceptD) of the 50 validation trials with acceptable C≤Caccept for the detector D for the three signal models and two SNRs using\n\n1. All detectors perform poorly for the -3dB Laplacian signal model. The highest value of racceptD is 0.22 for this signal model, which interestingly is from the AGLR-L detector designed for the Laplacian signal. Many detectors perform a little better with higher racceptD values for the -3dB Gaussian and biophysical signal models.\n\n2. The Modified Hodges detector is the most consistent detector across the different signal models and SNRs. It has an racceptD>0.8 for the three signal models at 0dB and the biophysical model at -3dB SNR.\n\n3. The Fuzzy Entropy detector performs as well as the Modified Hodges detector for the Gaussian and biophysical signal models, but not on the Laplacian model.\n\n4. In terms of the average value of racceptD, across the three signal models (last two columns of Table 3), the Modified Hodges detector performs the best for the 0dB signals, followed by the AGLR-G, AGLR-L, and Fuzzy Entropy detectors which have slightly lower but similar performance. For -3dB signals, the Modified Hodges, AGLR-G, and AGLR-L detectors result in similar performances.\n\nThe cells with proportions greater or equal to 0.8 are highlighted in gray.\n\nBased on these observations, the Modified Hodges appears to be the most consistent detector for low SNR signal models, irrespective of the EMG signal model. The two statistical detectors (AGLR-G, and AGLR-L) and the fuzzy entropy detectors provide similar but slightly lower performance than the Modified Hodges detector.\n\n\nDiscussion\n\nMovement intention-triggered robot-assisted therapy is one of the options available for severely impaired patients without residual movement. EMG for movement intent detection is a simpler, more direct and task-specific alternative to EEG-BCI.23 The investigation of EMG-triggered robot-assisted therapy requires a sensitive and robust method for the accurate and fast detection of movement intention from residual low SNR EMG signals. This study systematically investigated existing EMG detection algorithms in the literature until 2018. The investigation was carried out on simulated EMG signals using three different signal models with low SNR of 0dB and -3dB. These SNRs correspond to feeble EMG signals compared to regular surface EMG recordings from healthy individuals. Using three different signal models – two phenomenological and one biophysical – makes the study results robust to assumptions about the simulated EMG data.\n\nThe study by Staude et al. published in 200124 compared different EMG detectors for accurate EMG onset-time detection. They employed a Gaussian signal model with ramp variance profiles (with varying slopes) at SNR of 3dB to 12dB in their analysis24 and found the AGLR statistical detector to be the best in terms of onset detection, while the Hodges detector performed poorly.24 Although there are some similarities between the current study and those of Staude et al., the two differ in several ways: (a) the current study is focused on real-time detection, while Staude et al.’s primary goal was offline analysis; (b) the current study employed lower SNR signals, which is important considering its application to detect motion intention in severally affected stroke patients; (c) the current study tested three different signal models, while Staude et al. used only the Gaussian signal model; (d) the primary performance measure in Staude et al. was onset detection latency, while the current study used a composite performance measure (or cost) consisting of the false positive rate, false negative rate, and detection latency; (e) the rationale for the choice of the specific detector parameters was not explicitly mentioned in Staude et al.. In the current study, the detector parameters were optimized through a brute force search to ensure the best detectors from each detector type were compared; and (f) the current study investigates a wider class of detector types than Staude et al., including the detectors published after 2001.\n\nThe current study identified that the Modified Hodges detector performed consistently well with cost C≤0.2 for at least 80% of the validation trials, across the different signal models and SNRs, except for the -3dB Laplacian signal model, where all detectors fail. The modified Hodges detector – a simplified version of the Hodges detector – performs better than Hodges because it does not involve the additional averaging step in computing its test function. This reduces the detection latency for the modified Hodges detector without an appreciable increase in the false positive and false negative rates (Table S4 in the extended data in figshare (RRID:SCR_004328)). The AGLR-G, AGLR-L, and fuzzy entropy detectors perform slightly lower than modified Hodges but better than the rest of the detectors. The good performance of the statistical detectors agrees with that of Staude et al. even with the lower SNRs investigated in this study. The fuzzy entropy detector also performs well, unlike its counterpart – sample entropy. The sample entropy algorithm in this study used the local estimate of the signal’s standard deviation for normalizing the data. Sample entropy’s poor performance with the local estimate of the standard deviation was previously reported by Zhang et al. Sample entropy performs well only with the global estimate of the signal’s standard deviation.31 This is not suitable for real-time implementation as estimating the global standard deviation is a non-causal operation requiring the entire signal record. The use of the fuzzy similarity measure addresses this problem with sample entropy, allowing the fuzzy entropy detector to track changes in the overall signal amplitude. Interestingly, fuzzy entropy has a low cost of detection for both 0dB and -3dB biophysical signal models, which could be due to the additional structure of the motor unit action potentials (MUAPs) in the move-phase of the biophysical signal.\n\nInterestingly, the RMS detector we used previously to demonstrate the viability of EMG as an alternative to detect movement intention in severely impaired chronic stroke subjects23 was not one of the best performers, as seen in Figure 5 and Table 3. We note that the observed performance was for the RMS detector with optimized parameters (Table 2) using the training dataset. This optimized RMS detector had a relatively high false negative rate and higher detection latency which resulted in its poor performance. This could possibly explain the lack of agreement between the EMG and EEG detectors we had observed in our previous study, and a more sensitive detector might have identified EMG activity in a larger proportion of subjects. The current study results warrant further investigation with real EMG data from severely impaired patients using other detectors, such as the modified Hodges, AGLR-G/L, and fuzzy entropy.\n\nIn general, most detectors have a relatively lower cost of detection for the biophysical signal model, compared to the Gaussian and the Laplacian signal models. The reasons for the better performance on the biophysical model are not entirely clear, except for the fuzzy entropy detector, which might be sensitive to the temporal structure of the simulated data (MUAP) from the biophysical model. One possibility is the difference in the spectra of the signals from the biophysical model compared to the Gaussian or Laplacian modes (Figure 1); more signal energy is concentrated in the lower frequencies for the biophysical model than in the Gaussian or Laplacian models. Most detectors compute their test functions through a lowpass filtering or averaging operation, which could be retaining a relatively larger portion of the signal in the biophysical model compared to the Gaussian and Laplacian ones, thus resulting in improved performance with the biophysical model. If this is correct, then the difference in performances between the biophysical and the Gaussian/Laplacian models should disappear when an appropriate spectral shaping filter is used in the Gaussian and Laplacian models, yielding a spectrum like the biophysical model. Finally, among the Gaussian and Laplacian models, the relatively poorer performance with the Laplacian signal model could be due to the long tails of the Laplacian distribution.\n\nThe simulated data used in the current study relies on a step-change in the signal properties between the rest- and move-phase, and an EMG signal of fixed amplitude during the move phase. These assumptions will be violated when dealing with feeble surface EMG signals recorded from impaired participants with no residual movements. In such participants, movement attempts are likely to produce intermittent bursts of EMG activity with smooth transitions between the on and off states in the target muscles. The EMG signal might have time-varying amplitude even when the participant can continuously activate the muscle for sufficient duration. Although based on idealized simulated EMG data, the current results do provide some idea about the detector types that can potentially work on real low SNR EMG signals; a detector performing poorly on ideal data is likely to perform worse with real data. Furthermore, the results from the current analysis also indicate that modified Hodges, AGLR-G, AGLR-L, and fuzzy entropy detectors are likely to pick up even bursts of EMG signals since they have small detection latency ∆t≤50ms.\n\nThe detectors studied in this paper can only be used for on-off control of robotic assistance,54 where once EMG activity is detected, robotic assistance drives the limb towards the target in a preprogramed fashion. This is different from continuous control of the motion where robotic assistance is proportional to the level of EMG measured from the target muscles.36 Continuous control of robotic assistance is likely to be a more natural and engaging interaction for participants than simple on-off control. The most common EMG feature for continuous control has been the EMG amplitude estimate,36 however, the test functions employed by the different detector types in the current study could be potential alternatives. The choice of the best control variable depends on which one of these is sensitive, robust, and provides a natural human-robot interaction with minimal lag. However, it should be noted that it is unclear how well severely impaired participants, with no residual movements, can finely modulate their EMG activity. The choice of on-off versus continuous control of robotic assistance for a participant will require a screening procedure to evaluate the ability of the participant to modulate EMG activity in the target muscle.\n\nThe study has limitations that are worth noting to ensure that the results are interpreted appropriately. The study entirely relies on simulated data to investigate the different detectors. The conclusions are thus only as good as the assumed signal models and how well they represent the residual surface EMG signals of patients with no visible movements. This is the first study investigating detectors for low SNR EMG, and thus the use of simulated data was essential to gain some understanding of the performance of the different detectors. Simulated data also allows complete control of the ground truth, which provides a more truthful characterization of different detectors’ detection accuracy and latency. The use of three different signal models to investigate the different detectors also adds some robustness to the study’s findings. Additionally, this analysis allows us to exclude the poorly performing detectors and identify the ones that warrant further investigation with real data. Another potential limitation of the use of simulated data is the availability of complete information about the ground truth against which the different detectors are compared. However, the results of the current study can’t be verified with real data because we will never know the ground truth in the surface EMG from patients with no residual movements. This is a valid concern. Nevertheless, some form of an unsupervised approach will be required for verifying the results of the current study with real data. With real data, the best detector would be the one that consistently provides the maximum separation for the probability density function of the test function gn from the different detectors under the rest-phase and move-phase.\n\n\nConclusions\n\nThis paper systematically investigated existing EMG detection algorithms on low SNR EMG signals simulated using three different signal models (two phenomenological – Gaussian, Laplacian models and a biophysical model) at two different SNRs (0dB and -3dB). The Modified Hodges detector – a simplified version of the threshold-based Hodges detector, introduced in the current study – was found to be the most consistent detector across the different signal models and SNRs. This detector had false positive and false negative rates of lower than 20% and a detection latency of lower than 50 ms for almost 90% of the trials on which it was tested for 0 dB SNR and more than 40% of the trials for -3 dB SNR. The two statistical detectors (Gaussian and Laplacian Approximate Generalized Likelihood Ratio) and the Fuzzy Entropy detectors have a slightly lower performance than Modified Hodges. Overall, the modified Hodges, Gaussian and Laplacian approximate generalized likelihood ratio, and fuzzy entropy detectors were identified as potential candidates for further validation with real surface EMG data on a population of severely impaired patients. The current study forms the first step towards developing a simpler, practical, and robust EMG-based human-machine interface for triggered robot-assisted therapy in severely impaired patients.\n\nLet the parameter set for the given detector type be Π=p1p2…pm.\n\nSet the parameter ranges for the individual parameters pi in the parameter set P for the detector type, which results in K different parameters combinations.\n\nFor j=1 to K parameter combinations:\n\n- Compute the output of the detector yini=150for the chosen combination of parameter values for each of the 50 trials in the training dataset.\n\n- Compute the cost Cii=150 for each of the 50 trials.\n\n- Compute the median cmed and inter-quartile range ciqr of the cost values from the 50 trials.\n\n- Compute the overall detector performance for the jth trial as Pj=cmed2+ciqr2.\n\nGet the best parameter combination for the detector type as the following,\n\n\nAuthor contributions\n\nSB conceived and brainstormed the idea with EB and VSKM. PR worked on the initial literature search and the implementation of some of the detectors. MY implemented the different EMG signal models, all the detectors, optimization of detector parameters, and the analysis of the results. AD and SB provided scientific inputs for the implementation and analysis done by MY. EB and VSKM provided critical feedback for the methodology and results. MY, AD, and SB wrote the first draft of the manuscript. All authors reviewed and approved the final submitted manuscript.", "appendix": "Data availability\n\nFigshare - Dataset: A systematic investigation of detectors for low signal-to-noise ratio EMG signal, https://doi.org/10.6084/m9.figshare.22317658.v2. 53\n\nThe data used in the analysis is saved as csv file which is named based on the SNR and signal generating model as follows:\n\n• Example: EMGDataSNR0trail50dur13biophy.csv (EMG data generated using biophysical model having SNR 0).\n\n• TestEMGDataSNR0trail50dur13biophy.csv (Test data generated using biophysical model with SNR 0).\n\nFigshare: Supplementary material: A Systematic Investigation of Detectors for Low Signal-to-Noise Ratio EMG Signals.docx, https://doi.org/10.6084/m9.figshare.22232527.v3. 52\n\nThis project contains the following extended data:\n\n- Supplementary material.pdf (parameters for optimizing the detector)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors thank Prof. Suresh Devasahayam for providing us with the software he’d developed for simulating the EMG signals. This software was used for generating data for the biophysical EMG model.\n\n\nReferences\n\nWard NS, Brander F, Kelly K: Intensive upper limb neurorehabilitation in chronic stroke: outcomes from the Queen Square programme. J. Neurol. Neurosurg. Psychiatry. 2019; 90: 498–506. Publisher Full Text\n\nLanghorne P, Coupar F, Pollock A: Motor recovery after stroke: a systematic review. Lancet Neurol. 2009; 8: 741–754. Publisher Full Text\n\nYoung J, Forster A: Review of stroke rehabilitation. BMJ. 2007; 334: 86–90. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIsrael JF, Campbell DD, Kahn JH, et al.: Metabolic costs and muscle activity patterns during robotic- and therapist-assisted treadmill walking in individuals with incomplete spinal cord injury. Phys. Ther. 2006; 86: 1466–1478. PubMed Abstract \| Publisher Full Text\n\nReinkensmeyer DJ, Emken JL, Cramer SC: Robotics, Motor Learning, and Neurologic Recovery. Annu. Rev. Biomed. Eng. 2004; 6: 497–525. Publisher Full Text\n\nLewthwaite R, Wulf G: Optimizing motivation and attention for motor performance and learning. Curr. Opin. Psychol. 2017; 16: 38–42. PubMed Abstract \| Publisher Full Text\n\nKaelin-Lane A, Sawaki L, Cohen LG: Role of voluntary drive in encoding an elementary motor memory. J. Neurophysiol. 2005; 93: 1099–1103. PubMed Abstract \| Publisher Full Text\n\nLotze M, Braun C, Birbaumer N, et al.: Motor learning elicited by voluntary drive. Brain. 2003; 126: 866–872. PubMed Abstract \| Publisher Full Text\n\nJo I, Park Y, Lee J, et al.: A portable and spring-guided hand exoskeleton for exercising flexion/extension of the fingers. Mech. Mach. Theory. 2019; 135: 176–191. Publisher Full Text\n\nHornby TG, Reinkensmeyer DJ, Chen D: Manually-Assisted Versus Robotic-Assisted Body Weight−Supported Treadmill Training in Spinal Cord Injury: What Is the Role of Each? PM&R. 2010; 2: 214–221. PubMed Abstract \| Publisher Full Text\n\nJo I, Park Y, Lee J, et al.: A portable and spring-guided hand exoskeleton for exercising flexion/extension of the fingers. Mech. Mach. Theory. 2019; 135: 176–191. Publisher Full Text\n\nEthier C, Gallego JA, Miller LE: Brain-controlled neuromuscular stimulation to drive neural plasticity and functional recovery. Curr. Opin. Neurobiol. 2015; 33: 95–102. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVárkuti B, et al.: Resting state changes in functional connectivity correlate with movement recovery for BCI and robot-Assisted upper-extremity training after stroke. Neurorehabil. Neural Repair. 2013; 27: 53–62. PubMed Abstract \| Publisher Full Text\n\nPichiorri F, et al.: Brain-computer interface boosts motor imagery practice during stroke recovery. Ann. Neurol. 2015; 77: 851–865. PubMed Abstract \| Publisher Full Text\n\nOno T, et al.: Brain-computer interface with somatosensory feedback improves functional recovery from severe hemiplegia due to chronic stroke. Front. Neuroeng. 2014; 7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrauchle D, Vukelić M, Bauer R, et al.: Brain state-dependent robotic reaching movement with a multi-joint arm exoskeleton: combining brain-machine interfacing and robotic rehabilitation. Front. Hum. Neurosci. 2015; 9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRamos-Murguialday A, et al.: Brain–machine interface in chronic stroke rehabilitation: A controlled study. Ann. Neurol. 2013; 74: 100–108. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRamos-Murguialday A, et al.: Proprioceptive Feedback and Brain Computer Interface (BCI) Based Neuroprostheses. PLoS One. 2012; 7: e47048. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAng KK, et al.: A Randomized Controlled Trial of EEG-Based Motor Imagery Brain-Computer Interface Robotic Rehabilitation for Stroke. Clin. EEG Neurosci. 2015; 46: 310–320. PubMed Abstract \| Publisher Full Text\n\nBai O, et al.: Prediction of human voluntary movement before it occurs. Clin. Neurophysiol. 2011; 122: 364–372. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nObermaier B, Neuper C, Guger C, et al.: Information transfer rate in a five-classes brain-computer interface. IEEE Trans. Neural Syst. Rehabil. Eng. 2001; 9: 283–288. PubMed Abstract \| Publisher Full Text\n\nNorman SL, et al.: Movement Anticipation and EEG: Implications for BCI-Contingent Robot Therapy. IEEE Trans. Neural Syst. Rehabil. Eng. 2016; 24: 911–919. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBalasubramanian S, Garcia-Cossio E, Birbaumer N, et al.: Is EMG a Viable Alternative to BCI for Detecting Movement Intention in Severe Stroke? I.E.E.E. Trans. Biomed. Eng. 2018; 65: 2790–2797.\n\nStaude G, Flachenecker C, Daumer M, et al.: Onset Detection in Surface Electromyographic Signals: Journal on. Applied Signal Processing. 2001; 2: 67–81.\n\nYang D, Zhang H, Gu Y, et al.: Biomedical Signal Processing and Control Accurate EMG onset detection in pathological, weak and noisy myoelectric signals. Biomed Signal Process Control. 2017; 33: 306–315. Publisher Full Text\n\nTabie M, Kirchner EA: EMG onset detection: Comparison of different methods for a movement prediction task based on EMG EMG Onset Detection Comparison of different methods for a movement prediction task based on EMG.2017.\n\nVaisman L, Zariffa J, Popovic MR: Application of singular spectrum-based change-point analysis to EMG-onset detection. J. Electromyogr. Kinesiol. 2010; 20: 750–760. PubMed Abstract \| Publisher Full Text\n\nMing L, Xiong C, Zhang Q, et al.: Fuzzy Entropy-Based Muscle Onset Detection Using Electromyography (EMG). Intelligent Robotics and Applications. Xianmin Z, Liu H, Chen Z, et al. editors. Springer International Publishing; 2014; pp. 89–98.\n\nSolnik S, Devita P, Rider PM, et al.: Teager-Kaiser Operator improves the accuracy of EMG onset detection independent of signal-to-noise ratio. Acta Bioeng. Biomech. 2008; 10(2): 65–68. PubMed Abstract\n\nMerlo A, Farina D, Merletti R: A fast and reliable technique for muscle activity detection from surface EMG signals. I.E.E.E. Trans. Biomed. Eng. 2003; 50: 316–323. Publisher Full Text\n\nZhang X, Zhou P: Sample entropy analysis of surface EMG for improved muscle activity onset detection against spurious background spikes. J. Electromyogr. Kinesiol. 2012; 22(6): 901–907. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHu XL, et al.: Coordinated upper limb training assisted with an electromyography (EMG)-driven hand robot after stroke. 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). 2013; pp. 5903–5906. Publisher Full Text\n\nSarasola-Sanz A, et al.: EMG-based multi-joint kinematics decoding for robot-aided rehabilitation therapies. 2015 IEEE International Conference on Rehabilitation Robotics (ICORR). 2015; pp. 229–234. Publisher Full Text\n\nLan Y, Yao J, Dewald JPA: The impact of shoulder abduction loading on EMG-based intention detection of hand opening and closing after stroke. 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 2011; pp. 4136–4139. Publisher Full Text\n\nIrastorza-Landa N, et al.: EMG Discrete Classification Towards a Myoelectric Control of a Robotic Exoskeleton in Motor Rehabilitation. Biosystems and Biorobotics. 2017; 15: 159–163. Publisher Full Text\n\nHu XL, Tong KY, Song R, et al.: A comparison between electromyography-driven robot and passive motion device on wrist rehabilitation for chronic stroke. Neurorehabil. Neural Repair. 2009; 23: 837–846. PubMed Abstract \| Publisher Full Text\n\nDe Luca CJ: The Use of Surface Electromyography in Biomechanics. J. Appl. Biomech. 1997; 13: 135–163. Publisher Full Text\n\nBilodeau M, Cincera M, Arsenault AB, et al.: Normality and stationarity of EMG signals of elbow flexor muscles during ramp and step isometric contractions. J. Electromyogr. Kinesiol. 1997; 7: 87–96. PubMed Abstract \| Publisher Full Text\n\nParker PA, Stuller JA, Scott RN: Signal processing for the multistate myoelectric channel. Proc. IEEE. 1977; 65: 662–674. Publisher Full Text\n\nMerletti R, Lo Conte LR: Advances in processing of surface myoelectric signals: Part 1. Med. Biol. Eng. Comput. 1995; 33: 362–372. PubMed Abstract \| Publisher Full Text\n\nShwedyk E, Balasubramanian R, Scott RN: A Nonstationary Model for the Electromyogram. I.E.E.E. Trans. Biomed. Eng. 1977; BME-24: 417–424. Publisher Full Text\n\nClancy EA, Hogan N: Probability density of the surface electromyogram and its relation to amplitude detectors. I.E.E.E. Trans. Biomed. Eng. 1999; 46: 730–739. Publisher Full Text\n\nDevasahayam SR: Signals and systems in biomedical engineering: physiological systems modeling and signal processing.468.\n\nClancy EA: Electromyogram amplitude estimation with adaptive smoothing window length. I.E.E.E. Trans. Biomed. Eng. 1999; 46: 717–729. Publisher Full Text\n\nClancy EA, Hogan N: Single site electromyograph amplitude estimation. I.E.E.E. Trans. Biomed. Eng. 1994; 41: 159–167. Publisher Full Text\n\nBonato P, D’Alessio T, Knaflitz M: A statistical method for the measurement of muscle activation intervals from surface myoelectric signal during gait. I.E.E.E. Trans. Biomed. Eng. 1998; 45: 287–299. Publisher Full Text\n\nStaude G, Wolf W, Appel U: Automatic event detection in surface EMG of rhythmically activated muscles. Proceedings of 17th International Conference of the Engineering in Medicine and Biology Society. Vol. 2. 1995; pp. 1351–1352.\n\nLidierth M: A computer based method for automated measurement of the periods of muscular activity from an EMG and its application to locomotor EMGs. Electroencephalogr. Clin. Neurophysiol. 1986; 64: 378–380. PubMed Abstract \| Publisher Full Text\n\nStaude G, Wolf W, Appel U: Automatic event detection in surface EMG of rhythmically activated muscles. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings. Vol. 17. 1995; pp. 1351–1352.\n\nVaisman L, Zariffa J, Popovic MR: Application of singular spectrum-based change-point analysis to EMG-onset detection. J. Electromyogr. Kinesiol. 2010; 20: 750–760. PubMed Abstract \| Publisher Full Text\n\nYuvaraj M: 1608Moni/EMG_detectors: A systematic investigation of detectors for low sig-nal-to-noise ratio EMG signals (v1.0.0). [Code]. Zenodo. 2023. Publisher Full Text\n\nYuvaraj M, Raja P, David A, et al.: Supplementary material: A Systematic Investigation of Detectors for Low Signal-to-Noise Ratio EMG Signals.docx. [Data]. figshare. Figure. 2023. Publisher Full Text\n\nYuvaraj M, Raja P, David A, et al.: Dataset: A systematic investigation of detectors for low signal-to-noise ratio EMG signals. [Data]. figshare. 2023. Publisher Full Text\n\nHu XL, et al.: The effects of post-stroke upper-limb training with an electromyography (EMG)-driven hand robot. J. Electromyogr. Kinesiol. 2013; 23: 1065–1074. PubMed Abstract \| Publisher Full Text" }	[ { "id": "219586", "date": "06 Nov 2023", "name": "Vincent Crocher", "expertise": [ "Reviewer Expertise Rehabilitation robotics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors propose to evaluate and compare 13 sEMG onset detectors specifically on low signal-to-noise EMG (0db and -3db). The authors propose a thorough work and use an appropriate methodology (including generation of simulated EMG signals, wide range of detectors and tuning, outcome evaluation cost and analysis) which is aligned with the objective of the paper and the application (the use of EMG onset for rehabilitation robotics control).\nThe paper is clearly of interest in the field of neuro-rehabilitation robotics and I believe that both the results and the methodology used (and associated code provided, which is reasonably documented) are of direct interest to the field.\nSpecific comments:\nIntroduction:\nThe part on BCI drawbacks can be shorten into a simple sentence to keep the introduction more straightforward (this is not the focus of the paper).\n\n\"In this paper, EMG always refers to surface-recorded muscle\": this indeed makes sense for the neuro-rehabilitation application of interest here and even more generally given the wider adoption and ease of use of surface EMG.I would thus suggest to bring this statement as early as in the introduction and adopt the sEMG acronym across the paper as this is an unambiguous terminology widely used.\nMethods:\nIn the \"Simulation of surface EMG signal\" section, I would suggest to move the part of the last paragraph (\"The phenomenological models were based on the work of De Luca...\") to the next section to ease the reading. This part is relative to the Phenomenological models only.\n\nFigure 1 presenting examples of the three types of generated signals show the biophysical signal of a smaller (20 times) than the phenomenological ones. While the absolute amplitude likely does not affect the detectors, this is slightly confusing. Is there any valid reason for this difference or can these three signals be equalised to the same amplitude?\n\nIn Table 1, authors refer to 'Weights' for \\alpha whereas it appears that there is only a single value for each detector. Please clarify.\n\nIn Table 1, while RMS and Lidierth detectors do use a filter for the conditioning, those filters cut-off frequencies are not listed as parameters. Do authors intentionally chose fixed, non-optimised, frequencies for those (and if so, why)? or is this a simple oversight in the table?\n\nAfter Eq 12, authors should clearly introduce \\alpha and refer to it as weight as this is the fist time it is properly introduced. I would also recommend to explicit it earlier on, as the Weight (weights?) are introduced in Table 1 earlier and earlier in the text but without explanation making it hard to follow.\nMethods: On the cost definition:\nAccording to Eq. 16, f(deltat) is 0 (ideal) when the detection happens before the actual onset: \\deltat<0ms and so is effectively a False positive. While I understand that this cannot be avoided with the chosen structure of the cost: this suggests that the within the overall cost, the latency and the false negative rates are more redundant whereas the false negative rate is quite independent of the other two.\n\nMore generally, as the authors show that most detectors already behave quite poorly for such low SNR sEMG, the chosen cost bounds, and especially the 20% seems quite high for actual use. Given the application in mind where the objective is to detect one true onset as quickly as possible (and 50ms appears reasonable for a robotics assistance), I wonder if a cost accounting for a more strict false negative rate and more tolerant (if accounted at all) for false positive would make more sense. Indeed, only the earliest positive detection after onset can be considered useful for an application using this signal as a trigger. Wouldn't it make sense to also train and evaluate the detectors on a cost based solely on a very strict false positive rate (5%?) and not included FN in the cost (given that only the earliest detection after true onset matters)? Regarding the FP and FN rates, those are also calculated per trial, meaning that 20% (or even 5%) can mean that each trial has at least several FP before onset and not that 20% (or 5%) of the trials do have a FP. This is this latest figure that is of direct interest for the application. Authors should clearly discuss this point on how these results translate to real scenarios and provide results showing in what percentage of test trials FP detection happens before onset.\nDiscussion:\nIt could be interesting to discuss the possibility that the signal processing (detectors) might not be necessarily implemented at the same frequency than the one the sEMG data is collected. Indeed it is common in existing systems to have an EMG acquisition faster than the robotic controller (typically a >2kHz EMG sampling for a 1kHz controller). Does authors have clues on how that might differently affect the different detectors?\n\nWhile the use of simulated (generated) EMG signals to evaluate the performance of the detector is appropriate and allows for robust and repeatable outcomes, it would be an interesting addition to also perform a short evaluation on actual low signal-to-noise EMG datasets.\nOn that point of potential difference with actual EMG signals, authors rightly point that they here test the optimal behaviour of the detectors, i.e. they would likely all perform worst on actual signals, especially when muscle activation is not constant over a long period. Can authors infer and discuss some difference in performance between the detectors for short activation (typically flickers that can be encountered in rehabilitation applications)? Some detectors are based on relatively long windows of 150ms, and while authors explain in the discussion that the best detectors have a latency of <50ms and so likely suitable for short activation bursts, how this would affect the detectors with longer window? Could they be likely be optimised differently for such signals?\nMinor/typos:\n\n\"Devasahayam S43\" => \"Devasahayam43\"\n\nIn Table 2, some window sizes are in (ms) some in (s)\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10896", "date": "30 Jan 2024", "name": "Monisha Yuvaraj", "role": "Author Response", "response": "1. Summary Thank you very much for taking the time to review this manuscript. Please find the detailed responses below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files. 2. Point-by-point response to Comments and Suggestions for Authors In the following, the reviewer’s comments are in Italics. Each comment has the response and The changes in the manuscript are presented by first showing verbatima segment of the text from the previous manuscript followed by the modified text. Please find the response as a PDF file here. The authors propose to evaluate and compare 13 sEMG onset detectors specifically on low signal-to-noise EMG (0db and -3db). The authors propose a thorough work and use an appropriate methodology (including generation of simulated EMG signals, wide range of detectors and tuning, outcome evaluation cost and analysis) which is aligned with the objective of the paper and the application (the use of EMG onset for rehabilitation robotics control). The paper is clearly of interest in the field of neuro-rehabilitation robotics and I believe that both the results and the methodology used (and associated code provided, which is reasonably documented) are of direct interest to the field. Introduction: The part on BCI drawbacks can be shorten into a simple sentence to keep the introduction more straightforward (this is not the focus of the paper). Response: We have shortened this segment in the introduction section as suggested. Original text: They have a poor signal-to-noise ratio (SNR) with large trial-to-trial intra-subject variability. 20 The use of sophisticated signal processing techniques can increase the delay in intent detection, which can result in inappropriately timed robotic assistance leading to suboptimal recovery 12 , 21 EEG-BCI modalities do not precisely identify which limb segment is intended to move due to its low information rate. 21 Event-related desynchronization of the EEG sensorimotor rhythm may not necessarily reflect movement intention. 22 Critical for practical use, current EEG-BCI systems are too complex and time-consuming for clinical work. 23 Change in the manuscript: They often exhibit a poor signal-to-noise ratio, with significant trial-to-trial intra-subject variability [20]. Unlike EMG systems, EEG-BCI modalities lack task specificity [21]. Moreover, their complexity and time-consuming nature prevent their routine clinical use [23]. \"In this paper, EMG always refers to surface-recorded muscle\": this indeed makes sense for the neuro-rehabilitation application of interest here and even more generally given the wider adoption and ease of use of surface EMG. I would thus suggest to bring this statement as early as in the introduction and adopt the sEMG acronym across the paper as this is an unambiguous terminology widely used. Response: We have moved the sentence to the introduction and used “sEMG” throughout the paper. Change in the manuscript: In this paper, we consider surface-recorded muscle electromyogram activity (sEMG), as this modality will most likely be employed in routine robot-assisted therapy. sEMG could be used as a viable alternative to address the drawbacks of EEG-BCI for robot-assisted therapy. Methods: In the \"Simulation of surface EMG signal\" section, I would suggest to move the part of the last paragraph (\"The phenomenological models were based on the work of De Luca...\") to the next section to ease the reading. This part is relative to the Phenomenological models only. Response: We have moved the paragraph to the phenomenological models’ section as suggested. Change in the manuscript: “ The phenomenological models were based on the work of De Luca 37 where an sEMG signal from a muscle activated at a fixed level can be treated as zero-mean white noise followed by a shaping filter (electrode properties); this model is widely accepted in the literature. 24, 38 – 41… The first step in this model is the generation of the zero-mean unit-variance white Gaussian and Laplacian noise …” Figure 1 presenting examples of the three types of generated signals show the biophysical signal of a smaller (20 times) than the phenomenological ones. While the absolute amplitude likely does not affect the detectors, this is slightly confusing. Is there any valid reason for this difference or can these three signals be equalised to the same amplitude Response: The amplitude of biophysical model is in mV since it is modelled using physics of the EMG generation and recording process. Whereas with the phenomenological model the EMG signal is generated as bandpass filtered white noise, and thus its amplitude is in arbitrary units. We have now addressed this issue by scaling the biophysical models to have similar amplitudes to that of the phenomenological models to avoid any confusion. In Table 1, authors refer to 'Weights' for \\alpha whereas it appears that there is only a single value for each detector. Please clarify. Response: The optimal parameter for each detector type is selected by doing search over a range of values for each parameter. The performance of a detector is tested with different weights in the range α ∈{1,2,3,4,5}. However, only one value by detector is used for computing the threshold. “Weights” in Table 1 has been modified as “Weight”. In Table 1, while RMS and Lidierth detectors do use a filter for the conditioning, those filters cut-off frequencies are not listed as parameters. Do authors intentionally chose fixed, non-optimised, frequencies for those (and if so, why)? or is this a simple oversight in the table? Response: The Lidierth detector utilizes rectification for signal conditioning and does not incorporate a low-pass filter. This oversight in the table has been rectified. On the other hand, the RMS detector, as per the original paper, employed a band-pass filter between 10 Hz and 250 Hz (fs/2) on recoded raw EMG data to obtain the EMG signal within the required frequency spectrum. However, in this analysis, simulated data was generated by band-pass filtering white noise between 10 and 450 Hz. Therefore, the band-pass filter for signal conditioning in the RMS detector was redundant. Hence, we implemented the detector without the band-pass filter and achieved similar results. After Eq 12, authors should clearly introduce \\alpha and refer to it as weight as this is the first time it is properly introduced. I would also recommend to explicit it earlier on, as the Weight (weights?) are introduced in Table 1 earlier and earlier in the text but without explanation making it hard to follow. Response: Thank you, we have followed this suggestion as follows: Change in the manuscript: The threshold h is adaptive and is calculated for each trial by adding α times the standard deviation of first 3 seconds data (Figure 3) to the mean. α is termed as weight for threshold in this paper. Methods: On the cost definition: According to Eq. 16, f(deltat) is 0 (ideal) when the detection happens before the actual onset: \\deltat<0ms and so is effectively a False positive. While I understand that this cannot be avoided with the chosen structure of the cost: this suggests that the within the overall cost, the latency and the false negative rates are more redundant whereas the false negative rate is quite independent of the other two. Response: The response is with the understanding that the reviewer's comment is as follows: “This suggests that the within the overall cost, the latency and the false negative rates are more redundant whereas the false positive rate is quite independent of the other two.” We performed a correlation analysis between false negative rate and the latency, which showed that: Moderate positive correlation between false negative rate and latency with 0 dB SNR signal of Gaussian and biophysical model (Figure 1). No correlation between FNR and latency with -3 dB SNR across all three models (Figure 2). Therefore, the three factors are independent at lower SNR and there is a need to account for them separately in order to evaluate the performance of the detector. Scatter plots of FNR vs. latency at both 0dB and -3dB for one of the detector Hodges are presented in Figures 1 and 2, respectively. Similar results are observed for all other detectors. Fig.1. Correlation plot of false negative rate vs. latency of Hodges detector tested on the three signals model (from left: Gaussian, Laplacian and Biophysical) with 0dB SNR. Fig.2: Correlation plot of false negative rate v.s latency of Hodges detector tested on the three signal model (from left: Gaussian, Laplacian and Biophysical) with -3 dB SNR. The figures can be found here More generally, as the authors show that most detectors already behave quite poorly for such low SNR sEMG, the chosen cost bounds, and especially the 20% seems quite high for actual use. Given the application in mind where the objective is to detect one true onset as quickly as possible (and 50ms appears reasonable for a robotics assistance), I wonder if a cost accounting for a more strict false negative rate and more tolerant (if accounted at all) for false positive would make more sense. Indeed, only the earliest positive detection after onset can be considered useful for an application using this signal as a trigger. Wouldn't it make sense to also train and evaluate the detectors on a cost based solely on a very strict false positive rate (5%?) and not included FN in the cost (given that only the earliest detection after true onset matters)? Regarding the FP and FN rates, those are also calculated per trial, meaning that 20% (or even 5%) can mean that each trial has at least several FP before onset and not that 20% (or 5%) of the trials do have a FP. This is this latest figure that is of direct interest for the application. Authors should clearly discuss this point on how these results translate to real scenarios and provide results showing in what percentage of test trials FP detection happens before onset. Response: Firstly, we have modified the term EMG-triggered robot-assisted therapy to EMG-driven robot-assisted therapy to emphasise that we are interested in implementing a therapy modality where the robot-assisted movement is contingent on the presence or absence of sEMG. Continued assistance required the continued presence of sEMG. This has been modified in the manuscript. We have also changed “sEMG-triggered” to “sEMG-driven”. Original text: In sEMG-triggered robot-assisted therapy, robotic assistance is triggered whenever sEMG is detected in real-time in the target muscle during the move phase of a trial. Change in the manuscript: In sEMG-driven robot-assisted therapy, the robot remains inactive during the rest phase, while in the move phase the robot-assisted movement is contingent upon the presence or absence of sEMG at any given time, thus continued sEMG is required to continuously receive robotic assistance. Response: Making robot-assistance contingent on continued presence of sEMG is important to keep the subject actively involved during the entire duration of a task, and thus avoid slacking. Such a modality requires both the rejection of false positives, quick detection of sEMG onset, and the continued detection of sEMG when it is present (i.e. low false negatives). Low false negative rates may be essential for the user’s motivation and sense of agency. For higher SNR signals, the presence of the false negative rate may not be important in the cost function, but it is crucial for low SNR signals (0dB or -3dB) including the false negative rate. Also, the sample entropy, SSA and CWT detectors that performed worse across all three models had acceptable false positive rate and latency, but the false negative rate alone was more than 20% which contributed to higher cost. These detectors will also be considered suitable for application in robot assisted therapy if the false negative rate is not included in the cost. This suggest that it is important to optimised for false negative rate as well since we are looking at low SNR EMG signals. We have now included a short paragraph explaining why the three terms are included in the cost function: Original text: The performance of a detector must consider the accuracy (false positive and false negative rate) and the detection latency. Change in the manuscript: An optimal EMG detector designed for use in EMG-driven robot-assisted therapy should possess the capability to quickly identify the onset of sEMG, efficiently eliminate false positives, and consistently detect sEMG when it is present (lower false negatives). Such a detector is essential for maintaining user’s motivation and sense of agency. Response: We agree that the 20% false positive rate might be too high. But since we are looking at very low SNR signal a strict FPR of 5% might decide all the detectors as not suitable for application in robot-assisted therapy. Also optimising for such low FPR could lead to parameter choices that compromise the true positive rate and latency since we are working with low SNR signals. Therefore, we have decided to use a more sensitive detector. We do not think that choosing a sensitive detector is a problem because the output of the detector will not be used to directly drive robot-assistance. Some form of low-pass filtering, or time-based filtering will be employed to smooth out jittery outputs from the detector before activating robotic-assistance. Such filtering operations on the detector output is commonly employed (e.g. Ramos-Murguialday et al., 2013). This can help filter out most short-duration false-positive pulses from activating robotic assistance. This filtering operation will increase the latency, which can impact the sense of agency and the perception of the user about the system’s responsiveness. Previous work indicates that a 200-300ms delay is well tolerated when reporting agency. Starting with a sensitive detector, we can experiment with different levels of filtering of the output with feedback from patients to yield an optimal detector. Individualising the detector and the filtering block is likely to favour patients to feel in control of their own movements. We have now included this in the Discussion to explain the 20% cut-off choice for determining a good detector. Change in the manuscript: In this analysis, a cost of 0.2 was selected for the application in sEMG-driven robot-assisted therap, corresponding to a 50 ms latency, 20% FPR or 20% FNR. Permitting up to a 20% false positive rate might be too high, leading to the selection of a highly sensitive detector as the best choice. However, we believe that choosing a sensitive detector is not a problem, because the raw output of this detector is unlikely to be used directly to drive the robot-assistance. Some form of low-pass or time-based filtering (like the one employed by Ramos-Murguialday et al.1) will be employed to filter out show false positives/negative pulses before using it to drive robotic assistance. This filtering operation reduce the FPR and FNR at the expense of introducing an additional latency; a delay of 200-300ms are well tolerated when reporting for sense of agency2. The choice of amount of filtering of the chose detector’s output will need to be done through feedback from patients/users of the system. A 20% false positive rate does not imply that 20% of the trials have a false positive rate. Instead, we assessed the consistency of the detectors by determining the number of test trials with a cost less than 0.2. A suitable detector is identified as one that has 80% of test trials with a cost less than 0.2, as indicated by the grey boxes in Table 3. These highlighted detectors exhibit more than 80% of test trials with at most a 20% false positive rate. This means that every trial could have false positives, and in our analysis the best detectors are the ones that consistently show less than 20% false positives in each test trial. Discussion: It could be interesting to discuss the possibility that the signal processing (detectors) might not be necessarily implemented at the same frequency than the one the sEMG data is collected. Indeed, it is common in existing systems to have an EMG acquisition faster than the robotic controller (typically a >2kHz EMG sampling for a 1kHz controller). Do authors have clues on how that might differently affect the different detectors? Response: Although the EMG acquisition happens at faster rate when compared to the robotic controller, the performance of the different detectors is likely to be not affected by the sampling rate. Consider that the EMG detectors are implemented at the same frequency as the EMG acquisition system (1 kHz) but the robotic controller is running at lower sampling frequency of 100 Hz. Then the output of the EMG detector is to be down sampled to match the frequency of the robotic controller which might lead to increase in latency by few milliseconds (10 ms) which might not affect the overall behaviour of the EMG-triggered robot assistance system. While the use of simulated (generated) EMG signals to evaluate the performance of the detector is appropriate and allows for robust and repeatable outcomes, it would be an interesting addition to also perform a short evaluation on actual low signal-to-noise EMG datasets. Response: We believe that evaluating the performance of the detector with real EMG datasets is outside the scope of this paper, in part as the same analysis approach cannot be applied with real data since we do not have full control over the amplitude and timing of the real EMG data, and we might not always have the ground truth. However, we are investigating if the outcomes of this study are supported by real data from patients from a previously concluded study. On that point of potential difference with actual EMG signals, authors rightly point that they here test the optimal behaviour of the detectors, i.e. they would likely all perform worst on actual signals, especially when muscle activation is not constant over a long period. Can authors infer and discuss some difference in performance between the detectors for short activation (typically flickers that can be encountered in rehabilitation applications)? Some detectors are based on relatively long windows of 150ms, and while authors explain in the discussion that the best detectors have a latency of <50ms and so likely suitable for short activation bursts, how this would affect the detectors with longer window? Could they be likely be optimised differently for such signals? Response: From Table 3, we can see that the detectors that have more than 80% validation trials with cost consistently lower than 0.2 (latency < 50ms) have a window size of less than or equal to 100 ms as the optimised parameter (Table 2). AGLR-G detector under biophysical model (0dB and -3dB) and Laplacian model (-3dB) with window size of 150 ms do not fall under the detectors with acceptable cost. This shows that detectors with a larger window size are less likely suitable for short activation bursts. However, on an average across all three models AGLR-G detector had reasonable percentage of validation trials with cost less than 0.2, thus we have mentioned in the Discussion that it is also one of the detectors that is likely to pick up short bursts. We conducted an analysis on EMG signals with short pulses of 500 ms duration. The results indicated that optimised parameters differed for the step EMG and pulse EMG. We also included the offset time in evaluating the performance of the detector. When optimising for offset time, higher weights for the threshold and a greater cut-off frequency for the low-pass filter (smaller window sizes) were selected to minimise the offset time latency. Hence, the detectors that were optimised with step EMG with relatively longer window size may exhibit suboptimal performance on EMG, with intermittent muscle activity as they might miss to detect the short activation burst. Minor/typos: \"Devasahayam S43\" => \"Devasahayam43\" In Table 2, some window sizes are in (ms) some in (s) Response: These have been corrected in the manuscript." } ] }, { "id": "223113", "date": "19 Feb 2024", "name": "Werner Wolf", "expertise": [ "Reviewer Expertise Biosignal Processing - human motor control" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nFirst of all, I would like to confirm the detailled review of Vincent Crocher. But I would like to underline his criticism on the lengthy elaboration of the rehabilitation issue. The manuscript focusses on event detection in stochastic signals and, therefore, it can be mapped to the biosignal processing field. The EMG processing is only specificly addressed by the inclusion of the biophysical signal model. And the topic „robots in rehalitation“ is a separate field not really related main issue of this manuscrpt. Thus, the total rehabilitation part – not only the BCI passages - can be reduced – as Vincent already states – to a single sentence and a removal of about 25 references. It sounds also contradicting to refer to the case „without residual movement“ but to measure surface EMG. What presumably is addressed by the manuscript are combined muscle excitations; i.e. to generate stiffness in the arm when fingers are grasping an object. But such a stiffness in the forearm is ambiguous, because the same stiffness will be generated with different finger movements. I will not continue this rehabilitation issue, because it is not the concern of this manuscript. – as mentioned above. Summarizing: The main results are interesting and they should be provided in a compressed form.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11298", "date": "13 Apr 2024", "name": "Monisha Yuvaraj", "role": "Author Response", "response": "1. Summary Thank you very much for taking the time to review this manuscript. Please find the detailed responses below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files. 2. Point-by-point response to Comments and Suggestions for Authors In the following, the reviewer’s comments are in Italics which is followed by our response. First of all, I would like to confirm the detailled review of Vincent Crocher. But I would like to underline his criticism on the lengthy elaboration of the rehabilitation issue. The manuscript focusses on event detection in stochastic signals and, therefore, it can be mapped to the biosignal processing field. The EMG processing is only specificly addressed by the inclusion of the biophysical signal model. And the topic „robots in rehalitation“ is a separate field not really related main issue of this manuscrpt. Thus, the total rehabilitation part – not only the BCI passages - can be reduced – as Vincent already states – to a single sentence and a removal of about 25 references. Response: Our primary goal is to identify a suitable EMG detector for on-off control of robotic assistance during therapy. This paper focusses on the problem of event detection of EMG signals as this is the first step towards implementing an effective closed loop control of robotic assistance using EMG. The result of this analysis identifies the most promising detectors for application in EMG-driven robot assisted therapy. The “cost” for identifying the detectors is also designed accordingly. Therefore, in the introduction we have given the background about the necessity to identify the best detector that works well with low SNR EMG signals. However, we have reduced the introduction and discussion section which now highlights only the need for identifying the best detector for application such as EMG driven robot assisted therapy. Original text: Substantial recovery of sensory-motor function after a stroke is possible with high-intensity and high-dosage movement training. 1 Rehabilitation robots can facilitate such high-intensity movement training while providing physical assistance to the user for completing movements consistently and precisely. About 30% of stroke survivors are severely impaired 2 , 3 and require physical assistance to actively engage in movement training. While physical assistance from a robot can motivate such subjects to attempt and train movements, they can also provide inappropriately timed or too much assistance 4 , 5 leading to slacking, where patients reduce their voluntary effort and exploit robotic assistance to perform the movements. Inappropriately timed robotic assistance also alters the patient’s sense of agency or subjective awareness of control. This could lead to a lack of intrinsic motivation and attention, affecting motor learning and performance. 6 Positive therapeutic effects have been observed only when patients actively engage in therapy. 7 – 10 Jo et al. 11 reported no improvement in clinical scales with passive range of motion therapy. Thus, active patient participation during movement therapy is an essential ingredient for sensorimotor recovery. Robotic assistance contingent on a subject’s intention to move is an effective way to guide neuroplasticity. Reduced text in the manuscript: Active patient participation during movement therapy is an essential ingredient for sensorimotor recovery after a stroke. About 30% of stroke survivors are severely impaired 2 , 3 and require physical assistance to actively engage in movement training. Robotic assistance can motivate such subjects to attempt and train movements and when it is contingent on the intention to move it may be an effective way to guide neuroplasticity. 12 It sounds also contradicting to refer to the case „without residual movement“ but to measure surface EMG. What presumably is addressed by the manuscript are combined muscle excitations; i.e. to generate stiffness in the arm when fingers are grasping an object. But such a stiffness in the forearm is ambiguous, because the same stiffness will be generated with different finger movements. I will not continue this rehabilitation issue, because it is not the concern of this manuscript. – as mentioned above. Summarizing: The main results are interesting, and they should be provided in a compressed form. Response: The study by Balasubramanian et al [1], about 70% of severely impaired stroke patients without residual movement in fingers and wrist had residual EMG. The lack of residual movements despite the presence of EMG in stroke patients could be because of several reasons, one such is co-contraction in which case we could still pick up residual EMG. We agree with the reviewer that the same stiffness can be generated with different finger movements. However, our objective is not to decode stiffness, but to see if there is EMG activity in a muscle of interest – a muscle the patient is trying to activate while attempting a movement. The patient could be activating other (antagonists or unrelated) muscles as well, but this is not relevant to the question of whether the muscle of interest displays EMG activity when it is being activated. We are primarily interested in the most appropriate detector for low SNR EMG from any given muscle, irrespective of what happens with other muscles. Once such a detector is identified, different forms of therapeutic interventions become possible, where patients could be asked to attempt activation of certain muscles while suppressing others." } ] } ]	1	https://f1000research.com/articles/12-429
https://f1000research.com/articles/12-1281/v1	06 Oct 23	{ "type": "Research Article", "title": "Variables and instruments for assessing mental health in competitive swimmers: A narrative review", "authors": [ "Alfonso Trinidad" ], "abstract": "Background: Mental health issues are becoming increasingly prevalent among elite athletes, and during the Tokyo 2020 Olympic Games, this issue became a pressing concern. In particular, several athletes complained about their mental health in relation to the highly demanding demands of their sport. High-performance swimming exposes athletes to a variety of stressors due to the physical, technical and mental demands of the sport. The study has carried out a narrative review of the main variables related to mental health, their dimensions and evaluations in competitive swimmers. Methods: Clearly planned and ordered potential studies were identified using combined search methods. The search was carried out in different bibliographic databases (Dialnet, Web of Science and Scopus) between 1990 and 2023. We then searched Google Scholar and manually searched the reference lists of the retrieved studies to identify potentially eligible studies that were not included in the electronic searches. The studies were examined from three different perspectives. Firstly, the methodology, sample, swimming categories and their relationship with mental health were analysed. Secondly, the variables related to mental health symptoms and disorders. Finally, the main mental health analysis tools and the conclusions of the studies. Results: The concept of mental health in competitive swimmers needs to be clarified in the scientific literature, as different variables have been analysed and multiple instruments have been used with small samples of swimmers, without any intervention and prevention protocol. In addition, the bodies and institutions involved should work in an interdisciplinary and collaborative manner, establishing specific programmes to ensure effective prevention and care. Conclusions: Studies are needed to fill this gap and it is necessary to work under the same consensus and in collaboration with specified technical teams. In order to monitor, evaluate and provide services through detection tests and support to swimmers in their training and competitions.", "keywords": [ "Natación", "competición", "deporte", "bienestar", "evaluación", "supervisión", "detección", "prevención" ], "content": "Introduction\n\nMental health problems are increasingly present among elite athletes and it was during the Tokyo 2020 Olympics when it was an urgent call for this issue. In particular, several athletes complained about their mental health situation regarding the highly demanding inquiries about their sports modalities. Moreover, the World Health Organization defines “global health” as “a state of complete physical, mental, and social well-being,”. This definition explicitly stresses that mental health is vital to our ability to think, feel and interact among us (Jackson et al., 2022; World Health Organization, 2018). However, far from this definition in terms of health, we find that in high-competition swimming, the athletes are exposed to different stressors in high competition due to the physical, technical and mental demands (Hooper et al., 2022; Salazar et al., 1997; Trinidad et al., 2021). Likewise, it was also corroborated that psychological preparation and sports psychologists are essential factors within the technical teams with a view to the optimal performance of swimmers (Rice et al., 2016). It was not until 2017 that the International Olympic Committee (IOC) began to take care of the mental health of athletes, creating a specific working group (MHWG), to develop an evaluation and early recognition tool on the possible risks of suffering from mental health symptoms and disorders (Gouttebarge et al., 2021).\n\nSince the 1990s, the scientific literature has emphasised mental health’s role among competitive swimmers. This factor is as important as physical health in optimising the athlete’s performance and well-being. However, this concept has been unnoticed by sports coaches and psychologists, due to the limited literature on swimming and the benefits of this sport for mental health (Geamonond, 2018). The scarcity of research that has had competitive swimmers as an object of study has been a visible fact (Jackson et al., 2022; Rice et al., 2016). Even in a recent review study (Gouttebarge et al., 2019), the absence of these athletes is evidenced by not characterizing them specifically (Hughes & Leavey, 2012; Reardon & Factor, 2010). Similarly, high-quality systematic studies and intervention trials have been limited (Rice et al., 2016; Gouttebarge et al., 2021), as well as descriptive research on the extent of mental health symptoms and disorders (Gouttebarge et al., 2019). This evidence set off alarms among swimmers, coaches and technical teams, as high rates of highly prevalent mental disorders begin to appear (Rice et al., 2016). This is contrary to the statement that swimming causes the sensation of well-being and relaxation, as well as control of anxiety, stress and fatigue (Cordeiro et al., 2017). Some factors include intense physical activity, overtraining, injuries and exhaustion (Peluso & Andrade, 2005), proximity to sports retirement (Gouttebarge et al., 2016), a strict diet (Sundgot-Borgen & Torstveit, 2004), physical and competitive stress, along with pressure from the public, the media, and the social media (Bruner et al., 2008; Fletcher & Wagstaff, 2009; Hanton et al., 2005; Noblet & Gifford, 2002). Moreover, it should be added that athletes do not seek help for reasons such as a bad reputation, lack of understanding, the impact on performance and the perception that seeking help is a weakness (Reardon & Factor, 2010; Gulliver et al., 2012). This generates a high risk of mental illness that reduce sporting success (Rice et al., 2016).\n\nTherefore, something must be fixed since the literature has warned us of the importance of psychological preparation and mental training (Nideffer, 1985; Ryan, 1982). Moreover, putting up with the high training loads does not only depends on physical, technical and tactical preparation in order to achieve high performance (Salazar et al., 1997). Subsequently, the novelty of this study is to review the different works that examine the mental health of swimmers and the tools displayed to examine those characteristics of mental health in this population. To date, it seems that no previous review has examined the different tools and measures to portray competitive swimmers’ mental health situation. Therefore, this study aimed to carry out an analysis of the scientific tests taken with mental health in the discipline of swimming, as well as to examine the type of instrument used to evaluate and diagnose this situation in highly competitive swimmers.\n\n\nMethods\n\nCombined search processes identified potential studies, clearly planned and ordered. First, the following bibliographical databases were consulted: Dialnet, WOS (Web of Science) and Scopus with the following search terms included in Boolean search strategies: (mental[tiab] AND (health [tiab] AND competitive [tiab] AND swimmers [tiab]) OR (swimming [tiab]) or in Spanish (mental[tiab] AND (salud [tiab] AND competitivos [tiab] AND nadadores [tiab]) OR (natación [tiab]).\n\nBy using filter criteria of the respective databases, the search was limited to publication dates (from 1 January 1990 to 30 June 2023), species (humans), and English and Spanish languages. Moreover, we searched Google Scholar and manually searched the reference lists of retrieved studies to identify potentially eligible studies not captured by the electronic searches.\n\nTo avoid internal biases in studies and between studies, the following criteria were adopted:\n\n‐ Articles published from 1990 to 2023.\n\n‐ Full-text articles written in English or Spanish languages (to reduce the bias of the revised publication) and peer-reviewed (to guarantee a minimum of manuscript quality and a minimum of reliability).\n\n‐ Articles that analyzed competitive swimmers based on scientific methodology, with one or more measuring instruments in different variables.\n\nThose that did not meet these criteria were excluded, as were books, book chapters, theses, thesis reviews, case study presentations, conference notes, and studies focused on non-competitive, amateur or triathlon swimmers. Also, it is important to note that research were only taken after extensively searching for existing research in that field.\n\nFor collection and data organization, the tools offered by the different databases were used (text availability, article attributes, article type, publication date…). The data analysis was considered from three different points of view. Firstly, the methodology, sample, swimming categories (swimmers who competed in regional, university, national, international, masters championships and who had a minimum of 2 hours of training per week) were analysed and their relationship with mental health in competitive swimmers. Secondly, those variables (anxiety; motivation; self-esteem; goal orientation and goal setting; intensity and level of performance; importance of the test; coping; eating and depressive disorders; stress and recovery; exhaustion; tension, optimism and pessimism) that were related to mental health symptoms and disorders in competitive swimmers. Finally, the main analysis instruments for the mental health of competitive swimmers.\n\nTable 1 shows the main research, as well as the methodology used, the sample and the swimming category of the analysed swimmers. Particularly, most studies followed a cross-sectional design (n = 8), followed by longitudinal (n = 4), comparative (n = 5) and a review (n = 1). Moreover, the sample was made up of 1174 swimmers. On the other hand, the swimming categories were: elite (n = 7), national/international (n = 3), master (n = 1), national (n = 1), university/international (n = 1), international (n = 1) and regional/national (n = 1). The period in which the studies were published was in a range of 27 years (from 1994 until June 2023).\n\n\nResults\n\nSearches were made using titles, abstracts and keywords. The first comprehensive search yielded a total of 512 records. One additional article was identified by other means. After removing duplicates, 72 documents were identified, of which 41 were excluded as they were not directly related to the objective of the study. Finally, 59 articles were reviewed and, after applying the inclusion criteria, the 18 articles included in this review were selected (Figure 1).\n\nTable 2 shows the main variables that examined the symptoms and disorders of mental health in competitive swimmers. The main studies focused on analyzing different variables such as: performance anxiety, as well as before and after competition; individual and group motivation; the self-esteem; orientation and goal setting; intensity and level of performance; the importance of the test; coping; eating and depressive disorders; stress and recovery; exhaustion, as well as tension, optimism and pessimism.\n\nTable 3 shows the main instruments used in the literature to analyse the possible symptoms and disorders associated with mental health in competitive swimmers. Particularly, the main variables examined in the studies analysed were: Anxiety (performance, pre- and post-competition) (n = 1), Mood (n = 1), Motivation (individual and groups) (n = 1), Self-esteem (n = 1), Goal orientation (n = 1), Goal setting (n = 1), Training intensity (n = 1), Performance level (n = 1), Test Importance (n = 1), Perceived efficacy coping (n = 1), Task Coping (n = 1), Coping with the events’ cancelation (n = 1), Eating disorders (n = 1), Depressive disorders (n = 1), Stress and recovery (n = 1), Exhaustion (n = 1), Psychological tension (n = 1), and Optimism and pessimism (n = 1). Regarding the main instruments utilized it stands out the use of the modified CSAI-2 (n = 1), the direction scale (n = 1), the mental readiness form (MRF-3) (n = 1), modified COPE (n = 1), the MCOPE (n = 1), the performance strategies test (TOPS) (n = 1), the semi-structured follow-up telehealth interviews (n = 1), the mental training program (MTP) (n = 1), the perception of success questionnaire (POSQ) (n = 1), the DSM-IV-TRir semi-structured questionnaire (n = 1), the BDI-II self-report instrument (n = 1), the Depression Scale CESD-R-10 (n = 1) and an online survey (n = 1).\n\nTable 4 shows how the studies affirm that the high levels of physical activity that elite swimmers develop may cause high-stress levels, depression and anxiety, even after the competition cancellation, which psychological distress symptoms could follow. Other authors highlight that competitive swimming can lead to mental health problems, associated with other factors such as harassment and abuse, and the need to maintain a slim figure or a low body weight to compete. However, most of the studies agree that competitive swimmers should have a psychological support service and receive psychological preparation in this regard, which would help them as a tool for achieving goals and regulating anxiety in order to achieve a positive motivational climate that would allow them to reach a high degree of mental and physical well-being.\n\n\nDiscussion\n\nThis study aimed to carry out an analysis of the scientific tests taken in mental health in the discipline of swimming, as well as to examine the type of instrument used to evaluate and diagnose this situation in highly competitive swimmers. In competitive swimming, mental health has been assessed from different perspectives and with great scientific heterogeneity. One of the possible causes could be associated with the fact that swimming is related to other areas of knowledge (Navarro et al., 1990), among which is psychology. The range of variables studied in this area has generated some uncertainty and overlooked certain factors that may have influenced swimmers’ vulnerability to mental health symptoms and disorders (Bär & Markser, 2013). Likewise, some studies highlight that there are more than 640 different stressors (Arnold & Fletcher, 2012) and that together with the sports withdrawal, they could develop a high probability of suffering from symptoms and mental health disorders (Arnold & Fletcher, 2012; Wylleman & Reints, 2010). Therefore, it may be highlighted that mental health has not been analysed and evaluated in depth and rigour, according to the scientific literature. However, there are also controversies since other authors defend the idea that swimming positively affects general somatic health (Oja et al., 2015; Tanaka, 2009) and mental health (Cordeiro et al., 2017; Yfanti et al., 2014). On the contrary, these opinions differ from those other researchers give when discussing mental health in high-level sports and its stressors and conditioning factors (Henriksen et al., 2020). For this reason, this scientific diversity has generated some uncertainty among researchers, not knowing what to focus their studies on when evaluating and diagnosing due to the dimensional amplitude of variables.\n\nThe reviewed scientific literature shows how the concept of mental health could be clearer between the studies, since most of them have analysed different variables separately (Byrne & McLean, 2002; Didymus & Fletcher, 2014; Hammond et al., 2013; Hooper et al., 2022), to later refer to the term mental health in general. Likewise, most of these studies have focused mainly on variables such as: anxiety, coping, goal setting and depression (Abrahamsen et al., 2008; Nixdorf et al., 2013; Salazar et al., 1997; Simões et al., 2012), neglecting other factors (Arnold & Fletcher, 2012), which could also be analysed and give a more complete view in terms of mental health among swimmers. Therefore, it would be necessary to reach a consensus on mental health and work on these symptoms and disorders in an interconnected way with other factors (risk and recovery from injuries, sports performance, depression and anxiety) and relate them to other symptoms, injuries and physical illnesses (Jones & Hanton, 1996). This could further clarify what mental health is and how it could be extrapolated to swimming, since most of the studies analysed in the literature focus on the study of a reduced number of variables or in the analysis of aquatic disciplines displayed by FINA (Jackson et al., 2022).\n\nLikewise, the scientific literature seems to have not found a consensual categorization of the term mental health. Authors such as Rice et al. (2016) related mental health with: anger and aggression, anxiety, eating disorder and image, general prevalence studies, seeking help, sleep, stress and coping, substance use and well-being. In contrast, Gouttebarge et al. (2019) linked it to terms such as: distress, sleep, anxiety/depression, and alcohol abuse. Purcell et al. (2019) and Reardon et al. (2019) linked it with: high prevalence disorders (e.g., anxiety and mood symptoms) and more complex mental health disorders (e.g., bipolar and eating disorders). However, the International Olympic Committee (IOC) and its mental health working group (MHWG) have proposed a confidential mental health support service “Mentally Fit”. This service could help to clarify the term and establish different categories of analysis (pressure management, physical or psychological exhaustion, harmony between sport and life at home, management of life or career changes, stress management, communication improvement, how to deal with injuries, anxiety control, depression, eating disorders, bullying, harassment and abuse, and parenting). Also, this service could explain all the edges that make up mental health for future research, given the lack of consensus among researchers when categorising mental health. Furthermore, even the International Swimming Federation (FINA) does not have a program similar to that of the International Olympic Committee (IOC) and delegates, according to its general medical regulations, to the members of the Olympic movement. It is therefore questionable whether there is any concern on the part of this competent body for its swimmers in the area of mental health according to its current regulations.\n\nIt even reinforces the opinion of some researchers on the lack of concern on the part of federations and institutions (Reardon & Factor, 2010), in the face of this situation in high-level swimmers. Therefore, it would be recommended that the International Swimming Federation (FINA) implement a health program that will help both coaches and athletes to improve their knowledge of mental health problems (Mountjoy et al., 2019), extending this to other aquatic disciplines under FINA conditions (Jackson et al., 2022).\n\nConcerning the methodology used to detect mental health problems in swimmers, it has been shown that most cross-sectional, longitudinal and comparative studies do not correspond to high-quality research and intervention trials (World Health Organization, 2018). This situation also corroborates the need for more consensus among researchers when it comes to intervening, preventing and establishing action protocols, to which is added the scarcity of scientific literature (Trinidad et al., 2021; World Health Organization, 2018), being necessary the expansion in this field through specific studies. Furthermore, it would be necessary to increase the analysis sample for future comparative studies (Hainline & Reardon, 2019; Hammond et al., 2013; Purcell et al., 2019), since it was found that most research was at most 15 sample swimmers (Henriksen et al., 2020; Jackson et al., 2022; Oja et al., 2015; Tanaka, 2009).\n\nRegarding the revised instruments for the measurement and diagnosis of mental health in swimmers, there is great heterogeneity since most of them have used between three and four measurement tools. First, for anxiety the following were mainly used: the modified CSAI-2 (Ning et al., 2022; Martens et al., 1990), the direction scale, the mental readiness form (MRF-3) (Krane, 1994) and different self-report scales (Hooper et al., 2022). Regarding coping, the following were used: the career information questionnaire, modified COPE (Carver et al., 1989) and MCOPE (Crocker & Graham, 1995), the performance strategies test (TOPS) (Hardy et al., 2010) and the semi-structured follow-up telehealth interviews (Ning et al., 2022). In order to establish goals, the following were used: the scale of expectations of achieving objectives, the mental training program (MTP) and the perception of success questionnaire (POSQ) (Roberts et al., 1998). Finally, for depression, the following were used: the semi-structured interview based on the DSM-IV-TR criteria, the BDI-II self-report instrument (Beck & Steer, 1993), center for Epidemiological Studies Depression Scale revised (CESD-R-10) (Jackson et al., 2022) and an online survey. This diversity of resources demonstrates, once again, the lack of consensus and the need to establish a more homogeneous protocol among researchers, in order to know what tools should be used in each aspect of mental health. Therefore, it would be necessary to lay the foundations to reach viable conclusions that can be extrapolated to swimmers to measure and diagnose mental health. All this evidence makes it necessary to carry out specific studies with swimmers and ex-swimmers, in order to carry out intervention protocols and prevention of mental health, rather than waiting for symptoms to appear during sports life or even waiting for the testimonies of retired swimmers.\n\nIn conclusion, mental health problems are a salient topic in sports since 1990s. Studies that have analysed mental health symptoms and disorders in competitive swimmers have been insufficient in the scientific literature. They have even valued it from different dimensions and tools, masking the problem or simply reporting data that have not helped to clarify what mental health is. Therefore, it is necessary to fill this gap with studies that work under the same consensus and in collaboration with specified technical teams, in order to supervise, evaluate and provide services, through detection tests and support to swimmers in their training, as well as before and after competitions. Moreover, there should be a direct involvement by the competent bodies and institutions to tackle, instead of ignoring or mismanaging this situation, in order to respond to the needs of swimmers. Finally, mental health is everyone’s responsibility, from the swimmer himself to the bodies and institutions involved, and interdisciplinary and collaborative work should be done, establishing specific programs based on the sport in order to guarantee efficient prevention and care.\n\nThe author declares that he/she has not registered the study with an independent registry without a data analysis plan.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAcknowledgements\n\nThe present study was supported by the Aqualab Research Group (Department of Education and Humanities) of the Universidad Europea de Madrid, Madrid, Spain.\n\n\nReferences\n\nAbrahamsen FE, Roberts GC, Pensgaard AM: Achievement goals and gender effects on multidimensional anxiety in national elite sport. Psychol. Sport Exerc. 2008; 9(4): 449–464. Publisher Full Text\n\nArnold R, Fletcher D: A research synthesis and taxonomic classification of the organizational stressors encountered by sport performers. J. Sport Exerc. Psychol. 2012; 34: 397–429. PubMed Abstract \| Publisher Full Text\n\nBär K-J, Markser VZ: Sport specificity of mental disorders: the issue of sport psychiatry. Eur. Arch. Psychiatry Clin. Neurosci. 2013; 263(2): 205–210. Publisher Full Text\n\nBeck AT, Steer RA: Manual for the Beck Depression Inventory. San Antonio, TX: Psychological Corporation, Harcourt, Brace; 1993.\n\nByrne S, McLean N: Elite athletes: effects of the pressure to be thin. J. Sci. Med. Sport. 2002; 5(2): 80–94. PubMed Abstract \| Publisher Full Text\n\nBruner MW, Munroe-Chandler KJ, Spink KS: Entry into elite sport: a preliminary investigation into the transition experiences of rookie athletes. J. Appl. Sport Psychol. 2008; 20(2): 236–252. Publisher Full Text\n\nCarver CS, Scheier MF, Weintraub JK: Assessing coping strategies: A theoretically based approach. J. Pers. Soc. Psychol. 1989; 56: 267–283. Publisher Full Text\n\nCordeiro LMS, Rabelo PCR, Moraes MM, et al.: Physical exercise-induced fatigue: the role of serotonergic and dopaminergic systems. Braz. J. Med. Biol. Res. 2017; 50(12): e6432. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCrocker PRE, Graham TR: Coping by competitive athletes with performance stress: gender differences and relationships with affect. Sport Psychol. 1995; 9: 325–338. Publisher Full Text\n\nDidymus FF, Fletcher D: Swimmers’ experiences of organizational stress: exploring the role of cognitive appraisal and coping strategies. J. Clin. Sport Psychol. 2014; 8(2): 159–183. Publisher Full Text\n\nFletcher D, Wagstaff CRD: Organizational psychology in elite sport: its emergence, application and future. Psychol. Sport Exerc. 2009; 10: 427–434. Publisher Full Text\n\nGeamonond NL: Sports swimming and mental health: is there a relationship? Pensar en Movimiento: Revista de Ciencias del Ejercicio y la Salud. 2018; 18(2): e44034–e44222. Publisher Full Text\n\nGouttebarge V, Aoki H, Kerkhoffs GM: Prevalence and determinants of symptoms related to mental disorders in retired male professional footballers. J. Sports Med. Phys. Fitness. 2016; 56(5): 648–654. PubMed Abstract\n\nGouttebarge V, Bindra A, Blauwet C, et al.: International Olympic Committee (IOC) Sport Mental Health Assessment Tool 1 (SMHAT-1) and Sport Mental Health Recognition Tool 1 (SMHRT-1): towards better support of athletes’ mental health. Br. J. Sports Med. 2021; 55(1): 30–37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGouttebarge V, Castaldelli-Maia JM, Gorczynski P, et al.: Occurrence of mental health symptoms and disorders in current and former elite athletes: a systematic review and meta-analysis. Br. J. Sports Med. 2019; 53(11): 700–706. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGulliver A, Griffiths KM, Christensen H: Barriers and facilitators to mental health help-seeking for young elite athletes: A qualitative study. BMC Psychiatry. 2012; 12(1): 157. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHainline B, Reardon CL: Breaking a taboo: why the International Olympic Committee convened experts to develop a consensus statement on mental health in elite athletes. Br. J. Sports Med. 2019; 53(11): bjsports-2019-100681–bjsports-2019-100666. PubMed Abstract \| Publisher Full Text\n\nHammond T, Gialloreto C, Kubas H, et al.: The prevalence of failure-based depression among elite athletes. Clin. J. Sport Med. 2013; 23(4): 273–277. PubMed Abstract \| Publisher Full Text\n\nHanton S, Fletcher D, Coughlan G: Stress in elite sport performers: a comparative study of competitive and organizational stressors. J. Sports Sci. 2005; 23(10): 1129–1141. PubMed Abstract \| Publisher Full Text\n\nHanton S, Jones G: The effects of a multimodal intervention program on performers: II. Training the butterflies to fly in formation. Sport Psychol. 1999; 13(1): 22–41. Publisher Full Text\n\nHardy L, Roberts R, Thomas P, et al.: Test of Performance Strategies (TOPS): Instrument refinement using confirmatory factor analysis. Psychol. Sport Exerc. 2010; 11(1): 27–35. Publisher Full Text\n\nHatzigeorgiadis A, Chroni S: Pre-competition anxiety and in-competition coping in experienced male swimmers. Int. J. Sports Sci. Coach. 2007; 2(2): 181–189. Publisher Full Text\n\nHenriksen K, Schinke R, McCann S, et al.: Athlete mental health in the Olympic/Paralympic quadrennium: a multi-societal consensus statement. Int. J. Sport Exerc. Psychol. 2020; 18(3): 391–408. Publisher Full Text\n\nHooper NR, Reiber C, Cheatham SA: The psychological effects of event cancellation in Olympic-level swimmers: preliminary findings and mental health screening recommendations. J. Sports Med. Phys. Fitness. 2022; 62: 732–739. PubMed Abstract \| Publisher Full Text\n\nHughes L, Leavey G: Setting the bar: athletes and vulnerability to mental illness. Br. J. Psychiatry. 2012; 200(2): 95–96. PubMed Abstract \| Publisher Full Text\n\nJackson M, Kang M, Furness J, et al.: Aquatic exercise and mental health: A scoping review. Complement. Ther. Med. 2022; 66: 102820. PubMed Abstract \| Publisher Full Text\n\nJones G, Hanton S: Interpretation of competitive anxiety symptoms and goal attainment expectancies. J. Sport Exerc. Psychol. 1996; 18(2): 144–157. Publisher Full Text\n\nJones G, Hanton S, Swain A: Intensity and interpretation of anxiety symptoms in elite and non-elite sports performers. Personal. Individ. Differ. 1994; 17: 657–663. Publisher Full Text\n\nKrane V: The mental readiness form as a measure of competitive state anxiety. Sport Psychol. 1994; 8(2): 189–202. Publisher Full Text\n\nMartens R, Burton D, Vealey RS, et al.: Development and validation of the Competitive State Anxiety Intentory-2.Martens R, Vealey RS, Burton D, editors. Competitive anxiety in sport. Champaing, Illinois: Human Kinetics; 1990; pp. 127–140.\n\nMountjoy M, Junge A, Budgett R, et al.: Health promotion by International Olympic Sport Federations: priorities and barriers. Br. J. Sports Med. 2019; 53(17): 1117–1125. PubMed Abstract \| Publisher Full Text\n\nMountjoy M, Junge A, Magnusson C, et al.: Beneath the Surface: Mental Health and Harassment and Abuse of Athletes Participating in the FINA (Aquatics) World Championships, 2019. Int. J. Sport Exerc. Psychol. 2022; 32(2): 95–102. PubMed Abstract \| Publisher Full Text\n\nNavarro F, Arellano R, Carnero C, et al.: Swimming. Madrid: COE; 1990.\n\nNideffer RM: Athletes’ Guide to Mental Training. Champaign, Ill: Human Kinetics; 1985.\n\nNing JH, Hao QW, Huang DC: Effects of “Mindfulness Acceptance Insight Commitment” Training on Flow State and Mental Health of College Swimmers: A Randomized Controlled Experimental Study. Front. Psychol. 2022; 13: 799103. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNixdorf I, Frank R, Hautzinger M, et al.: Prevalence of depressive symptoms and correlating variables among German elite athletes. J. Clin. Sport Psychol. 2013; 7(4): 313–326. Publisher Full Text\n\nNoblet AJ, Gifford SM: The sources of stress experienced by professional Australian footballers. J. Appl. Sport Psychol. 2002; 14(1): 1–13. Publisher Full Text\n\nOja P, Titze S, Kokko S, et al.: Health benefits of different sport disciplines for adults: systematic review of observational and intervention studies with meta-analysis. Br. J. Sports Med. 2015; 49(7): 434–440. PubMed Abstract \| Publisher Full Text\n\nPeluso M, Andrade L: Physical activity and mental health: the association between exercise and mood. Clinics. 2005; 60(1): 61–70. Publisher Full Text\n\nPotdevin F, Vanlerberghe G, Zunquin G, et al.: Evaluation of global health in master swimmers involved in French national championships. Sports Med. Open. 2015; 1(1): 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPurcell R, Gwyther K, Rice SM: Mental health in elite athletes: Increased Awareness requires an early intervention framework to respond to athlete needs. Sports Med. Open. 2019; 5: 46. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReardon CL, Factor RM: Sport psychiatry: a systematic review of diagnosis and medical treatment of mental illness in athletes. Sports Med. 2010; 40(11): 961–980. Publisher Full Text\n\nReardon CL, Hainline B, Aron CM, et al.: Mental health in elite athletes: International Olympic Committee consensus statement . Br. J. Sports Med. 2019; 53(11): 667–699. PubMed Abstract \| Publisher Full Text\n\nRice SM, Purcell R, De Silva S, et al.: The mental health of elite athletes: A narrative systematic review. Sports Med. 2016; 46: 1333–1353. Publisher Full Text\n\nRoberts GC, Treasure DC, Balague G: Achievement goals in sport: The development and validation of the perceptions of success questionnaire. J. Sports Sci. 1998; 16: 337–347. PubMed Abstract \| Publisher Full Text\n\nRomberg K, Tufvesson E, Bjermer L: Asthma is more prevalent in elite swimming adolescents despite better mental and physical health. Scand. J. Med. Sci. Sports. 2012; 22(3): 362–371. PubMed Abstract \| Publisher Full Text\n\nRyan F: Sports and Psychology. Publigraphics S.A: Mexico; 1982.\n\nSalazar R, Solís A, Barboza R: Effect of Mental Health in sports performance in elite swimmers. Revista Costarricense de Salud Pública. 1997; 6(10): 29–37.\n\nSimões P, Vasconcelos-Raposo J, Silva A, et al.: Effects of a Process-Oriented Goal Setting Model on Swimmer’s Performance. J. Hum. Kinet. 2012; 32: 65–76. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSundgot-Borgen J, Torstveit MK: Prevalence of eating disorders in elite athletes is higher than in the general population. Clin. J. Sport Med. 2004; 14(1): 25–32. Publisher Full Text\n\nTanaka H: Swimming Exercise. Sports Med. 2009; 39(5): 377–387. Publisher Full Text\n\nTorstveit MK, Rosenvinge JH, Sundgot-Borgen J: Prevalence of eating disorders and the predictive power of risk models in female elite athletes: a controlled study. Scand. J. Med. Sci. Sports. 2008; 18(1): 108–118. PubMed Abstract \| Publisher Full Text\n\nTrinidad A, González-García H, López-Valenciano A: An Updated Review of the Epidemiology of Swimming Injuries. PM R. 2021; 13(9): 1005–1020. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Mental health: Strengthening our Response. WHO; 2018, March 30. int. Reference Source\n\nWylleman P, Reints A: A lifespan perspective on the career of talented and elite athletes: perspectives on high-intensity sports. Scand. J. Med. Sci. Sports. 2010; 20(2): 88–94. PubMed Abstract \| Publisher Full Text\n\nYfanti M, Samara A, Kazantzidis P, et al.: Swimming as physical activity and recreation for women. TIMS. Acta. 2014; 8(2): 137–145. Publisher Full Text" }	[ { "id": "213018", "date": "16 Nov 2023", "name": "Miguel Ángel Gómez Ruano", "expertise": [ "Reviewer Expertise Sport Sciences" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe narrative review submitted is quite interesting, well-prepared, and useful for coaches and researchers interested in improving the mental health of their swimmers. I have some comments and suggestions in order to improve the meaning and readability of the manuscript.\n\nPlease use the impersonal form when writing through the manuscript.\n\nIntroduction, first paragraph, line 3, please write (WHO) after World Health Organization.\n\nMethods, authors should describe what type of review they are conducting, in this case, a narrative review. I suggest using the following reference to justify the methodology used: Grant, M. J., & Booth, A. (2009). A typology of reviews: an analysis of 14 review types and associated methodologies. Health Information and Libraries Journal, 26, 91-1081.\n\nMethod, please add the date when the search was made.\n\nFigure 1, should consider only 3 phases according to PRISMA 2020 guidelines, please modify it accordingly.\n\nTable 1 should be presented by pooling the studies that used the same methodology, then this would clarify the visual inspection of every study.\n\nThe discussion could be enriched using an infographic that summarizes the main factors and variables under analysis.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10684", "date": "22 Mar 2024", "name": "Alfonso Trinidad", "role": "Author Response", "response": "Dear Reviewer, Thank you very much for your comments and suggestions. The changes have been made according to your instructions: Please use the impersonal form when writing through the manuscript. The manuscript has been revised and the erroneous verb tenses have been changed to impersonal. Apologies for this. Introduction, first paragraph, line 3, please write (WHO) after World Health Organization. Corrected. Thanks for the comment. Moreover, the World Health Organization (WHO) defines “global health” as “a state of complete physical, mental, and social well-being,”. Methods, authors should describe what type of review they are conducting, in this case, a narrative review. I suggest using the following reference to justify the methodology used: Grant, M. J., & Booth, A. (2009). A typology of reviews: an analysis of 14 review types and associated methodologies. Health Information and Libraries Journal, 26, 91-1081. The type of review used in the methodology was described. For this, the suggested reference was taken into account. Subsequently, the References section was updated. A narrative review or literature review was carried out where the materials published in the literature (tests and instruments to evaluate and diagnose mental health in highly competitive swimmers) were described, in order to perform a textual, tabular or graphic synthesis of Your results. and contributions (Grant & Booth, 2009). Method, please add the date when the search was made. Corrected. Thanks for the comment. The start of the study was in February 2023 through combined search processes, in which potential studies, clearly planned and ordered, were identified. In orden to perform that, the following bibliographical databases were consulted: Dialnet, WOS (Web of Science) and Scopus with the following search terms included in Boolean search strategies: (mental[tiab] AND (health [tiab] AND competitive [tiab] AND swimmers [tiab]) OR (swimming [tiab]) or in Spanish (mental[tiab] AND (salud [tiab] AND competitivos [tiab] AND nadadores [tiab]) OR (natación [tiab]). Figure 1, should consider only 3 phases according to PRISMA 2020 guidelines, please modify it accordingly. Corrected. Thanks for the comment. Table 1 should be presented by pooling the studies that used the same methodology, then this would clarify the visual inspection of every study. Corrected. Thanks for the comment. The discussion could be enriched using an infographic that summarizes the main factors and variables under analysis. Thanks for the suggestion. I will ask the magazine if this option is possible within the discussion section." } ] } ]	1	https://f1000research.com/articles/12-1281
https://f1000research.com/articles/13-294/v1	18 Apr 24	{ "type": "Research Article", "title": "The impact of perceived social support and social self-efficacy on resilience ‎among single mothers", "authors": [ "Baha' Suhail Shawaqfeh" ], "abstract": "Background In Jordan, the number of single mothers is rising, constituting a distinct and neglected population sector. Single women encounter several obstacles as primary carers for their children. Since it is a complicated experience that may affect woman's resilience, influenced by social self-efficacy (SSE) and perceived social support (PSS), this study aims to determine how SSE and PSS influence resilience among single mothers.\n\nMethods This research employs a quantitative method. A volunteer group of 534 women in Jordan selected. Three scales were developed to meet the study objectives: PSS, SSE, and resilience.\n\nResults The study results indicate that PSS and SSE have a bearing on the resilience of single mothers, that there are no differences in PSS and resilience levels by social status, and that there is a difference in SSE levels by social class, favoring widows.\n\nConclusions The PSS and SSE influence the resiliency of single women, which offers us the key to assisting them in reintegrating with the community following a family break. These women are also impacted by psychological and physical stress.", "keywords": [ "Perceived Social Support", "Social Self-Efficacy", "Resilience", "Single Mothers‎" ], "content": "Introduction\n\nThe world community’s wetness changes in the family structure, which has grown very fast in the last century, especially in Jordan. The absence of the father becomes a significant problem that faces family structure, which can be caused by death, divorce, or abandonment, so the mother becomes the only maintainer for the family, necessitating taking more responsibility for the children with the psychological and social stresses. The percentage of single mothers in Jordan has risen because of the wars around integration and divorce, and the statistics show 47 cases daily (Department 2020).\n\nSingle mothers suffer from many psychological stresses, such as low levels of psychological safety, physiological, cognitive, and emotional problems (Khwaiter 2010; Al-Muzaini 2011), loneliness, and low economic status (Alwan 2008) that they must be recouping with the new life events.\n\nThe transformation from a regular family to a broken one is complicated. The single mother must reorganize her personal and social life by coping with the main changes in her life's characteristics. The perceived social support (PSS), social self-efficacy (SSE), and resilience can help her to manage (Yilmaz and Fişiloglu 2005).\n\nResilience is a person's ability to deal with adverse situations or stressful life events that can lead to a lower coping level (Ariapooran and Khezeli 2018). Resilience is vital and significant in preventing the negative impacts of stressful life conditions on the capacity to recover of a woman living alone. She is vulnerable due to her low resilience, which causes her to have challenging, unpleasant emotions, react badly to terrible life experiences, and be unable to interact with others, lack responsibility, and be prone to psychological and physiological problems (Zidan 2013).\n\nPSS significantly impacts resilience among single mothers, regardless of the source, whether from family, friends, or a new relationship (Greeff and Van Der Merwe 2004). Furthermore, it is a valuable resource that every individual needs every day. Nonetheless, single mothers require this assistance more than others from family, friends, coworkers, social rehabilitation groups, etc., to combat the negative effect (Khalil 2018; Naz et al. 2020).\n\nHaving someone we can depend on in times of need is the difference between feeling safe and secure and lonely. Social relationships contribute to the formation of PSS, which reduces stress through emotional support such as listening, compassion, and warmth, material support such as financial assistance and meeting basic needs, and informational support such as problem-solving assistance and raising awareness (Blonna 2006).\n\nPSS is related to SSE (Karademas 2006), and SSE mediates the relationship between PSS and certain psychological factors (Aune et al. 2021). SSE reflects an individual's confidence in his ability to engage in the social interaction required to initiate and maintain interpersonal relationships (Bandura and Watts 1996; Satici et al. 2013), as the positive expectation of a single mother's ability to solve her problems is an essential component of SSE. Bandura highlighted that it conveys the individual's self-perception in overcoming challenges he faces while engaging in a particular social activity and his self-expectations based on his talents (Bandura 1977).\n\nA single mother's high expectations of her social and emotional competence (SSE) help her succeed in various social settings, including overcoming adversity, managing anxiety and despair, and solving problems via analytical thinking (Tras et al. 2013). The research by (Tras et al. 2013) showed a predictive association between SSE and resilience; nevertheless, SSE depends on the single mother using her strengths to the utmost degree (Bandura 1993).\n\nThe single mother goes through three stages after losing her husband or separating from him until she can adapt to her new situation. The first stage is shock, characterized by a tense reaction and denial. The second stage is tension, in which the mother feels persecuted, pessimistic, has low self-confidence, is dissatisfied with life, and attempts to withdraw and feel lonely. The third stage is the recoping stage. Here, the single mother begins to rearrange her life, reconsider matters in general, search for sources of support, and start dealing with her new responsibilities (Al-Jawfi 2014). Thus, the researcher analyzed the link between SSE and PSS and their effect on resilience among single mothers.\n\n\n\n1. What is the PSS, SSE, and resilience level among single mothers?\n\n2. Is there an impact of PSS and SSE on resilience among single mothers?\n\n3. Due to social status, are there differences among single women's PSS, SSE, and resilience levels?\n\n\nMethods\n\nThis research employs a quantitative technique of prediction. A volunteer selected five hundred thirty-four women in Jordan as subjects; all participants supplied written informed permission with the scales. The research ethics committee authorized the institution's study.\n\nThe study sample consists of 534 women chosen by volunteering in Jordan, The distribution of participants by socioeconomic rank is as follows: 297 Divorced ladies and 237 widows.\n\nPerceived social support scale\n\nThe researcher developed a scale of 8 items from (Hapke 2015; Tashtoush 2015; Watson et al. 2019). Participants rated each item on a four-Likert scale, from 1 (‘Always’) to 4 (‘Never’). Higher scores reflect a higher level of PSS. The researcher extracted the validity and reliability and found that the discriminate evidence ranged between 0.483 and 0.834. Cronbach's alpha was 0.845, then 0.937 at the retest two weeks later.\n\nSocial self-efficacy scale\n\nThe researcher developed a scale of 7 items from (Smith and Betz 2000; Ahmad et al. 2014). Participants rated each item on a four-Likert scale, from 1 (‘strongly disagree’) to 4 (‘strongly agree’). Higher scores reflect a higher level of SSE. The researcher extracted the validity and reliability and found that the discriminate evidence ranged between 0.590 and 0.789. Cronbach's alpha was 0.804, then 0.828 at the retest two weeks later.\n\nResilience scale\n\nThe researcher developed a scale of 17 items from (Connor and Davidson 2003; Alsheikh Ali 2014). Participants rated each item on a four-Likert scale, from 1 (‘strongly disagree’) to 4 (‘strongly agree’). Higher scores reflect a higher level of resilience. The researcher extracted the validity and reliability and found that the discriminate evidence ranged between 0.300 and 0.963. Cronbach's alpha ranged between 0.746-0.908. The retest two weeks later ranged between 0.794-0.886.\n\nThe researcher obtained approval for this study from the Institutional Review Board at the University of Jordan. The registration number 2376271/744/2021/1. The date was 3/3/2021. Anonymized data was collected by associations concerned with women's affairs, the survey was conducted by paper instruments.\n\nThe researcher entered the data into SPSS data sheet, and used IBM SPSS Statistics for Windows, version 22 (IBM corp., Armonk, N.Y., USA) to analyze the data. Means, standard deviations, Pearson’s correlation, multi-regression, and independent T-test were calculated. All missing data was planned to be reported as missing.\n\n\nFindings and Discussion\n\nMeans, standard deviations, and Person correlations between PSS, SSE, and resilience are shown in Table 1.\n\n* Correlation is significant at the 0.01 level (2-tailed).\n\nTable 1 shows a positive correlation between PSS, SSE, and resilience. Also, the PSS, SSE, and resilience levels were low, the PSS mean was (1.92±0.62), SSE mean was (1.82±0.61), and (1.69±0.57).\n\nTo investigate the impact of PSS and SSE on resilience among single mothers, multi- regression test was calculated, and Table 2 shows the results.\n\nTable 2 shows the impact of PSS and SSE on resilience among single mothers, which was 47.1%, while the correlation was 0.868. Also, The SSE has a more substantial influence on resilience, and the relationship between the variables was positive.\n\nSSE is associated with positive expectations and the ability to solve social problems. With its decline, single mothers try to avoid complex tasks and issues and attribute their inappropriate performance to their personal inability. Thus, persistence and self-confidence decrease, they seek loneliness and separation from others (Pajares and Schunk 2001), and they are exposed to depression and anxiety. With these negative emotions, they look at situations pessimistically, and thus, resilience decreases (Tras et al. 2013).\n\nThe single mother is expected to fulfill paternal and maternal responsibilities, which might strain her relationships with those around her. Therefore, she loses the social and informational support that helps her solve her challenges and difficulties, leading to unfavorable and distressing outcomes, a diminished capacity for resilience, and an environment devoid of positive reinforcement. As a result, a woman's ability to cope with social, psychological, and material stresses is diminished, and she develops a diminished sense of safety in her relationships with others and her community.\n\nIn modern-day Jordan, women have achieved economic and social parity with males. Yet, the stigma arising from a culture that looks at women with suspicion and distrust following a separation or the husband's death restricts the help they get. They are SSE drops because she cannot maintain appearances, and the relationships suffer. Consequently, her anxiety, loneliness, and feeling of isolation due to her focus on her children and other domestic and professional duties all increase as her PSS and SSE drop.\n\nSince communication is a fundamental human need, her lack of it has a negative impact on her adaptability and prevents her from interacting with others, lowering her psychological immunity. So, her resilience is diminished since she cannot fulfill one of humanity's most fundamental needs—the urge to connect with others (Ariapooran and Khezeli 2018).\n\nThe difference in SSE between widows and non-widows may be related to the widow's husband's death. As for the divorced lady, her marriage life ended due to frequent disagreements and her inability to resolve these marital issues, which influenced her perception of her effectiveness since she saw herself as a relationship failure. Rather, she may feel guilt, helplessness, and inferiority. Furthermore, with divorce, the partners' friends between the spouses begin to move away due to their bias towards one of the parties, especially the husband, as they blame the woman most of the time; this causes the loss of relationships and the inability to maintain them. That is one of the primary requirements for SSE.\n\nAs for the no differences in PSS and resilience, widows and divorced women suffer from pressures related to caring for their children and trying to meet their material, emotional and physical needs, including food and housing.\n\n\nConclusion\n\nThis study found an impact of PSS and SSE on resilience among single mothers, which gives us the key to helping them to recoup with the community after the family break. They are affected by psychological and physical stress. In addition, there are no variations in PSS and resilience based on social position. However, there is a difference in SSE based on social class that favors widows. Families and organizations must provide more significant assistance to divorced women to boost their SSE, which may help them find support and be more resilient. Thus, future research should consider social status as a potentially important variable.\n\nMore effective intervention may be achieved and the benefits of this family structure can be better understood if single mothers are regarded as a complex group worthy of independent study. Overall, I argue that a better understanding of how single mothers are able to remain resilient in the face of the challenges of single parenting is necessary, and I present interventions that specifically target the needs of single mothers and have the potential to have a lasting, positive impact on both the mothers' and their children's lives.\n\nThis study was conducted with a sample of single women enrolled in 2022 in Capital Amman in Jordan. The study results were interpreted from the participants’ responses to the PSS, SSE, and resilience scales. The researcher recommend further research on the resilience variable and how it helps single mothers recoup with the community. It will only increase in importance because it will lower the effect on children and build a healthy society. Future research might also relate resilience to personality types and techno wellness variables. The creation of counselling and guidance programs to improve SSE and PSS among single women because they positively impact resilience.\n\nThe researcher obtained approval for this study from the Institutional Review Board at the University of Jordan. The registration number 2376271/744/2021/1. The date was 3/3/2021. Anonymized data was collected by associations concerned with women's affairs, the survey was conducted by paper instruments. A volunteer selected five hundred thirty-four women in Jordan as subjects; all participants supplied written informed permission with the scales. The research ethics committee authorized the institution's study.", "appendix": "Data availability statement\n\nfigshare. PSS & SSE on Resilience.sav http://doi.org/10.6084/m9.figshare.25376581.\n\nData is available under the terms of the CC0.\n\nfigshare. CROSS Checklist for the impact of perceived social support and social self-efficacy on resilience among single mothers, http://doi.org/10.6084/m9.figshare.25432384\n\nData is available under the terms of the CC0.\n\nfigshare. Scales for the impact of perceived social support and social self-efficacy on resilience among single mothers, https://doi.org/10.6084/m9.figshare.25483366.v1\n\nData is available under the terms of the CC0.\n\n\nAcknowledgements\n\nThe researcher would like to thank the participants and the organizations to help him in collecting the data\n\n\nReferences\n\nAhmad ZR, Yasien S, Ahmad R: Relationship between perceived social self-efficacy and depression in adolescents. Iran. J. Psychiatry Behav. Sci. 2014; 8(3): 65.\n\nAl-Jawfi A: The degree of prevalence of cognitive distortions among divorced and widowed female teachers and its relationship to their social sufficiency in the Tabuk region in the Kingdom of Saudi Arabia. Karak, Jordan: Mutah University; 2014.\n\nAl-Muzaini: The psychological suffering of the wives of the martyrs of the 2008 Gaza war in the light of some variables. IUG J. Humanit. Res. 2011; 19(2): 273–304.\n\nAlsheikh Ali A: Resilience levels and their relationship to academic adjustment and achievement among graduates of orphanages. Jordan J. Educ. Sci. 2014; 10(4): 411–430.\n\nAlwan N: Satisfaction with life and its relationship to psychological loneliness (a field study on Aymaneh from the wives of Palestinian martyrs). J. Islamic Univ. 2008.\n\nAriapooran S, Khezeli M: Suicidal ideation among divorced women in Kermanshah, Iran: the role of social support and psychological resilience. Iran J. Psychiatry Behav. Sci. 2018; 12(4): 1–5. Publisher Full Text\n\nAune T, Juul EML, Beidel DC, et al.: Mitigating adolescent social anxiety symptoms: the effects of social support and social self-efficacy in findings from the Young-HUNT 3 study. Eur. Child Adolesc. Psychiatry. 2021; 30: 441–449. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBandura A: Self-efficacy: toward a unifying theory of behavioral change. Psychol. Rev. 1977; 84(2): 191–215. PubMed Abstract \| Publisher Full Text\n\nBandura A: Perceived self-efficacy in cognitive development and functioning. Educ. Psychol. 1993; 28(2): 117–148. Publisher Full Text\n\nBandura A, Watts RE: Self-efficacy in changing societies. Springer; 1996.\n\nBlonna R: Coping with stress in a changing world. McGraw-Hill Humanities/Social Sciences/Languages; 2006.\n\nConnor KM, Davidson JR: Development of a new resilience scale: The Connor-Davidson resilience scale (CD-RISC). Depress. Anxiety. 2003; 18(2): 76–82. Publisher Full Text\n\nDepartment JSJ: Annual Statistical Report for the Year 2020.2020.\n\nGreeff AP, Van Der Merwe S: Variables associated with resilience in divorced families. Soc. Indic. Res. 2004; 68: 59–75. Publisher Full Text\n\nHapke L: Social support networks among children with intellectual and developmental disabilities.2015.\n\nKarademas EC: Self-efficacy, social support and well-being: The mediating role of optimism. Personal. Individ. Differ. 2006; 40(6): 1281–1290. Publisher Full Text\n\nKhalil AHS: Social support and its relationship to the ability to solve social problems among students of the preparatory stage in the schools of Erbil Governorate. Qay Zanst Scientific Journal. 2018.\n\nKhwaiter: Psychological security and a sense of psychological loneliness among Palestinian women (divorced and widowed) and their relationship to some variables. Gaza, Palestine: Islamic University; 2010. Forthcoming.\n\nNaz I, Fatima K, Anjum R: Prevalence and correlates of adjustment disorder in single parent mothers. Pak. Armed Forces Med. J. 2020; 70(3): 830–834.\n\nPajares F, Schunk DH: Self-beliefs and school success: Self-efficacy, self-concept, and school achievement. Perception. 2001; 11(2): 239–266.\n\nSatici SA, Kayis AR, Akin A: Investigating the predictive role of social self-efficacy on authenticity in Turkish university students. Eur. J. Psychol. 2013; 9(3): 572–580. Publisher Full Text\n\nSmith HM, Betz NE: Development and validation of a scale of perceived social self-efficacy. J. Career Assess. 2000; 8(3): 283–301. Publisher Full Text\n\nTashtoush R: life Satisfaction with and perceived social support and the relation-ship between them among a sample of breast cancer patients. Jordan J. Educ. Sci. 2015; 11(4): 449–467.\n\nTras Z, Arslan C, Hamarta E: AN EXAMINATION OF RESILIENCE IN UNIVERSITY STUDENTS IN TERMS OF SELF-ESTEEM AND SOCIAL SELF-EFFICACY. Int. J. Acad. Res. 2013; 5(3): 325–330. Publisher Full Text\n\nWatson RJ, Grossman AH, Russell ST: Sources of social support and mental health among LGB youth. Youth Soc. 2019; 51(1): 30–48. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYilmaz AE, Fişiloglu H: Turkish Parents' Post-Divorce Adjustment: Perceived Power/Control Over Child-Related Concerns, Perceived Social Support, and Demographic Characteristics. J. Divorce Remarriage. 2005; 42(3-4): 83–107. Publisher Full Text\n\nZidan.: Psychological Immunity: Its Concept, Dimensions and Measurement - A Global Study. J. Fac. Educ. 2013; 51: 811–882." }	[ { "id": "272561", "date": "14 May 2024", "name": "Ola Alhwayan", "expertise": [ "Reviewer Expertise Counseling psychology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe connection between the paragraphs is excellent. but I think the reference (Department 2020) is not right; please check.\nThe last paragraph in the introduction needs to improve spatially the stages and responsibilities that women faced.\n\nThe method and analysis are good and achieve the purpose of the study.\nThe differences between widows and divorced ladies must be improved. You should add how the Arabian culture effect the women.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "272558", "date": "31 May 2024", "name": "Brenda Geiger", "expertise": [ "Reviewer Expertise single mothers women resistance to abuse" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nBackground\nToo many value judgements such as the regular family ? \"single mothers require this assistance more than others from family, friends, coworkers, social rehabilitation groups, etc., to combat the negative effect of what ??(Khalil 2018; Naz et al. 2020). WHAT NEGATIVE EFFECTS ?? STIGMA? ECONOMIC DIFFICULTY LEAVING AN ABUSIVE PARTNER??(Khalil 2018; Naz et al. 2020).\nThe percentage of single mothers in Jordan has been on the rise due to the wars around integration?\n\nTHE PHRASE WARS AROUND INTEGRATION DOES NOT MEAN ANYTHING UNLESS YOU SPECIFY WHAT WARS MAYBE STRUGGLES OR CHALLENGES AND INTEGRATION IN WHAT\n\nNonetheless, single mothers require this assistance more than others from family, friends, coworkers, social rehabilitation groups, etc.,\" to combat the negative effect of what ??(Khalil 2018; Naz et al. 2020).\"(Khalil 2018; Naz et al. 2020). Expand Bandurah on self efficacy perception and reciprocal determinism. Sentence need grammatical structuring. Single mothers in plural Mix between he and she Sentences no completed Too many one sentence paragraph\nMethods inadequate\nvariables in Scale are not specified Sample description and the background information of the participants is not sufficient especially on their employment status SES and number of children\n\nThe design is not specified not only quantitative but also comparative study between single and married women Statistical tools\nVariable entered in the regression analysis not specified What are the independent variable aside from martial status?? Results and discussion\nToo many extrapolations not based on data\n\nsuch as stress Too many value judgements which reflect the authors bias concerning that is the right family namely the traditional family as exemplified below. Rather, she may feel guilt, helplessness, and inferiority About What Furthermore, with divorce, the partners' friends between the spouses begin to move away due to their bias towards one of the parties, especially the husband, as they blame the woman most of the time; this causes the loss of relationships and the inability to maintain them. That is one of the primary requirements for SSE.??\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/13-294
https://f1000research.com/articles/13-292/v1	18 Apr 24	{ "type": "Study Protocol", "title": "A cross-sectional study on the impact of bedside echocardiography in critically ill pediatric patient’s management in the pediatric intensive care unit", "authors": [ "Sri Sita Naga Sai Priya K", "Amar Taksande", "Amar Taksande" ], "abstract": "Background Bedside echocardiography has emerged as a valuable diagnostic tool in intensive care units, aiding the prompt evaluation of cardiovascular function in critically ill patients. However, its application in the pediatric population, particularly within rural healthcare settings, still needs to be explored. This study aims to assess the influence of bedside echocardiography on the management and outcomes of critically ill pediatric patients admitted to a tertiary care center in rural Maharashtra, India.\n\nMethods A cross-sectional study will be conducted in the Pediatric Intensive Care Unit (PICU) of Acharya Vinoba Bhave Rural Hospital from July 2022 to July 2024 on 88 participants. The study will enroll critically ill pediatric patients aged one month to 18 years who meet the inclusion criteria. Data collection will involve comprehensive clinical assessments, echocardiography performed by pediatric cardiologists, and documentation of demographic information, clinical history, interventions, and outcomes. Statistical analyses will encompass descriptive statistics, correlation assessments, and significance testing.\n\nExpected results This study aims to elucidate the indications and necessity of echocardiography in pediatric patients, correlate echocardiographic findings with clinical interventions, and assess their impact on patient outcomes. It seeks to contribute valuable insights into the utility of bedside echocardiography in rural PICUs and its potential to inform clinical decision making.", "keywords": [ "Bedside echocardiography", "Pediatric intensive care", "critically ill patients", "Cardiac assessment", "Clinical outcomes", "Rural Healthcare" ], "content": "Introduction\n\nThe care of critically ill pediatric patients demands continuous advancements in diagnostic and therapeutic strategies to optimize outcomes. Bedside echocardiography has emerged as a powerful diagnostic tool in intensive care settings, allowing for rapid and noninvasive assessment of cardiovascular function.1 While its utility in adult critical care has been well established, its impact on the management of critically ill pediatric patients, particularly within rural healthcare settings, remains a subject of significant interest and exploration.2\n\nTimely and accurate assessment of cardiac function in pediatric critical care is paramount. Cardiac dysfunction can manifest in various forms, from structural anomalies to functional impairments, and often requires prompt intervention to mitigate adverse outcomes.3 Bedside echocardiography, with its ability to provide real-time information about cardiac anatomy, function, and hemodynamics, has the potential to revolutionize the care of critically ill children.4\n\nThis study protocol outlines a comprehensive investigation of the impact of bedside echocardiography on the management and outcomes of critically ill pediatric patients in the Pediatric Intensive Care Unit (PICU) at Acharya Vinoba Bhave Rural Hospital, a tertiary care center located in the state of Maharashtra, India. This study aims to bridge the existing gap in knowledge by examining the utilization and effectiveness of echocardiography in this specific patient population.\n\nBy assessing the indications and necessity of echocardiography, correlating echocardiographic findings with clinical interventions, and evaluating the subsequent impact on patient outcomes, this study endeavors to provide valuable insights into the role of echocardiography in critically ill pediatric patients. These insights can inform clinical decision making, enhance diagnostic accuracy, and ultimately improve the quality of care for vulnerable patients in rural healthcare settings.5\n\nAs demand for advanced critical care services continues to grow, particularly in regions with limited healthcare resources, understanding the value of bedside echocardiography in pediatric intensive care has become increasingly critical. This study represents a significant step towards unraveling the potential benefits of this diagnostic modality to enhance the care and outcomes of critically ill children.6\n\nThis study aims to evaluate the impact of bedside echocardiography on the management and outcomes of critically ill pediatric patients in a Pediatric Intensive Care Unit (PICU).\n\n\n\n1. To determine the indications and necessity of echocardiography assessment and therapeutic interventions in critically ill patients.\n\n2. To correlate the echocardiographic findings of patients admitted to the PICU with a systematic clinical examination.\n\n3. Correlation of cardiac dysfunction with the pediatric outcome.\n\n\nMethods\n\nThis study will employ a cross-sectional design to assess the impact of bedside echocardiography on the management of critically ill pediatric patients in a Pediatric Intensive Care Unit (PICU).\n\nThe study population will consist of critically ill pediatric patients aged one month to 18 years admitted to the PICU at Acharya Vinoba Bhave Rural Hospital, associated with Jawaharlal Nehru Medical College, Maharashtra, India, between July 2022 and July 2024.\n\nThe study will be conducted at the Pediatric Intensive Care Unit (PICU) of Acharya Vinoba Bhave Rural Hospital, a tertiary care center in Maharashtra, India.\n\n\n\n• Aged between one month and 18 years.\n\n• Critically ill status as determined by the treating healthcare team.\n\n\n\n• Post-operative patients requiring PICU admission.\n\n• Patients who do not meet the age criteria (< one month or > 18 years).\n\nTo minimize bias, the study will adhere to rigorous methodologies. Patient selection will be based on explicit inclusion and exclusion criteria, and data collection will follow standardized procedures. Researchers involved in data collection will be trained to minimize observer bias and patient anonymity will be maintained to reduce reporting bias.\n\nEnrollment will be initiated after obtaining informed consent from the parents or legal guardians of eligible pediatric patients admitted to the PICU. The enrollment process will involve obtaining consent, confirming the eligibility criteria, and documenting patient demographics.\n\nFormula\n\nPrevalence of patients who underwent echocardiographic evaluation = 35.4%.\n\nP =35.4% (As per reference article5)\n\nMinimum sample size required 88.\n\nThe data collection process for this study will be comprehensive and meticulously conducted to ensure the accuracy and reliability of the gathered information. This process will involve several steps and methods.\n\nUpon admission to the PICU, critically ill pediatric patients meeting the inclusion criteria will be identified. Informed consent will be obtained from their parents or legal guardians before commencing the data collection procedures, ensuring full compliance with ethical standards.\n\nOnce consent is obtained, patient demographics including age, sex, and clinical history will be recorded by using data collection proforma. This will provide a baseline understanding of the patient population. Subsequently, a team of experienced pediatric cardiologists will conduct echocardiographic assessments of the enrolled patients. Echocardiographic evaluations will include parameters such as ejection fraction, fractional shortening, and systolic and diastolic cardiac function assessments. These assessments will be performed according to the clinical necessity, and the findings will be thoroughly documented.\n\nIn addition to echocardiographic data, relevant clinical information will be collected and recorded, including vital signs on admission, complaints, initial diagnosis, final diagnosis, type of ventilation, length of PICU stay, and the Pediatric Risk of Mortality (PRISM) score.7\n\nThe necessity for echocardiography will be assessed based on clinical indications, which include a variety of factors, such as the presence of cardiac murmurs, suspected cardiac diseases, hypotension or shock, hypertension, arrhythmia, signs of congestive heart failure, and several other clinical situations. Therapeutic interventions following echocardiography, such as changes in fluid management, vasopressor therapy, antihypertensive therapy, and cardiac surgery, will also be meticulously recorded.\n\nTo maintain data accuracy and quality control, research personnel involved in data collection will receive training in standardized data collection procedures. Patient confidentiality will be strictly maintained throughout the process.\n\nDescriptive statistical analysis will summarize the data, including the mean, standard deviation, median, interquartile range, and percentages. Parametric or non-parametric statistical tests, such as chi-square, Fisher’s exact test, independent t-test, Spearman’s rank correlation coefficient, or Pearson’s correlation coefficient, will assess the relationships between variables. Statistical significance will be set at P < 0.05. Data analysis will be conducted using the appropriate statistical software, R Studio version 2023.03.0-daily+82. pro2.\n\nThe Institutional Ethics Committee of the Datta Meghe Institute of Higher Education and Research (DU) has granted its approval to the study protocol (Reference number: DMIMS (DU)/IEC/2022/1073) Date: 27/06/2022. Before commencing the study, we will obtain written informed consent from all participants, providing them with a comprehensive explanation of the study’s objectives.\n\nAfter completion of the study, we will publish it in an indexed journal or conference.\n\nThe study has not yet started. After the publication of the protocol, we will begin recruitment for the study.\n\n\nDiscussion\n\nUsing bedside echocardiography in pediatric intensive care is paramount. Critically ill pediatric patients often present with complex and rapidly evolving cardiac issues, and timely and accurate assessment is crucial for their management. This study addresses the pressing need to evaluate the role of echocardiography in pediatric intensive care, particularly in a rural healthcare setting.8\n\nBedside echocardiography can potentially transform the diagnosis and management of cardiac conditions in critically ill children. Providing real-time information on cardiac anatomy, function, and hemodynamics enables clinicians to rapidly make informed decisions. This study aims to shed light on the diagnostic value of echocardiography, including its indications, necessity, and the extent to which it correlates with clinical interventions.9\n\nThe primary aim of this study is to correlate the cardiac functional or structural abnormalities identified through echocardiography with pediatric outcomes. This aspect of the research is critical, as it can elucidate whether echocardiography significantly improves patient outcomes in the PICU. If it demonstrates a positive impact, it could lead to a more widespread adoption of this diagnostic tool.10\n\nA unique aspect of this study is its location in a rural healthcare setting. Rural areas often require more resources and access to advanced medical technology. Assessing the applicability and effectiveness of bedside echocardiography in such a setting is particularly relevant and could provide insights directly applicable to similar healthcare environments worldwide.11\n\nThis study will also explore how echocardiography influences clinical decision-making. This includes assessing whether echocardiographic findings lead to changes in therapeutic interventions such as medication adjustments or surgical procedures. Understanding its impact on clinical decisions is essential for determining the practical value of echocardiography in the PICU.12\n\nThe findings of this study are expected to have implications for clinical practice, healthcare policies, and further research. Positive results may encourage healthcare facilities in rural areas to invest in echocardiographic equipment and training, potentially leading to improved outcomes. Additionally, the study may stimulate further research into optimizing echocardiography protocols and expanding their use in pediatric critical care.\n\nIt is important to acknowledge the potential limitations of this study. Cross-sectional studies provide valuable insights into prevalence and associations but do not establish causality. Additionally, the findings of this study may be influenced by various factors, such as the experience of the healthcare team and availability of resources.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Proforma for the data collections ‘A cross-sectional study on the impact of bedside echocardiography in critically ill pediatric patient’s management in the pediatric intensive care unit ’. https://zenodo.org/doi/10.5281/zenodo.10275599. 13\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nBeaulieu Y: Bedside echocardiography in the assessment of the critically ill. Crit. Care Med. 2007; 35: S235–S249. Publisher Full Text\n\nLosonczy LI, Papali A, Kivlehan S, et al.: White Paper on Early Critical Care Services in Low Resource Settings. Ann. Glob. Health. 87: 105. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlexander PM, Checchia PA, Ryerson LM, et al.: Cardiovascular Dysfunction Criteria in Critically Ill Children: The PODIUM Consensus Conference. Pediatrics. 2022; 149: S39–S47. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTissot C, Muehlethaler V, Sekarski N: Basics of Functional Echocardiography in Children and Neonates. Front. Pediatr. 2017; 5: 235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nŞahin S, Yazıcı MU, Ayar G, et al.: Clinical impact and efficacy of bedside echocardiography on patient management in pediatric intensive care units (PICUs): A prospective study. Anatol. J. Cardiol. 2017; 18: 136–141. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYildizdas D, Aslan N: A trend skill that makes pediatric intensivists stand out: Critical care echocardiography. Australas J. Ultrasound Med. 2021; 24: 78–81. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnjali MM, Unnikrishnan DT: Effectiveness of PRISM III score in predicting the severity of illness and mortality of children admitted to pediatric intensive care unit: a cross-sectional study. Egypt. Paediatr. Assoc. Gaz. 2023; 71: 25. Publisher Full Text\n\nGaspar HA, Morhy SS: The Role of Focused Echocardiography in Pediatric Intensive Care: A Critical Appraisal. Biomed. Res. Int. 2015; 2015: 1–7. Publisher Full Text\n\nPellegrini JAS, Mendes CL, Gottardo PC, et al.: The use of bedside echocardiography in the care of critically ill patients - a joint consensus document of the Associação de Medicina Intensiva Brasileira, Associação Brasileira de Medicina de Emergência and Sociedade Brasileira de Medicina Hospitalar. Part 2 - Technical aspects. Crit. Care Sci. 2023; 35: 117–146. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurton L, Bhargava V, Kong M: Point-of-Care Ultrasound in the Pediatric Intensive Care Unit. Front. Pediatr. 2022; 9: 830160. Publisher Full Text\n\nCoombs NC, Campbell DG, Caringi J: A qualitative study of rural healthcare providers’ views of social, cultural, and programmatic barriers to healthcare access. BMC Health Serv. Res. 2022; 22: 438. Publisher Full Text\n\nLiu J, Banchs J, Mousavi N, et al.: Contemporary Role of Echocardiography for Clinical Decision Making in Patients During and After Cancer Therapy. JACC Cardiovasc. Imaging. 2018; 11: 1122–1131. Publisher Full Text\n\nSri Sita Naga Sai Priya K: Proforma for the data collections ‘A cross-sectional study on the impact of bedside echocardiography in critically ill pediatric patient’s management in the pediatric intensive care unit’. [Dataset]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "341395", "date": "20 Nov 2024", "name": "Andrea Sonaglioni", "expertise": [ "Reviewer Expertise Cardiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this interesting paper, the Authors have described the potential usefulness of bedside echocardiography for rapid assessment of cardiovascular function in critically ill pediatric patients, particularly within rural healthcare settings.\nThe Authors have proposed a research protocol that aims at evaluating the impact of bedside echocardiography on the management of critically ill pediatric patients in a Pediatric Intensive Care Unit.\nThe Authors primarily focused on the assessment of conventional echocardiographic parameters, such as ejection fraction, fractional shortening and parameters of diastolic function.\nThe Authors aim at evaluating how bedside echocardiography influences clinical decision-making. The research protocol is very interesting.\n\nI have only one suggestion for the Authors.\nThe Authors could mention also innovative echocardiographic techniques.\nIn the Discussion section, paragraph \"Diagnostic value of bedside echocardiography\", the Authors could also state that recent advances in cardiovascular imaging have led to the introduction of speckle tracking echocardiography. This imaging modality may allow the clinicians to detect subclinical impairment in myocardial strain parameters, which occur earlier than ejection fraction reduction. The implementation of conventional transthoracic echocardiography with strain echocardiographic imaging may provide incremental diagnostic and prognostic information not only in adults but also in pediatric patients (refer 1 and 2).\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-292
https://f1000research.com/articles/13-290/v1	18 Apr 24	{ "type": "Research Article", "title": "Comparison of treatment planning for stereotactic radiosurgery and stereotactic body radiation therapy techniques with 2.5 mm and 5 mm multileaf collimator (MLC): A pilot study", "authors": [ "Rechal Nisha Dsouza", "Krishna Sharan", "Suresh Sugumar", "Srinidhi G C", "Shreekripa Rao", "Shirley Lewis Salins", "Umesh V", "Senthil Manikandan", "Rechal Nisha Dsouza", "Srinidhi G C", "Shreekripa Rao", "Shirley Lewis Salins", "Umesh V", "Senthil Manikandan" ], "abstract": "Background The Elekta Apex micro-multileaf collimator (mMLC) for planning stereotactic radiosurgery (SRS)/stereotactic body radiation therapy (SBRT) provides excellent dose distribution; however, it offers disadvantages such as prolonged treatment duration and technical errors in terms of mMLC and gantry calibration, which adds to the total treatment duration. Hence, we aimed to compare the treatment planning performed with the 2.5 mm Apex mMLC and 5 mm MLC (Elekta Agility) for brain and lung targets treated with SRS and SBRT in Elekta Versa high definition (HD).\n\nMethods The study included 10 patients, five each with brain and lung targets. Two treatment plans were performed for each case using Elekta’s Monaco (5.11.03) treatment planning system (TPS) with 2.5 mm and 5 mm MLC. An X-ray photon beam of energy 6FFF was used for planning purposes with various gantry, couch, and collimator combinations. These two plans were compared using target coverage (TC), conformity index (CI), homogeneity index (HI), gradient index (GI), and organ at risk (OAR) doses.\n\nResults No significant differences were found in the target coverage, CI, HI, or OAR doses in either MLC design. Volumetric modulated arc therapy (VMAT) with a 5 mm MLC provided equivalent tumor coverage with an additional number of monitor units. OAR doses were comparable in both MLC widths for brain targets, whereas for lung targets, OAR doses were slightly lower with 2.5 mm mMLC. GI was superior in the 2.5 mm mMLC compared to the 5 mm MLC giving a steep falloff in the dose distributions (p = 0.158).\n\nConclusions The TC, CI, HI, and OAR doses were similar in both 2.5 and 5 mm based VMAT plans. The gradient index was better in the 2.5 mm mMLC resulting in steep dose gradients, which further reduced the isodose volumes. Therefore, a 5 mm MLC (agility) can also be used for SRS/SBRT treatment planning, with a further reduction in the gradient index. However, the study must be extended further with more samples and multiple comparison parameters. Clinical Trials Registry - India, registration number CTRI/2021/11/037842, registration date. 8th November, 2021.", "keywords": [ "Stereotactic Radiotherapy", "Stereotactic Body Radiotherapy", "micro multileaf collimator(mMLC)", "Multi leaf collimator (MLC)", "Treatment planning", "Volumetric Modulated Arc Therapy", "Dynamic Conformal Arc Therapy" ], "content": "Introduction\n\nCancer is considered one of the leading causes of death worldwide, and its incidence and mortality rates may rise to approximately 29 million and 16 million people, respectively, by 2040.1 In India, the incidence rate of brain or nervous system-related cancers is the leading cause of death and is ranked 13th in males and 11th in females among all cancers.1 Radiotherapy is an extremely cost-effective treatment modality, and almost 50% of cancer patients receive radiation therapy during their course of cancer treatment.2 In radiotherapy, high-energy photons such as X-rays, gamma radiation, or high-energy particles are used to deliver treatment externally using external beam radiation therapy (EBRT), or they can be administered internally using radioactive sources such as brachytherapy.3\n\nStereotactic radiosurgery (SRS) is a radiotherapy treatment technique in which a high radiation dose is delivered in a single fraction, using multiple radiation beams or arcs. If the same treatment is delivered in multiple fractions, it is called stereotactic radiotherapy (SRT).4 For selected intracranial lesions, SRS/SRT is performed as it delivers a high amount of radiation to the tumor volume, and the dose gradient is steep so that the surrounding uninvolved structures are spared.5 Lars Leksell, a Swedish neurosurgeon, initially introduced SRS in 1969 for treating intracranial lesions and has successfully shown positive results in managing intracranial lesions and brain metastasis. It has increased the tumor control rate, survival rate, and quality of life. An SRS system based on a linear accelerator (LINAC) was developed in 1980, which allowed the treatment of SRS, SRT, and stereotactic body radiation therapy (SBRT) with high precision and accuracy.6 Similar to SRS, SBRT is an SRT procedure that is used to treat extracranial lesions where hypofractionated radiation is administered in a fewer number of fractions. SBRT has been regularly incorporated as a better treatment option for metastatic and primary tumors such as lung cancer, liver lesions, and prostate cancer.7\n\nSBRT is one of the best therapeutic options for inoperable liver and other metastases of the body. Patients with primary and metastatic liver lesions treated with 46–50 Gy in four–six fractions have shown better local tumor control as well as overall survival.8 For brain tumors less than 3 cm, treatment with SRS given in a single fraction has shown the best results as it has various advantages such as a greater decrease in tumor size, sparing of normal tissues due to rapid dose fall-off, minimum radiation-related side effects, lesser duration of radiotherapy, and better tumor response. If the tumor size is greater than 3 cm, SRS must be delivered in multiple fractions (SRT) so that normal tissue toxicity is minimized.9\n\nSRS/SRT/SBRT are complicated treatment procedures that include various steps such as immobilization of the patient, patient imaging, delineation of the target (tumor) and critical structures, treatment planning, performing patient-specific quality assurance (QA) checks, and delivering radiation therapy to the patient, including patient follow-up.10 As high radiation doses are delivered in a smaller fraction of treatments, very small error margins are given compared to conventional radiation therapy. A small error in the localization of the tumor, even in a single fraction, can lead to an underdosage of the tumor by 20% or more, and at the same time, it can overdose the surrounding normal tissues, thereby resulting in potentially serious injuries to the organs involved.11\n\nThe treatment delivery of stereotaxy has generally utilized dedicated specialized equipment such as Gamma Knife and CyberKnife. Medical LINACs have been increasingly adopted as a mode for delivering hypofractionated radiotherapy schedules. There are important advantages to using a LINAC for SRS/SRT/SBRT treatment, including increased versatility, cost benefits, and higher throughput. Technological advances have made use of LINAC and are increasingly accurate in stereotaxic treatment. One such device, designed to improve conformity to the target, is an externally attached additional collimating device with an mMLC.12 The mMLC had a high-resolution collimation system with a width of less than 3 mm at the isocenter. This would facilitate the delivery of a conformal radiation dose to the tumor with a steep dose gradient beyond the tumor, thus better sparing the surrounding normal tissues. However, there is a disadvantage of reduced clearance between the patient and collimator, which limits the utilization of non-coplanar beam directions.13\n\nUsing the Elekta Apex mMLC for planning SRS/SRT/SBRT provides excellent dose distribution, but also offers technical errors in terms of mMLC and gantry calibration, which adds to the total treatment duration. If the same plan with excellent output is available without the use of Apex mMLC but with flattening filter free (FFF) photon beam energies, then the treatment duration is expected to be reduced compared to Apex-based delivery.\n\nThis study aimed to compare SRS/SRT/SBRT treatment plans with and without the mMLC, using FFF radiation beams to compare the generated treatment plans in terms of various indices of planning target volume (PTV) coverage and organ-at-risk doses.\n\n\nMethods\n\nTen patients were retrospectively considered for the study after approval from the Institutional Ethics Committee, Kasturba Medical College and Kasturba Hospital, Manipal Academy of Higher Education Manipal (IEC427-2021) 8th August 2021, Clinical Trials Registry, India; registration number CTRI/2021/11/037842, 8th November 2021. population included five patients each with brain and lung targets who were treated in the year 2021 at our institute. The eligibility criteria for the patient selection was based on the guidelines given.14–17 The selected cases were planned using SRS and SBRT treatment techniques following the guidelines prescribed by the Radiation Therapy Oncology Group (RTOG) and Stereotactic Ablative Body Radiotherapy (SABR) guidelines using the Monaco 5.11.03 (Elekta, 2016) treatment planning system (TPS). For every patient, two plans were generated with the Apex mMLC (2.5 mm) and the other without the mMLC (i.e., with the Elekta Agility, 5 mm). The gantry, collimator, and couch angles were determined based on the tumor location and kept constant in both treatment plans.\n\nThe selected patients were immobilized with a Fraxion patient-specific cranial immobilization device (Fraxion, P10106-103) consisting of a computed tomography (CT) adaptor, tabletop adaptor, vacuum cushion, thermoplastic mask, and Fraxion stereotactic frame. Vacuum cushions from Fraxion are specially used as head rests for patients, and they provide precise positioning of the head and reproducibility of the treatment setup. Each cushion was molded individually for each patient and used throughout the course of treatment.18 Each patient was immobilized using a thermoplastic mask. A CT scan of the patient was performed with the Fraxion stereotactic frame and marking sheet. A stereotactic frame was used to locate the tumor in SRS/SRT. It has three Z-shaped radiopaque markers that are visible in the axial cut CT image as nine dots that act as fiducials for the identification of the target coordinates. The marking sheet has three coordinates, that is, x, y, and z, which are used to locate the tumor in the coordinate system. This makes it convenient to position patients according to the treatment isocenter. The acquired CT images were exported to the Monaco TPS. Magnetic resonance imaging (MRI) is considered superior to CT in soft-tissue discrimination of the brain. Image registration was performed, and mapping of the structures was carried out. Contouring of the MRI image onto the CT image was performed for the exact delineation of the target and critical structures such as the normal brain, optic nerves, optic chiasma, brainstem, eyes, lens, cochlea etc.19\n\nSelected patients were immobilized using a thermoplastic mask. An active breathing coordinator (ABC) (Elekta limited, 201510) was used to implement effective respiratory motion management throughout the treatment.20 An ABC is used to control respiratory motion by applying simple and efficient breath-holds at an applicable threshold level. A CT image of the patient was obtained with the same setup using a thermoplastic mask and ABC.21 Image fusion using MRI and CT was performed to properly delineate the tumor volume and critical structure, where appropriate.\n\nA CT image with a slice thickness of 1 mm for the brain and 2 mm for the lungs was acquired using suitable immobilization devices. For SBRT cases, CT images with deep inspiration breath-hold (DIBH) were acquired.22 The CT images were then exported to Monaco (5.11.03 version) TPS.23 Contouring of the target volume and organ at risk (OAR) was accomplished by oncologists, and a later treatment plan was planned based on the site of the tumor using Monaco TPS.24 For this study, two separate treatment plans for SRS and SBRT were generated retrospectively.\n\nThe first plan for SRS/SBRT was developed using the dynamic conformal arc therapy (DCAT) technique with a 6FFF photon beam energy using a 2.5 mm Apex mMLC. The Apex mMLC is an additional attachment to the collimator of the Elekta Versa high-definition LINAC consisting of an MLC with a 2.5 mm width at the isocenter. This high-resolution collimating device is especially used for SRS treatment delivery to facilitate conformal dose distribution around the tumor. The maximum field size provided by the mMLC is 12 × 14 cm2.25 The isocenter was placed at the center of the target volume. The number and direction of the arcs were chosen based on the location of the tumor. Couch movement was restricted in some cases, wherever it was practically impossible to move the gantry with the Apex to reduce the risk of collision of the gantry with the couch and patient. The second plan was generated without using Apex mMLC. The LINAC has an inbuilt MLC with a 5 mm width at the isocenter, which is also called Agility. The SRS/SBRT treatment plans in this case were performed with agility using a 6FFF photon beam energy. The treatment plan was implemented using the same gantry couch combinations. Multiple optimizations in both techniques were performed to achieve the prescribed tumor dose and to bring the dose to the OARs within the given limits. The Monte Carlo algorithm was used to calculate the dose distribution.26 For the included cases, SRS was planned with 16 Gy in one fraction (Figure 1) and SBRT with 60 Gy in five fractions (Figure 2).\n\nRed: 100% prescribed dose; Green: 95% prescribed dose; Blue: 50% prescribed dose; Yellow: 115% prescribed dose.\n\nRed: 100% prescribed dose; Green: 95% prescribed dose; Blue: 50% prescribed dose; Blue (inside): 115% prescribed dose.\n\nThe treatment plans performed using APEX mMLC and agility were compared using Monaco TPS. The quality of the treatment plans was checked using quality indices such as target coverage (TC), conformity index (CI), homogeneity index (HI), gradient index (GI), and organ at risk (OAR) doses. CI was calculated using the formula TVPIV2/ (TV × PIV). Here, TV is the target volume, and PIV is the prescription isodose volume. GI was calculated using the formula PV50%/PIV. PV50% represents 50% of the prescribed dose covered by the patient volume. The HI was calculated as the ratio of the maximum target dose to the prescribed dose.27 The ideal value for HI and CI is 1, and as it decreases from 1, the quality of the plan also decreases. A value greater than 1 indicates that the tumor volume is overirradiated, and a value less than 1 indicates a reduction in the dose to the target volume. The smaller the GI value, the steeper the dose gradient. If multiple targets are close to each other, then combined GI will be performed for the lowest dose prescribed target in the patient. A clinically acceptable plan will have a lower GI value, higher CI value, and higher TC (>95%). Such a plan will provide better tumor coverage and maximum sparing of the normal brain.\n\nJamovi 2.3.2628 statistical software was used for statistical analysis and descriptive data for all continuous variables were presented as mean ± standard deviation (SD). Multivariate ANOVA and independent t-test were performed to compare the treatment plans generated with 5 mm and 2.5 mm MLC for brain SRS and lung SBRT. A value of p<0.05 was considered as a statistically significant difference between variables.\n\n\nResults\n\nThe volume of the GTV and PTV in the selected brain targets were ranging between 0.6 cm3 to 6.0 cm3 and 1.2 cm3 to 8.5 cm3 respectively. Similarly, in the lung targets the GTV and PTV volumes were ranging between 4.3 cm3 to 7 cm3 and 8.5 cm3 to 12.5 cm3 respectively. Among the selected ten cases, 50% of the patients were treated at the metastatic sites, and in the remaining cases, treatments were administered at the primary sites. Both treatment planning techniques showed excellent tumor dose distribution and the PTV coverage was comparable in both treatment planning techniques. For brain SRS cases, the mean target coverage in agility (5 mm MLC) was 98.85±0.78692 and in APEX (2.5 mm) it was 99.196±0.43592(p=0.415) (Figure 3). In lung SBRT cancers, the target coverage in Agility and APEX was 97.934±2.02090 and 99.076±1.17980(p=0.307) respectively (Figure 4) which shows that the APEX-based treatment plans showed slightly better target coverage, although both planning techniques provided a target coverage of more than 97%.\n\nCI in both the SRS and SBRT plans yielded excellent results. These values were found to be similar for both the planning techniques. In the 5 mm and 2.5 mm width MLC the mean CI for the brain targets were 0.972±0.01924 and 0.9780±0.04970 respectively (p=0.808) and for the lung targets were 0.9520±0.01789 and 0.9060±0.04615 respectively (p=0.071) which indicates that the target area is optimally covered (Figure 5) and there is no significant difference in the CI for brain and lung targets in both MLC designs. The HI values in case of 2.5 mm and 5 mm MLC in brain targets were 1.150±0.16093 and 1.1180±0.13293 respectively (p=0.741) and for the lung targets the values were 1.1620±0.14220 and 1.1380±0.12677 respectively (p=0.785). The HI values were also found to be close to unity, indicating a homogenous dose distribution across the tumor volume (Figure 6). The GI values for 5 mm and 2.5 mm MLC in brain targets were 5.1660±0.47732 and 4.3880±1.00912, respectively (p=0.158), and for the lung targets 4.670±1.33318 and 4.5720±1.05611, respectively(p=0.895). Although there was no significant difference between the GI values, the obtained results showed that GI was better in the 2.5 mm APEX based plans compared to 5 mm MLC (Figure 7). The mean and maximum doses to the OARs in both treatment planning techniques for both 2.5 mm and 5 mm MLC based plans were found to be close to each other. Although there was no significant difference between the two, it has been shown that the doses were slightly lower in most of the OARs in lung targets, whereas in brain targets, we received mixed results, indicating that both techniques are comparable (Tables 1 and 2). Data on the same have been made available online.29\n\n\nDiscussion\n\nAlmost 10–30% of all carcinoma patients have a risk of brain metastasis, which can originate from primary sites such as the lung, renal cell cancer, breast cancer, colorectal cancer, and melanoma.30 Multiple options are available for the treatment of brain metastasis, including radiation therapy to the whole brain, surgical resection of the tumor, SRS, and fSRT. SRS is considered the first-line treatment for tumors that can be destroyed without invasive techniques. SRS is recommended if the patient has a minimum number of sites of metastasis in the brain and is preferably used for patients with a good overall physical condition. SRS and fSRT have been shown to have potential benefits in terms of good tumor control and reduced toxicity.31 SRS administered in single and multiple fractions (fSRT) has provided good local control, with a lower risk of radiation-related necrosis. SRS can be used if the diameter of the tumor is less than 3 cm, and SRT in two to five fractions is basically used for larger lesions or when surgical removal of the tumor is not advisable. Therefore, the ultimate goal of SRT is the reduction of adverse effects due to the large size of the tumor and the improvement of local control.32\n\nThe lung is one of the most common sites of metastasis in various primary regions. On average, approximately 20–54% of cancer patients will suffer from lung metastasis in their lifetime.22 Radiotherapy administered in multiple fractions plays an important role in terms of overall survival and high tumor control rates compared to other palliative care, including treatment cost, which is less than or equal to that of surgery. Respiratory management is considered during imaging and treatment to prevent tumor movement. This reduces the toxicity that occurs in relation to the treatment and shoots the target in the exact position in every breathing cycle. Various modalities, such as 4D CT, Active Breathing Coordinator (ABC), and deep inspiration breath-hold (DIBH), Image-guided radiotherapy (IGRT) and cone-beam computed tomography (CBCT)-based treatment delivery help to accurately treat the tumor with very less to no error margin.33 Advanced technology in the LINAC, such as the use of FFF photon beams, lesser width MLC, advanced treatment planning techniques such as Volumetric Modulated Arc Therapy (VMAT), SRS, SBRT, DCAT, and the option of respiratory gating during simulation and treatment, have made SRS/SBRT treatment more optimal and accurate.34\n\nIn the current study, ABC was used for SBRT to manage the breathing of patients, and CBCT was used for verification. Accurate treatment was delivered with an error margin of ±1 mm. Contouring of the brain and lung lesions was performed by the physicians after fusing the CT (Philips, 16 slice) images with MRI to draw accurate tumor volume and the OAR. CT is considered the first-line imaging modality used to diagnose the disease and to determine the true extent of the disease. However, the brain and mass in the lung are soft tissues, and the approximate and true spatial extent of the disease cannot be identified using CT images alone. MRI is superior to CT for the identification of soft tissues, definite tumor size, exact tumor location, number of lesions in the brain, and peritumoral edema. Therefore, both CT and MRI images were combined. The actual tumor volume was contoured on MRI and automatically mapped onto the CT image, which was then used for planning purposes.32\n\nThis study identified dosimetric differences in the treatment plans performed with the addition of mMLC (2.5 mm) and agility (5 mm). It is important to conform the radiation dose to the target volume in SRS/SRT/SBRT because of the size of the lesion and proximity of the OAR so that the dose distribution is bound tightly to the tumor volume. For this reason, dedicated machines are now available, including standard LINAC with added mMLC.35 However, the addition of this device prolongs the total treatment duration and reduces the clearance between the collimator and patient because of restrictions in choosing the appropriate and required gantry angles most of the time. It has limitations in the placement of noncoplanar arc angles.36 The LINAC (Elekta HD Versa) used in the current study was equipped with an built-in 160 MLC with a width of 5 mm at the isocenter. To deliver treatment plans performed with a 2.5 mm MLC using the same LINAC, an additional collimating device (APEX) must be attached to the machine. APEX consists of 56 pairs of MLC with a 2.5 mm width at the isocenter, which provides a field size of 12 × 14 cm2.\n\nThe SRS and SBRT treatment plans performed with a 2.5 mm MLC were considered as the benchmark in this study, and these plans were compared with a 5 mm MLC. The plans with a 2.5 mm MLC were optimized to deliver the best possible treatment with more than 95 to 98% coverage of the target volume with other parameters to be within the prescribed limits. In the plans with a 5 mm MLC, the gantry, couch, and collimator combinations were kept constant, and the treatment plans were optimized to deliver the same dose distribution by keeping all the dose constraints to the OARs minimum. The resulting PTV coverage was equivalent in the 2.5 mm and 5 mm treatment plans. The obtained results were comparable to the results obtained by Wu et al., in which three planning techniques were used for the comparison, and the plans were performed using 2.5 mm and 5 mm MLC. They suggested that the PTV coverage, HI, and CI were better in IMRT-based HD MLC plans; however, as the size of the tumor increased and the OARs were closer to the target, the scope of HD MLC also became less noticeable.36\n\nThe treatment plan quality was compared using HI, CI, and GI.27 The HI and CI values for both the plans were comparable. Heather et al. conducted a study in which they compared MLC of three different widths, 2.5, 5, and 10 mm, for the SBRT spine. With respect to tumor coverage, CI, and HI, the results of the study were comparable irrespective of leaf width.37 Joablot et al. conducted a study wherein they performed SRS/SRT plans using 2.5 mm, 5 mm and 10 mm MLC. With respect to HI, they found no clinically significant differences in any of the different MLC widths. In addition, there was no difference in the CI between 5 mm and 2.5 mm for PTV volumes greater than 1cc. However, for PTV volumes lesser than 1cc, the dose conformity was less in the 5 mm MLC, but the amount of reduction was clinically acceptable. The OAR doses were found to be comparable irrespective of leaf width. The dose falloff was steep in the 2.5 mm MLC which was clinically acceptable.12 This result was also observed in the current study in terms of GI, which showed a steep dose fall off in the 2.5 mm MLC. The GI was slightly higher in the 5 mm MLC compared in the 2.5 mm MLC which indicates a steeper dose fall in the 2.5 mm MLC.37 The GI is an important factor that indicates the surrounding normal tissue dose. The lesser the GI, the more the surrounding OARs are spared.38 In a study conducted by Ferrer et al., three SRS cases were planned with a 5 mm and 2.5 mm MLC. They obtained similar results for conformation indices and OARs. The target coverage in VMAT is also better at the cost of more monitoring units. They found satisfactory results with VMAT, but in order to have more comparisons between VMAT and APEX, planning must be performed with a larger sample size.29\n\nThis study adds to the literature by showing that a 5 mm MLC may suffice in most cases of SRS and SBRT and will be beneficial in reducing the treatment time. This study was limited by the sample size and its retrospective nature.\n\n\nConclusions\n\nThere was no clinically significant difference found in the target coverage, CI, HI and OAR doses in ten patients planned for SRS and SBRT using 2.5 mm (APEX mMLC) or 5 mm (agility) MLC with 6FFF photon beam energy. The target coverage was comparable for both the plans. VMAT with agility provided equivalent tumor coverage with an additional number of MUs. The CI and HI values were almost similar in both plans, resulting in a conformal and homogenous dose distribution to the entire PTV. OAR doses were comparable in both MLC for brain cases, whereas for the lung targets, OAR doses were slightly lower with 2.5 mm mMLC. GI was superor in the 2.5 mm mMLC compared to the 5 mm MLC giving a steep dose fall off in the dose distributions. Hence, a 5 mm MLC is also preferred for SRS and SBRT, with GI being an important consideration during planning.", "appendix": "Data availability\n\nHarvard Dataverse: Underlying data for ‘Comparison of treatment planning for stereotactic radiosurgery and stereotactic body radiation therapy techniques with 2.5 mm and 5 mm multileaf collimator (MLC): A pilot study’, https://www.doi.org/10.7910/DVN/CFNQEX. 29\n\nHarvard Dataverse: STROBE checklist for ‘Comparison of treatment planning for stereotactic radiosurgery and stereotactic body radiation therapy techniques with 2.5 mm and 5 mm multileaf collimator (MLC): A pilot study’, https://www.doi.org/10.7910/DVN/CFNQEX. 29\n\nData are available under the terms of the Creative Commons Zero “No rights reserved’ data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nI would like to acknowledge the contribution of Ms. Sneha Ravichandran in editing and reviewing this study.\n\n\nReferences\n\nKulothungan V, Sathishkumar K, Leburu S, et al.: Burden of cancers in India - estimates of cancer crude incidence, YLLs, YLDs and DALYs for 2021 and 2025 based on National Cancer Registry Program. BMC Cancer. 2022; 22(1): 512–527. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaskar R, Lee KA, Yeo R, et al.: Cancer and radiation therapy: Current advances and future directions. Int. J. Med. Sci. 2012; 9(3): 193–199. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmerican Cancer Society: Cancer Treatment and Survivorship Facts and Figures 2019-2021. Am. Cancer Soc. 2019; 1–48.\n\nKhan FMGJ: The Physics of Radiation Therapy.2014.\n\nYip HY, Mui WLA, Lee JWY, et al.: Evaluation of radiosurgery techniques-Cone-based linac radiosurgery vs tomotherapy-based radiosurgery. Med. Dosim. 2013; 38(2): 184–189. PubMed Abstract \| Publisher Full Text\n\nSaglam Y, Bolukbasi Y, Atasoy AI, et al.: Quality Assurance in Stereotactic Radiosurgery and Stereotactic Body Radiotherapy. Adv. Dent. Res. 2020; 21(7): 22–33.\n\nMalouff TD, Seneviratne D, Stross WC, et al.: Public interest in stereotactic body radiation therapy (SBRT) and stereotactic radiosurgery (SRS) in the United States. J Radiosurg. SBRT. 2020; 6(1): 311–315. Reference Source\n\nKirichenko A, Gayou O, Parda D, et al.: Stereotactic body radiotherapy (SBRT) with or without surgery for primary and metastatic liver tumors. HPB. 2016; 18(1): 88–97. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRashid A, Memon MA, Ahmed U, et al.: Multisession stereotactic radiosurgery for large benign brain tumors of >3cm-early clinical outcomes. J. Radiosurg. SBRT. 2012; 2(1): 29–40. Reference Source\n\nLi K: Aperture effect for LINAC-based SRS in small target treatment. J. Radiosurg. SBRT. 2016; 4(1): 21–29.\n\nSolberg TD, Balter JM, Benedict SH, et al.: Quality and safety considerations in stereotactic radiosurgery and stereotactic body radiation therapy: Executive summary. Pract. Radiat. Oncol. 2012; 2(1): 2–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJalbout W, Zahr JA, Youssef B, et al.: On the feasibility of stereotactic radiosurgery with 5.0 and 10.0 mm mlc leaves as a function of target size and shape. Front. Oncol. 2019; 9(AUG): 3–10. Publisher Full Text\n\nMarrazzo L, Zani M, Pallotta S, et al.: Comparison of stereotactic plans for brain tumors with two different multileaf collimating systems. J. Appl. Clin. Med. Phys. 2014; 15(1): 27–37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDawson LA, Anderson UMD: Radiation Therapy Oncology Group Rtog 1112 Randomized Phase Iii Study Of Sorafenib Versus Stereotactic Body Radiation Therapy Followed By Sorafenib In Hepatocellular Randomized Phase Iii Study Of Sorafenib Versus Stereotactic Body Radiation Therapy Follow.1818.\n\nFatima N, Meola A, Pollom E, et al.: Stereotactic Radiosurgery for Large Benign Intracranial Tumors. World Neurosurg. 2020; 134: e172–e180. PubMed Abstract \| Publisher Full Text\n\nHanna GG, Murray L, Patel R, et al.: UK Consensus on Normal Tissue Dose Constraints for Stereotactic Radiotherapy. Clin. Oncol. 2018; 30(1): 5–14. PubMed Abstract \| Publisher Full Text\n\nSABR UK Consortium: UK SABR Consortium Guidance.2019;(January). Reference Source\n\nFerrer C, Huertas C, Plaza R, et al.: Dosimetric effects of a repositioning head frame system and treatment planning system dose calculation accuracy. J. Appl. Clin. Med. Phys. 2018; 19(6): 124–132. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDjan I, Petrović B, Erak M, et al.: Planiranje radioterapije: Značaj registracija i fuzije CT-MR slike za odredivanje zapremine tumora. Vojnosanit. Pregl. 2013; 70(8): 735–739. PubMed Abstract \| Publisher Full Text\n\nEldredge-hindy H, Lockamy V, Crawford A, et al.: Cancer: Report of a Prospective Trial.2016; 5(1): 4–10.\n\nTeboh RF, Srinivasan S, Ng SP, et al.: Setup Management for Stereotactic Body Radiation Therapy of Patients With Pancreatic Cancer Treated via the Breath-Hold Technique. Pract. Radiat. Oncol. 2020; 10(4): e280–e289. PubMed Abstract \| Publisher Full Text\n\nGutiérrez E, Sánchez I, Díaz O, et al.: Current evidence for stereotactic body radiotherapy in lung metastases. Curr. Oncol. 2021; 28(4): 2560–2578. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWolff D, Monaco TPS: 2003 November.\n\nhttp\n\nGodwin GA, Simpson JB, Mugabe KV: Characterization of a dynamic multi-leaf collimator for stereotactic radiotherapy applications. Phys. Med. Biol. 2012; 57(14): 4643–4654. PubMed Abstract \| Publisher Full Text\n\nSchulz RJ, Kagan AR: New technology in radiation oncology. Oncology. 2004; 18: 249, 253; author reply 253–249, 253; author reply 254. PubMed Abstract\n\nPandu B, Khanna D: A Phantom Study on Feasibility of Manual Field - in - Field Clinical Implementation for Total Body Irradiation and Comparison of Midplane Dose with Different Bilateral TBI Techniques.2023; 59–67.\n\nhttp\n\nNisha R: Comparison of treatment planning for Stereotactic Radiosurgery (SRS) and Stereotactic Body Radiation Therapy (SBRT) techniques with 2.5mm and 5mm multileaf collimator (MLC) - a Pilot Study. [Dataset]. Harvard Dataverse. 2023. Publisher Full Text\n\nKrist DT, Naik A, Thompson CM, et al.: Management of brain metastasis. Surgical resection versus stereotactic radiotherapy: a meta-analysis. Neuro-oncol. Adv. 2022; 4(1): 1–14. Publisher Full Text\n\nMatsuda R, Hasegawa M, Tamamoto T, et al.: Linac-based stereotactic radiosurgery and fractionated stereotactic radiotherapy with a micro-multileaf collimator for brain metastasis in the primary motor cortex. J. Radiat. Res. 2022; 63(1): 63–70. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLupattelli M, Tini P, Nardone V, et al.: Stereotactic radiotherapy for brain oligometastases. Rep. Pract. Oncol. Radiother. 2022; 27(1): 15–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFalcinelli L, Menichelli C, Casamassima F, et al.: Stereotactic radiotherapy for lung oligometastases. Rep. Pract. Oncol. Radiother. 2022; 27(1): 23–31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLaoui S, Roa DE, Kuo J, et al.: Flattening filter free beam energy selection and its impact in multitarget intracranial stereotactic radiosurgery treatments. Med. Dosim. 2020; 45(4): 363–367. PubMed Abstract \| Publisher Full Text\n\nPérez Curbelo J, Diaz Moreno R, Caballero PR: Test cases for commissioning an add-on micro multi-leaf collimator Apex for stereotactic radiosurgery treatments. Rev. Bras. Física Médica. 2020; 14: 533. Publisher Full Text\n\nJackie QJ, Wang Z, Kirkpatrick JP, et al.: Impact of collimator leaf width and treatment technique on stereotactic radiosurgery and radiotherapy plans for intra- and extracranial lesions. Radiat. Oncol. 2009; 4: 1–10.\n\nPetroccia HM, Malajovich I, Barsky AR, et al.: Spine SBRT with HalcyonTM: Plan quality, modulation complexity, delivery accuracy, and speed. Front. Oncol. 2019; 9(APR): 1–8. Publisher Full Text\n\nWang D, DeNittis A, Hu Y: Strategies to optimize stereotactic radiosurgery plans for brain tumors with volumetric-modulated arc therapy. J. Appl. Clin. Med. Phys. 2020; 21(3): 45–51. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "286443", "date": "05 Jun 2024", "name": "Michele Zeverino", "expertise": [ "Reviewer Expertise I am a Medical Physicist with >15 years of experience in the field of Radiation Oncology. My expertise covers different topics of interest spanning from the implementation of new treatment planning and optimization strategies to the most recent innovations brought by the artificial intteligence in this domain." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIntroduction\nThe first paragraph should also encompass some clinical data regarding the incidence of lung cancers since it is one of the treatments under evaluation. I would not mention the use of brachytherapy. Although it is true that it is an option in radiation therapy, I do not see its application in the specific context. I would avoid introducing treatment site such as the liver to explain the use of SBRT. Please keep the focus of the paper sticked on the main topic mentioning the use of SBRT for lung cancers instead. SRS provides better tumor response with respect to what? The various steps listed to describe SRS/SBRT as complicated procedures actually apply also to fractionated EBRT. Please be more specific. The authors stated, “As high radiation doses are delivered in a smaller fraction of treatments, very small error margins are given compared to conventional radiation therapy”. Well, the margins for SRS/SBRT are smaller because of the use of high precision machines and/or the use of immobilization devices. Please reformulate this sentence, accordingly. Spell out the word mMLC as it was firstly introduced in the manuscript. Why did the authors write that the leaf width of the mMLC is less than 3mm instead of reporting its real measure (2.5mm)? Which are the technical errors and gantry calibration issues the authors refer to? If this is a limitation of the system that lead them to justify the use of the 5mm MLC instead, then more arguments are needed to support the aim of the study. The vendors name and country should be cited in brackets after each medical device listed in the Introduction section.\nMethods Patient selection\nWhich RTOG? And what are the SABRT guidelines used? Please include at least the references.\nPatient immobilization for SRS\nWhich kind of MRI was used? I also suggest reporting that rigid image registration was carry out between MRI and CT to avoid any misinterpretation.\nImmobilization for SBRT\nWhich kind of MRI was used? Was it registered rigidly or not to the CT?\nContouring and treatment planning\nI suggest moving the first paragraph in the previous sections as it looks more appropriate to define slice thickness and structure delineation in the description of imaging protocol. Was the dose prescribed to the same isolines for both rival plans. This is a very important element to report within a planning comparison study! And in the specific case of SRS, SBRT this may have a serious impact on the results! Looking at Figure 1, I have the feeling that this was not the case (i.e. same dose but different isolines prescriptions). Please report the PTV margins used and to which structure they were applied (CTV or GTV).\nPlan evaluation\nI would recommend to authors using throughout the text the same definition for the mMLC and MLC plans to avoid confusion. Here there is a problem concerning the HI definition. In SRS/SBRT, the dose is typically prescribed to the 80% or smaller isolines to increase the steep dose fall-off outside of the PTV. Therefore, HI will always be larger than unity as reported in the results. The sentence concerning the over/underdosage of the target with respect to values larger/smaller than unity applies only to CI and not to both HI and CI.\nStatistical analysis\nDue to the small sample size, the use of a t-test looks not appropriate. Did the authors check the normality of their distributions? If not, I would recommend using a non-parametric test instead to assess any statistical difference.\nResults\nPlease avoid the term “excellent” as these results are aligned with a typical treatment planning evaluation protocol for SRS/SBRT. I would recommend using only one decimal digit for mean and SD target coverage (by the way add also the unit of measure (%)). The same suggestion applies also for HI, CI, and GI. Why in Figures 5,6, and 7 the results are reported with no distinctions between brain and lung cases? I would also add the resulting MU comparison, or if they were very similar between plans this should be reported at least in the Discussion section.\nDiscussion\nI found the three initial paragraphs of the Discussion section useless as they are not focused on the discussion of the results but rather, they look like a repetition of the Introduction section. What do the authors mean when they claim, “Accurate treatment was delivered with an error margin of ±1 mm”? Was it the setup error of the delivery system or what else? Please be more specific. I believe that a fairer comparison should have also included targets located more adjacent to OARs. In that case, mMLC is expected to outperform MLC. As this was not done in the study, please comment on that in the Discussion section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "281423", "date": "26 Sep 2024", "name": "Mary Joan", "expertise": [ "Reviewer Expertise Radiological Physics", "radiotherapy", "treatment planning", "dosimetry", "radiobiology", "quality assurance", "research methodology", "radiation protection", "emergency management" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have compared SRS and SBRT treatment plans with 2.5 mm and 5 mm MLCs by evaluating target coverage (TC), conformity index (CI), homogeneity index (HI), gradient index (GI), and organ at risk (OAR) doses. The paper is well structured and systematically written. The observations made by the authors add to the existing knowledge and confidence. One drawback with the study is the small number of patients plans recruited for evaluation. As this is a pilot study, the report could be accepted for indexing. The authors are encouraged to continue further with the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-290
https://f1000research.com/articles/13-289/v1	18 Apr 24	{ "type": "Systematic Review", "title": "A Systematic Review and Meta-Analysis of the Timing of Vasopressor Therapy in Patients with Septic Shock: Assessing Clinical Outcomes and Implication", "authors": [ "Hany A. Zaki", "Mohamed Elgassim", "Eman E. Shaban", "Amina Ahmed", "Thamir Hashim", "Mazin Sharafeldien Elsayed Mohamed", "Amro Abdelrahman", "Kaleem Basharat", "Mohammed Abdurabu", "Ahmed Shaban", "Hany A. Zaki", "Eman E. Shaban", "Amina Ahmed", "Thamir Hashim", "Mazin Sharafeldien Elsayed Mohamed", "Amro Abdelrahman", "Kaleem Basharat", "Mohammed Abdurabu", "Ahmed Shaban" ], "abstract": "Background Septic shock, is associated with a high mortality rate and increased expenses. Currently, the first-line therapy for septic shock entails administering resuscitation fluids followed by infusing vasopressors when the blood pressure goal is not achieved. The recommended first-line vasopressor is norepinephrine, followed by vasopressin, epinephrine, angiotensin II, and dopamine. There is still a controversy on when each vasopressor should be administered. Therefore, we conducted this review to determine the impact and implications of vasopressor timing in septic shock patients.\n\nMethods PubMed, Medline, Cochrane Library, Web of Science, and Google Scholar databases were comprehensively searched for potential studies until October 2023. The methodological quality and bias assessment of valid records was examined with the Newcastle Ottawa Scale and Cochrane’s risk of bias tool. Additionally, all the meta-analyses were performed with Review Manager software.\n\nResults Twelve articles were eligible for review and analysis. Pooled analyses of data from 7 of these studies demonstrated lower incidence of mortality and shorter duration to achieve target mean arterial pressure in the early vs. late epinephrine groups (OR:0.44; 95%CI: 0.35–0.55; p<0.00001 and MD:-1.17; 95%CI:-2.00– -0.34; p=0.0006). However, the length of ICU stay didn’t differ between the early and late norepinephrine group (MD:0.55; 95%CI: -0.52–1.62; p=0.31). The subgroup analyses show that early vasopressin is associated with a decreased mortality than late administration (OR:0.60; 95%CI:0.41–0.90; p=0.01). Similarly, the pooled analysis has shown that early concomitant administration of vasopressin and norepinephrine is associated with a shorter duration to achieve target MAP than norepinephrine alone (MD:-3.15; 95%CI:-4.40– -1.90;p<0.00001).\n\nConclusion Early administration of norepinephrine has a mortality benefit and improves the duration taken to attain and sustain the goal MAP. Furthermore, early vasopressin possesses the potential to lower the fatality rate in individuals experiencing septic shock. However, further research is required to validate this finding.", "keywords": [ "vasopressor", "septic", "shock" ], "content": "Introduction\n\nSepsis is a health condition in which the body responds adversely to an infection. If it is overlooked or left untreated, it can quickly deteriorate into septic shock, characterized by persistent hypotension and the presence of tissue hypoperfusion.1,2 Research indicates that up to 50% of septic shock patients experience mortality.3 However, the death rate in this group might range from 30-50% depending on demographic characteristics such as age, sex, comorbid diseases, and the presence of organ dysfunction.4 Moreover, the condition has been linked with higher medical expenses, with data revealing that in the United States alone, about $20 billion has been spent to manage it.5 Therefore, updating the recommendations and improving the therapy of septic shock may assist in minimizing the mortality of susceptible patients and the expenses.\n\nGenerally, the first-line treatment for septic shock entails administering intravenous fluids followed by vasopressor infusion when the blood pressure objective is not attained.6,7 The recommended first-line vasopressor medication is norepinephrine.6 Research has demonstrated that norepinephrine is an effective vasopressor. A recent meta-analysis of 2811 septic shock patients indicated that norepinephrine was associated with a lower death rate compared to dopamine alone.8 However, the meta-analysis suggested that dopamine should not be ruled out as a therapy option since it may have a role in treating individuals who exhibit minimal risk of arrhythmias. Additionally, a meta-analysis of 43 randomized studies found minimal occurrences of arrhythmias among individuals taking norepinephrine (8.33%).9\n\nOn the other hand, the Surviving Sepsis Campaign (SSC) guidelines have recommended vasopressin as a second-line vasopressor medication.6 Data from preclinical and small clinical studies suggests that vasopressin may be superior in maintaining glomerular filtration rate and increasing creatinine clearance than norepinephrine.10,11 In addition, a recent large clinical study indicated that using vasopressin as an adjuvant to norepinephrine had no significant difference in mortality compared to norepinephrine alone; however, the death rate was substantially minimized when vasopressin was used to treat patients with less severe shock.12\n\nOther vasopressors such as terlipressin (an analog of vasopressin), epinephrine, dopamine, and angiotensin II also have a place in managing different subsets of septic shock patients. Research has shown that terlipressin at low dosage is effective in attaining and maintaining target MAP and provides extra advantage of less severe impact on variceal hemorrhage in septic shock patients with an existing diagnosis of liver cirrhosis.13 Furthermore, a combination therapy of terlipressin and norepinephrine has shown some promise in improving survival and achieving the objective MAP within a shorter duration than norepinephrine alone.14 Epinephrine is also a second-line vasopressor recommended as an adjunct to norepinephrine.6,7 Because to its formidable β1-adrenergic action, this vasopressor is frequently suggested in patients with heart dysfunction. However, it has been linked with more fatalities in the setting of cardiogenic shock.15 Dopamine, which was prescribed in previous years as the primary vasopressor for septic shock patients, is currently recommended in case of bradycardia.7 However, its use is limited due to the higher risk of arrhythmias.16,17 Additionally, research has shown that angiotensin II has equal mortality benefit as norepinephrine without any increase in adverse events.6 However, it does not qualify as the primary treatment but can be used as a supplementary vasopressor therapy.\n\nDespite the plethora of literature on the efficacy of various vasopressors, there is still an existing controversy on whether the timing of administration could impact patient outcomes. Therefore, the current systematic review was conducted to assess the implications and impact of vasopressor timing on the clinical outcomes of septic shock patients.\n\n\nMethods\n\nPubMed, Medline, Cochrane Library, Web of Science, and Google Scholar databases were comprehensively searched for potential studies published from inception until October 2023. Moreover, the bibliographies of articles from these databases were scrutinized for additional studies. Articles were retrieved from the electronic databases if they had the following MeSH terms and keywords: (Timing OR timely OR delay OR early) AND (vasopressors OR vasopressor therapy OR norepinephrine OR vasopressin OR vasoconstrictor agents OR epinephrine OR dopamine) AND (Septic shock). Furthermore, to avoid publication bias and improve our scientific research, we did not retrieve grey literature.\n\nTwo independent reviewers analyzed the potential studies according to the predefined eligibility criteria. Articles were included in the present review if they were non-randomized or randomized studies with full articles and published in English, included adult patients with septic shock, and compared any vasopressor therapy according to the timing of administration. On the other hand, research articles that did not meet these criteria or were designed as reviews, conference abstracts, case reports, and editorials were excluded. Any discrepancy during this process was resolved via constructive debates between the two reviewers.\n\nThe data used for review and analysis was abstracted into separate Excel files by two independent reviewers. The differences in extracted data was initially resolved via constructive debates between the two reviewers, and if they failed to agree, an additional reviewer was engaged. The data abstracted included Author ID (surname of the primary author and date of publication), Study design, Study location, pertinent characteristics of the included patients (sample size, distribution of sex, and the number of patients receiving early or delayed vasopressor therapy), Vasopressor agents used, timing of vasopressor administration and outcomes.\n\nThe key endpoints of the current study were mortality rate and the duration needed to attain the goal mean arterial pressure (MAP) (≥65 mmHg), whereas the supplementary endpoints were the duration spent in ICUs and the incidence of new-onset arrhythmias. Mortality encompassed 28-day, 30-day, and in-hospital death rates.\n\nThe present review included randomized and non-randomized studies; therefore, assessment of methodological quality and risk of bias was performed using the Newcastle Ottawa Scale (NOS) and Cochrane’s risk of bias (RoB) tool, respectively. Using the NOS, articles were assessed according to the selection, comparability, and outcome domains. For each domain, a maximum of one star was assigned to each criterion fully addressed; otherwise, no star was assigned. For the selection domain, a maximum of four stars could be achieved, while the maximum number of stars that could be attained under the comparability and outcome domains were 2 and 3, respectively.\n\nOn the other hand, risk of bias assessment was performed according to the risk of selection, attrition, performance, reporting, and other biases. A low risk of bias was assigned to a domain that was sufficiently addressed within the study, while a high and unclear risk was assigned to domains not addressed entirely or with insufficient information to make a judgment.\n\nAll quantitative statistical analyses in the present systematic review were conducted using the Review Manager software (RevMan 5.4.1). These analyses were pooled together using the DerSimonian and Laird random-effect model, which provides conservative effect sizes and counteracts the interstudy heterogeneity. Moreover, the dichotomous outcomes, such as mortality and incidences of new-onset arrhythmias, were pooled together using the simple odds ratio (OR), while continuous outcomes, such as ICU stay and time taken to achieve target MAP (≥65 mmHg), were pooled using the mean difference (MD) calculations. For studies in which the continuous outcomes were presented as median, interquartile ranges, and ranges, the formula provided by Hozo and colleagues was used to calculate the mean and standard deviations.18 In addition, the 95% confidence interval was employed for calculations, and a p-value of less than 0.05 was considered significant. Interstudy heterogeneity was calculated using the I2 statistics, of which values greater than 50% were considered high or significant. During the analyses, we grouped the outcomes according to the type of vasopressor therapy used, and whenever possible, subgroup analyses were performed.\n\n\nResults\n\nWith the predefined keywords and MeSH terms, 2021 potential studies were identified from the electronic databases. A review of these articles led to the exclusion of 989 close or exact duplicates. Afterward, the remaining studies were screened based on their titles and abstracts, of which 917 deemed to be unrelated to our topic were excluded. Eventually, 12 studies were deemed eligible for review and analysis, while the remaining 64 articles were excluded as follows: 8 were animal studies, 12 did not have comparative groups, 4 included pediatric patients, 7 included patients with other conditions such as hemorrhagic shock and sepsis without evidence of shock, and 26 compared various vasopressin without showing the effect of the time of administration (Figure 1).\n\nTwelve studies with 2721 septic shock patients were included in the present review. Four of these studies were randomized controlled trials (RCT), and 8 were cohort studies. Furthermore, seven studies evaluated the timing of norepinephrine, and 5 assessed the timing of vasopressin as an adjunct treatment (Table 1).\n\nThe risk of bias outcomes are summarized in Figure 2. The bias assessment showed that most of the studies had a high risk of other bias because they were performed in single institutions. On the other hand, methodological quality of cohort studies is presented in Table 2. Most of the studies were carried out in single institutions; therefore, the could not attain maximum stars in the selection domain. Furthermore, two of the studies did not attain any stars in the comparability domain because they did not adjust any cofounders.\n\nOf the 12 studies, 7, including 1678 septic shock patients, evaluated the impact of administering norepinephrine early or late on the clinical outcomes. The pooled data from these studies showed that patients receiving norepinephrine in the early stage had significantly lower mortality rates than those who received norepinephrine late (OR: 0.44; 95% CI: 0.35 – 0.55; p<0.00001) (Figure 3). Similarly, the data pooled from 4 studies showed that patients in the early group took significantly less time (in hours) to achieve the target MAP than those in the late group (MD: -1.17; 95% CI: -2.00 – -0.34; p=0.0006) (Figure 4). However, the length of ICU stay did not differ statistically between the two groups (MD: 0.55; 95% CI: -0.52 – 1.62; p=0.31) (Figure 5).\n\nFive studies, including 1043 patients, assessed the impact of vasopressin as an adjunct therapy for septic shock. Data pooled from two studies showed that the early addition of vasopressin to norepinephrine has no significant mortality benefit compared to monotherapy norepinephrine (OR: 0.87; 95% CI: 0.48 – 1.58; p=0.65) (Figure 6). Similarly, data from the study in which vasopressin was administered in combination with hydrocortisone showed that early administration has no significant mortality benefit compared to norepinephrine in combination with hydrocortisone (OR: 1.20; 95% CI: 0.79 – 1.82; p=0.39) (Figure 6). However, the pooled data from two studies showed that early initiation of vasopressin significantly reduces mortality of septic shock patients compared to late initiation (OR: 0.60; 95% CI: 0.41 – 0.90; p=0.01) (Figure 6).\n\nIn addition, our statistical analyses show that early addition of vasopressin to norepinephrine is associated with a significant reduction in the time taken to achieve target MAP compared to monotherapy norepinephrine (MD: -3.15; 95% CI: -4.40 – -1.90; p<0.00001) (Figure 7). However, this early addition shows no significant difference compared with norepinephrine alone on the incidence of new-onset arrhythmias (OR: 1.31; 95% CI: 0.45 – 3.78; p=0.62) or ICU length of stay (MD: -0.45; 95% CI: -3.25 – 2.36; p=0.75) (Figures 8 & 9).\n\nThe statistical analyses also suggest that early vasopressin in combination with hydrocortisone shows no significant difference compared to norepinephrine on the incidence of new-onset arrhythmias (OR: 0.39; 95% CI: 0.08 – 2.04; p=0.27) (Figure 8) and length of ICU stay (MD: 0.50; 95% CI: -0.01 – 1.01; p=0.05) (Figure 9). Similarly, patients receiving early or late vasopressin have statistically equal length of ICU stays (MD: -0.41; 95% CI: -3.64 – 2.82; p = 0.80) (Figure 9) and incidences of new-onset arrhythmias (OR: 0.69; 95% CI: 0.18 – 2.58; p=0.58) (Figure 8).\n\n\nDiscussion\n\nThe present review sought to determine whether the time of vasopressor administration impacts the clinical outcomes of septic shock patients. We found that early norepinephrine initiation resulted in a mortality decrease and shorter time to achieve target MAP than delayed administration. However, the duration of ICU stay did not vary statistically among patients receiving norepinephrine early or late. Furthermore, timely addition of vasopressin to norepinephrine considerably decreases the time to attain goal MAP than monotherapy norepinephrine. Early addition of vasopressin to catecholamine therapy also results in a considerable decrease in mortality than late addition.\n\nThe SSC guidelines have recommended using norepinephrine as the first-line vasopressor for septic shock.6,7 The goal of this therapy is usually to attain and maintain a MAP of above 65 mmHg.31,32 MAP is a crucial measure of pressure because if it goes excessively low, it can cause organs not to be perfused, causing the cells to start dying and organs not function properly.7 Furthermore, MAP below 65mmHg results in an elevated mortality risk because of the inadequate amount of oxygen delivered to the organs.7 Therefore, it is essential to assess how the timing of norepinephrine initiation affects MAP. Our statistical analysis indicated that early initiation of norepinephrine significantly decreases the time to achieve target MAP. This finding collaborates with what was already reported in a previous meta-analysis of 5 studies. According to that study, the duration it took to attain target MAP was shorter with early administration of norepinephrine (MD: -1.39; 95% CI: -1.81 – -0.96; p<0.00001).33 Similarly, Hamzaoui and colleagues found that among patients with severe shock, early norepinephrine (within 6 hours of septic shock) was effective in obtaining the target MAP.34 This decrease in the duration to attain MAP goal is particularly important as studies have shown that MAP is a key determinant of patients’ outcomes.35,36\n\nThe current research has also revealed that early shock treatment with norepinephrine results in a considerable reduction in mortality. In similar fashion, Li and colleagues discovered that short-term mortality was lower when norepinephrine was administered early as opposed to late (p<0.00001).33 The survival benefit reported in these studies can be attributed to faster achievement of MAP with early norepinephrine administration. In contrast, a 2019 double-blinded RCT recorded an insignificant difference in crude 28-day mortality between early and late norepinephrine use (p=0.15).21 However, the mortality benefit of early norepinephrine cannot be inferred from this study due to various limitations. First, the trial was not designed to assess mortality. Secondly, the fluid resuscitation rate was not controlled, and this might have affected the mortality outcomes. Finally, the trial was performed in a single center, and its findings cannot be generalized to other care facilities.\n\nEarly administration of norepinephrine also displays other benefits over late administration. Research has shown that early norepinephrine can boost cardiac output via multiple methods. One of these methods is the elevation of cardiac preload and reduction of preload reliance34,37 during the initial stages septic shock by elevating mean systemic filling pressure and dispersing blood out of the disproportionately bumped unstressed volume to the stressed volume via α-adrenergic-mediated reduction of venous capacitance.38 Additionally, norepinephrine can elevate cardiac output by boosting the ventricular contractility.39 Hamzaoui and colleagues found that early norepinephrine administration in septic shock patients receiving adequate intravenous fluid might enhance the left ventricular ejection fraction and other indicators of left and right systolic function.39 This effect was attributed to an improvement in coronary perfusion pressure via an increased diastolic blood pressure and β-adrenergic stimulation of cardiomyocytes at the initial stages of septic shock when the β-adrenergic receptors are poorly controlled.\n\nEarly norepinephrine administration can also prevent fluid overload. Research has shown that positive fluid balance is independently associated with poor outcomes in septic shock.40,41 Therefore, early initiation of norepinephrine can result in a reduced amount of infused fluids, thus lowering the risk of fluid overload. This hypothesis is evident in the study by Li and colleagues, where patients receiving early norepinephrine had significantly lower amounts of infused fluids within the first 24 hours than those receiving norepinephrine late (p=0.03).28 Similarly, Bai and colleagues found that the volume of intravenous fluids at 24 hours was significantly lower in patients receiving norepinephrine within 2 hours of septic shock onset than those receiving the therapy after 2 hours (p<0.001).27 In contrast, permpikul and colleagues found that the amount of infused resuscitation fluids did not differ between patients in the early and late norepinephrine groups.21 This insignificant difference can be explained by the fact the study was performed during the 2013 – 2017 period when the SSC guidelines were used, meaning that fluid was given towards a target intravascular volume and central venous pressure. Additionally, early initiation of norepinephrine in cases of severe hypotension might recruit microvessels and improve microcirculation by increasing organ perfusion pressure. This is evident in the study by Georger and colleagues, who found that early norepinephrine significantly improved the tissue muscle oxygen saturation alongside MAP in septic shock patients.42\n\nAlthough we have shown that early administration of norepinephrine may be beneficial in septic shock patients, it is not without consequences. One of the well-known adverse events associated with vasopressor therapy is the development of arrhythmias. Permpikul et al. reported that early norepinephrine was associated with significantly lower incidences of new-onset arrhythmias and cardiogenic pulmonary edema than late norepinephrine (p=0.03 and 0.004, respectively).21 However, no other study has collaborated this finding, meaning that further high-quality trials are required to investigate whether administering norepinephrine in the early phase of septic shock might reduce the occurrence of new-onset arrhythmias and other adverse events.\n\nVasopressin is an antidiuretic drug that attaches onto the arginine vasopressin receptors. Currently, this medication is recommended as a supplementary treatment option for septic shock patients who are incapable of attaining or maintaining a MAP goal of more than 65mmHg on norepinephrine alone. In our analysis, we observed that the prompt addition of vasopressin to norepinephrine resulted to a considerable decrease in the time taken to achieve target MAP than norepinephrine alone. This faster achievement of target MAP suggests that resolving vasopressin insufficiency sooner could lessen the duration spent on the initial stages of septic shock. Since prior research has revealed that delay in obtaining objective MAP can raise the overall mortality of septic shock patients, the findings of this meta-analysis might provide clinicians with a therapy that can be employed to attain and sustain the target MAP within a shorter period. However, subsequent studies should concentrate on a precision therapeutic strategy to identify patients more likely to benefit from the early addition of vasopressin.\n\nThe pooled analyses have also shown that despite early vasopressin reducing the time to target MAP, it has no significant difference to norepinephrine alone in terms of mortality, ICU stay, and incidence of new-onset arrhythmias. These findings are collaborated by a previous meta-analysis of 5 studies which found that early vasopressin did not improve short-term mortality (p=0.60), length of ICU stay (p=0.77), and incidence of new-onset arrhythmias (p=0.10).43 Therefore, there is still a need for further large-scale trials to evaluate the benefit of early concomitant vasopressin and norepinephrine therapy in septic shock patients.\n\nIn addition, evidence suggests that early induction of vasopressin as a supplement to norepinephrine might aid in resolving organ dysfunction. A 2017 study noted that patients who were managed with concomitant early vasopressin and norepinephrine had considerable decreases in Sequential Organ Failure Assessment (SOFA) scores within 72 hours than those who received the initial norepinephrine monotherapy (-4 vs. -1; p=0.12, respectively).24 However, a 2018 randomized trial did not demonstrate any substantial variations in SOFA scores among patients receiving early vasopressin combined with norepinephrine and those receiving norepinephrine alone (p=0.29).23 The evidence in these trials has shown contradictions, meaning that the early initiation of vasopressin to norepinephrine has the potential to decrease morbidity and time taken to resolve septic shock phase by resolving organ failure, but this potential benefit should be investigated further in large high-quality randomized trials.\n\nOur subgroup analysis has also shown that early initiation of vasopressin as an adjunct therapy for septic shock patients receiving catecholamines is associated with a significant decrease in mortality than late initiation. However, the analyses have indicated a high interstudy heterogeneity, which suggests variation in outcomes. Reardon et al.20 found no significant difference in mortality rate between the early and late vasopressin groups. On the other hand, Rydz and colleagues found that the in-hospital mortality was significantly higher in patients receiving vasopressin after 7 hours.30 The difference between these studies may be attributed to the fact that Rydz and colleagues administered vasopressin at lower doses of norepinephrine, which might have statistically reduced the composite outcome of in-hospital mortality. This hypothesis is supported by a previous study which found that for every 10 ug/min increase in norepinephrine dose equivalents, less than 60 ug/min at the time of vasopressin initiation was associated with an increase in mortality by 20.7%.44\n\nThe present study has also demonstrated a negligible variation in the occurrence of new-onset arrhythmias between the early and delayed vasopressin groups. In contrast, Reardon and colleagues reported a significantly lower incidence of new-onset arrhythmias when vasopressin was administered in the initial stages of septic shock.20 This finding may be attributed to the fact that most patients in the early group were younger than those in the late group and were not necessarily at equal risk for developing arrhythmias. However, the outcomes of this research might not be applied to other healthcare institutions since it was undertaken in only one institution. Therefore, more RCTs are required to validate these findings.\n\nAlthough we did not assess the effect of vasopressin timing on organ dysfunction, it is worth noting the effect on acute kidney injury (AKI), which is a common complication of sepsis and septic shock. A previous meta-analysis focusing on the clinical outcomes of septic shock patients receiving early vasopressin found that patients receiving vasopressin had a reduced need for renal replacement therapy (RRT).43 Similarly, Rydz and colleagues reported that the incidence of AKI and the need for RRT was significantly lower for patients receiving adjunct vasopressin within 7 hours of stroke onset.30 On the other hand, a previous meta-analysis focusing on the renal outcomes of distributive shock patients found that vasopressin and its analogs is associated with reduced AKI incidences and the need for RRT.45 Therefore, vasopressin administration seems to be beneficial in resolving organ dysfunction, especially AKI. However, further large-scale RCTs are still needed to validate this important finding.\n\nFrom a practical standpoint, early administration of norepinephrine can rapidly increase MAP and lower the death rate of septic shock patients. Therefore, expedited norepinephrine infusion may be a logical therapy for improving organ perfusion, and we can recommend that norepinephrine is initiated concurrently with resuscitation fluids at the initial stages of septic shock. However, this technique ought not to hinder sufficient fluid resuscitation as clinicians should be aware of the ‘vasoconstrictor-masked hypovolemia’.46 Timely infusion of vasopressin as an additional treatment in septic shock might decrease mortality. However, further randomized trials are needed to validate this finding. Furthermore, early introduction of vasopressin as a supplement to norepinephrine rapidly improves the achievement of target MAP than norepinephrine alone. Therefore, we recommend early concomitant administration of vasopressin and norepinephrine in patients who are unable to attain the goal MAP or those with presumed or proven deficit of vasopressin.\n\nOur contemporary qualitative review has also identified gaps that should be addressed in future research. First, the definition of early vasopressor initiation varied across the studies. In studies on norepinephrine, early initiation was either referenced to the onset of septic shock or administration of loading fluid, while for studies on vasopressin, early initiation referred to the time between administration of first-line vasopressor to the addition of vasopressin. Therefore, future studies should look to harmonize the definition of early initiation to determine the optimal time at which vasopressor therapy can have improved outcomes. Secondly, evidence suggests that early initiation of norepinephrine might reduce the incidences of new-onset arrhythmias; however, further research is required to establish this finding. Finally, there is a suggestion that early administration of vasopressin might aid in resolving organ dysfunction; however, rigorous reporting is still required to validate this finding.\n\nThe present review article has several limitations that should be accounted for when interpreting our findings. First, we observed high heterogeneity in some of the statistical analyses. This heterogeneity might be a result of varied sample sizes, different dosages, and methodological designs. However, the random effect model employed in our analyses was justified and countered the heterogeneity to provide conservative outcomes. Second, our eligibility criteria excluded articles of pediatric patients; hence, our findings can only be inferred for adult septic shock patients. Thirdly, due to limited data, we were unable to carry out a meta-analysis on organ dysfunction, which is an important clinical outcome in septic shock. However, we have addressed this outcome by reviewing the literature qualitatively. Fourth, our study was designed to evaluate the effect of various vasopressor timing on clinical outcomes; however, we only identified articles reporting the timing of norepinephrine and vasopressin. Finally, most of the studies in this review were non-randomized and conducted in single centers; hence, the bias that comes with such study designs was transferred to our analyses.\n\n\nConclusion\n\nEarly initiation of norepinephrine in septic shock patients is associated with a significant reduction in mortality and a shorter duration to achieve the MAP goal. However, it does not reduce the duration spent in ICU compared to late admission. Therefore, our findings suggest that norepinephrine should continue to be used as the first-line vasopressor for septic shock and can be initiated during the early phase of septic shock. Furthermore, early administration of vasopressin as an adjunct to norepinephrine should be considered for patients with an absolute or relative vasopressin deficiency.", "appendix": "Data availability statement\n\nFigshare: A Systematic Review and Meta-Analysis of the Timing of Vasopressor Therapy in Patients with Septic Shock: Assessing Clinical Outcomes and Implication, DOI: 10.6084/m9.figshare.25405330. 47\n\nThis project contains the following underlying data:\n\n• PRISMA flow chart and all other data pertaining this article can be found in Figshare under the title matching the title of the article.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nDellinger RP: Cardiovascular management of septic shock. Crit. Care Med. 2003; 31: 946–955. Publisher Full Text\n\nAngus DC, Linde-Zwirble WT, Lidicker J, et al.: Epidemiology of severe sepsis in the United States: Analysis of incidence, outcome, and associated costs of care. Crit. Care Med. 2001; 29: 1303–1310. Publisher Full Text\n\nMayr FB, Yende S, Linde-Zwirble WT, et al.: Infection rate and acute organ dysfunction risk as explanations for racial differences in severe sepsis. JAMA. 2010; 303: 2495–2503. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnnane D, Bellissant E, Cavaillon J-M: Septic shock. Lancet. 2005; 365: 63–78. Publisher Full Text\n\nSinger M, Deutschman CS, Seymour CW, et al.: The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3). JAMA. 2016; 315: 801–810. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEvans L, Rhodes A, Alhazzani W, et al.: Surviving sepsis campaign: international guidelines for management of sepsis and septic shock 2021. Intensive Care Med. 2021; 47: 1181–1247. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRhodes A, Evans LE, Alhazzani W, et al.: Surviving Sepsis Campaign: International Guidelines for Management of Sepsis and Septic Shock: 2016. Intensive Care Med. 2017; 43: 304–377. PubMed Abstract \| Publisher Full Text\n\nOba Y, Lone NA: Mortality benefit of vasopressor and inotropic agents in septic shock: A Bayesian network meta-analysis of randomized controlled trials. J. Crit. Care. 2014; 29: 706–710. PubMed Abstract \| Publisher Full Text\n\nCheng L, Yan J, Han S, et al.: Comparative efficacy of vasoactive medications in patients with septic shock: a network meta-analysis of randomized controlled trials. Crit. Care. 2019; 23: 168. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLauzier F, Lévy B, Lamarre P, et al.: Vasopressin or norepinephrine in early hyperdynamic septic shock: a randomized clinical trial. Intensive Care Med. 2006; 32: 1782–1789. Publisher Full Text\n\nPatel BM, Chittock DR, Russell JA, et al.: Beneficial effects of short-term vasopressin infusion during severe septic shock. Anesthesiology. 2002; 96: 576–582. PubMed Abstract \| Publisher Full Text\n\nRussell JA, Walley KR, Singer J, et al.: Vasopressin versus norepinephrine infusion in patients with septic shock. N. Engl. J. Med. 2008; 358: 877–887. Publisher Full Text\n\nChoudhury A, Kedarisetty CK, Vashishtha C, et al.: A randomized trial comparing terlipressin and noradrenaline in patients with cirrhosis and septic shock. Liver. Int. 2017; 37: 552–561. PubMed Abstract \| Publisher Full Text\n\nXiao X, Zhang J, Wang Y, et al.: Effects of terlipressin on patients with sepsis via improving tissue blood flow. J. Surg. Res. 2016; 200: 274–282. PubMed Abstract \| Publisher Full Text\n\nTarvasmäki T, Lassus J, Varpula M, et al.: Current real-life use of vasopressors and inotropes in cardiogenic shock - adrenaline use is associated with excess organ injury and mortality. Crit. Care. 2016; 20: 208. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRegnier B, Safran D, Carlet J, et al.: Comparative haemodynamic effects of dopamine and dobutamine in septic shock. Intensive Care Med. 1979; 5: 115–120. Publisher Full Text\n\nDe Backer D, Biston P, Devriendt J, et al.: Comparison of dopamine and norepinephrine in the treatment of shock. N. Engl. J. Med. 2010; 362: 779–789. Publisher Full Text\n\nWan X, Wang W, Liu J, et al.: Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range. BMC Med. Res. Methodol. 2014; 14: 135. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOspina-Tascón GA, Hernandez G, Alvarez I, et al.: Effects of very early start of norepinephrine in patients with septic shock: a propensity score-based analysis. Crit. Care. 2020; 24: 52. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReardon DP, DeGrado JR, Anger KE, et al.: Early vasopressin reduces incidence of new onset arrhythmias. J. Crit. Care. 2014; 29: 482–485. PubMed Abstract \| Publisher Full Text\n\nPermpikul C, Tongyoo S, Viarasilpa T, et al.: Early Use of Norepinephrine in Septic Shock Resuscitation (CENSER). A Randomized Trial. Am. J. Respir. Crit. Care Med. 2019; 199: 1097–1105. PubMed Abstract \| Publisher Full Text\n\nGordon AC, Mason AJ, Thirunavukkarasu N, et al.: Effect of Early Vasopressin vs Norepinephrine on Kidney Failure in Patients With Septic Shock: The VANISH Randomized Clinical Trial. JAMA. 2016; 316: 509–518. PubMed Abstract \| Publisher Full Text\n\nHammond DA, Ficek OA, Painter JT, et al.: Prospective Open-label Trial of Early Concomitant Vasopressin and Norepinephrine Therapy versus Initial Norepinephrine Monotherapy in Septic Shock. Pharmacotherapy. 2018; 38: 531–538. PubMed Abstract \| Publisher Full Text\n\nHammond DA, Cullen J, Painter JT, et al.: Efficacy and Safety of the Early Addition of Vasopressin to Norepinephrine in Septic Shock. J. Intensive Care Med. 2019; 34: 910–916. PubMed Abstract \| Publisher Full Text\n\nElbouhy MA, Soliman M, Gaber A, et al.: Early Use of Norepinephrine Improves Survival in Septic Shock: Earlier than Early. Arch. Med. Res. 2019; 50: 325–332. PubMed Abstract \| Publisher Full Text\n\nColon Hidalgo D, Patel J, Masic D, et al.: Delayed vasopressor initiation is associated with increased mortality in patients with septic shock. J. Crit. Care. 2020; 55: 145–148. PubMed Abstract \| Publisher Full Text\n\nBai X, Yu W, Ji W, et al.: Early versus delayed administration of norepinephrine in patients with septic shock. Crit. Care. 2014; 18: 532. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi Y, Guo J, Li H, et al.: Effect of timing of norepinephrine application on prognosis of patients with septic shock: a prospective cohort study. In Review.2023. Publisher Full Text\n\nJouffroy R, Hajjar A, Gilbert B, et al.: Prehospital norepinephrine administration reduces 30-day mortality among septic shock patients. BMC Infect. Dis. 2022; 22: 345. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRydz AC, Elefritz JL, Conroy M, et al.: EARLY INITIATION OF VASOPRESSIN REDUCES ORGAN FAILURE AND MORTALITY IN SEPTIC SHOCK. Shock. 2022; 58: 269–274. PubMed Abstract \| Publisher Full Text\n\nDellinger RP, Levy MM, Rhodes A, et al.: Surviving Sepsis Campaign: international guidelines for management of severe sepsis and septic shock, 2012. Intensive Care Med. 2013; 39: 165–228. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDellinger RP, Levy MM, Carlet JM, et al.: Surviving Sepsis Campaign: International guidelines for management of severe sepsis and septic shock: 2008. Intensive Care Med. 2008; 34: 17–60. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi Y, Li H, Zhang D: Timing of norepinephrine initiation in patients with septic shock: a systematic review and meta-analysis. Crit. Care. 2020; 24: 488. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHamzaoui O, Georger J-F, Monnet X, et al.: Early administration of norepinephrine increases cardiac preload and cardiac output in septic patients with life-threatening hypotension. Crit. Care. 2010; 14: R142. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVarpula M, Tallgren M, Saukkonen K, et al.: Hemodynamic variables related to outcome in septic shock. Intensive Care Med. 2005; 31: 1066–1071. Publisher Full Text\n\nVincent J-L, Nielsen ND, Shapiro NI, et al.: Mean arterial pressure and mortality in patients with distributive shock: a retrospective analysis of the MIMIC-III database. Ann. Intensive Care. 2018; 8: 107. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMonnet X, Jabot J, Maizel J, et al.: Norepinephrine increases cardiac preload and reduces preload dependency assessed by passive leg raising in septic shock patients. Crit. Care Med. 2011; 39: 689–694. PubMed Abstract \| Publisher Full Text\n\nPersichini R, Silva S, Teboul J-L, et al.: Effects of norepinephrine on mean systemic pressure and venous return in human septic shock. Crit. Care Med. 2012; 40: 3146–3153. PubMed Abstract \| Publisher Full Text\n\nHamzaoui O, Jozwiak M, Geffriaud T, et al.: Norepinephrine exerts an inotropic effect during the early phase of human septic shock. Br. J. Anaesth. 2018; 120: 517–524. PubMed Abstract \| Publisher Full Text\n\nVincent J-L, Sakr Y, Sprung CL, et al.: Sepsis in European intensive care units: results of the SOAP study. Crit. Care Med. 2006; 34: 344–353. PubMed Abstract \| Publisher Full Text\n\nBoyd JH, Forbes J, Nakada T, et al.: Fluid resuscitation in septic shock: a positive fluid balance and elevated central venous pressure are associated with increased mortality. Crit. Care Med. 2011; 39: 259–265. PubMed Abstract \| Publisher Full Text\n\nGeorger J-F, Hamzaoui O, Chaari A, et al.: Restoring arterial pressure with norepinephrine improves muscle tissue oxygenation assessed by near-infrared spectroscopy in severely hypotensive septic patients. Intensive Care Med. 2010; 36: 1882–1889. PubMed Abstract \| Publisher Full Text\n\nHuang H, Wu C, Shen Q, et al.: The effect of early vasopressin use on patients with septic shock: A systematic review and meta-analysis. Am. J. Emerg. Med. 2021; 48: 203–208. PubMed Abstract \| Publisher Full Text\n\nSacha GL, Lam SW, Wang L, et al.: Association of Catecholamine Dose, Lactate, and Shock Duration at Vasopressin Initiation With Mortality in Patients With Septic Shock. Crit. Care Med. 2022; 50: 614–623. PubMed Abstract \| Publisher Full Text\n\nNedel WL, Rech TH, Ribeiro RA, et al.: Renal Outcomes of Vasopressin and Its Analogs in Distributive Shock: A Systematic Review and Meta-Analysis of Randomized Trials. Crit. Care Med. 2019; 47: e44–e51. PubMed Abstract \| Publisher Full Text\n\nHinder F, Stubbe HD, Van Aken H, et al.: Early multiple organ failure after recurrent endotoxemia in the presence of vasoconstrictor-masked hypovolemia. Crit. Care Med. 2003; 31: 903–909. PubMed Abstract \| Publisher Full Text\n\nElgassim M, Zaki HA, Shaban E, et al.: A Systematic Review and Meta-Analysis of the Timing of Vasopressor Therapy in Patients with Septic Shock: Assessing Clinical Outcomes and Implication. figshare. 2024. Publisher Full Text" }	[ { "id": "271514", "date": "08 May 2024", "name": "Zhongheng Zhang", "expertise": [ "Reviewer Expertise critical care" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis systematic review found that early administration of norepinephrine has a mortality benefit and improves the duration taken to attain and sustain the goal MAP. Furthermore, early vasopressin possesses the potential to lower the fatality rate in individuals experiencing septic shock. However, further research is required to validate this finding. I have several comments as follows: 1. In the abstract, the key component of a systematic review should be reported in PICO, at least, the intervention and control should be explicitly described. 2. There can be heterogenous definitions for early versus late use of epinephrine. 3. \"Pooled analyses of data from 7 of these studies demonstrated lower incidence of mortality and shorter duration to achieve target mean arterial pressure in the early vs. late epinephrine groups (OR:0.44; 95%CI: 0.35–0.55; p<0.00001 and MD:-1.17; 95%CI:-2.00– -0.34; p=0.0006).\"--in this sentence, the epinephrine should be norepinephrine? 4. Early use of norepinephrine means less fluid infusions in the resuscitation phase. The fluid volume should also be compared between the two groups. 5. It should also be acknowledged that the septic shock population can be heterogenous and some may respond well to early use of NE and others are better suited for late NE. The heterogeneity of the study population should be acknowledged so that future work are needed to explore how subgroups of patients can have different results/conclusions 1. There has been numerous studies in this field and the authors may need to discuss this issue in interpreting current findings.\n\n6. I do not think non-randomized studies can be pooled with RCTs because the level of evidence is far different. 7. \"However, the length of ICU stay did not differ statistically between the two groups (MD: 0.55; 95% CI: -0.52 – 1.62; p=0.31)\"--the unit should be added to the length of ICU stay, since it is a mean difference.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [] }, { "id": "276798", "date": "29 Aug 2024", "name": "Francesca Innocenti", "expertise": [ "Reviewer Expertise Sepsis", "management of the critical patient in the Emergency Medicine Setting" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI thank for having the opportunity to review this paper. The topic is hot and large areas of debate persist.\nI would have some concerns.\nThe review seems unbalanced in the sense of recognizing a survival benefit of early noradrenaline use. The paper by Permpikul is undervalued and the paper by Yeo and coll, \"Vasopressor Initiation Within 1 Hour of Fluid Loading Is Associated With Increased Mortality in Septic Shock Patients: Analysis of National Registry Data\" in Critical Care Medicine 2022 was not included. I was not able to understand the reasons for this choice.\nIt has to be demonstrated if results are confirmed by the inclusion of this prospective multicenter study, which included one of the largest populations among those included in the present meta-analysis.\nI would invite the authors to detail what they intend for early NA and early vasopressin, also considering differences among different studies.\nThe discussion is very long and repetitive; it should be shortened and focused on the main finding of the study. For example, the long explanation about pathophysiology of MAP is not so pertinent.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-289
https://f1000research.com/articles/13-288/v1	18 Apr 24	{ "type": "Data Note", "title": "A data set of Japanese corporates’ green transformation technologies patents", "authors": [ "Jiaming Jiang", "Yu Zhao", "Junshi Feng", "Yu Zhao", "Junshi Feng" ], "abstract": "Abstract* In 2020, the Government of Japan declared 2050 “carbon neutral” and launched a long-term strategy to create a “virtuous cycle of economy and environment.” Japanese corporations possess many technologies that contribute to decarbonization, which is important for expanding investments in green transformation technology inventory (GXTI) development. Patent data are the most reliable measure of business performance for applied research and development activities when investigating knowledge domains or technological evolution. Our paper describes a Japanese patent dataset of Japanese corporations’ green transformation (GX) patent applications on the Japan Platform for Patent Information, using a search method of bombinating International Patent Classification (IPC) codes and keywords. The dataset contains 37,476 GX patent applications from 298 corporations during the period 1999–2022.", "keywords": [ "Green transformation technology", "innovation", "Japanese corporates", "environment", "patents" ], "content": "Introduction\n\nCurrently, we are expected to shift economic, social, and industrial structures, which have depended on fossil fuels since the Industrial Revolution, into structures driven by clean energy through green transformation (GX). With the Paris Agreement of 2015, the world has been moving toward carbon neutrality. As pointed out by Sueyoshi and Goto (2019), Japan has historically faced various environmental problems, along with industrialization. Therefore, Japan has also made a “2050 Carbon Neutrality Declaration” in 2020. The declaration indicated that “the goal is to reduce overall greenhouse gas emissions to zero by 2050, that is, to achieve a carbon-neutral, decarbonized society in 2050”. The trend toward a decarbonized society has become irreversible in Japan. Most recently, based on the “GX Promotion Law” enacted in May of the previous year, the GX Promotion Strategy was approved by the Cabinet of Ministers, and all the moves toward GX are taking shape. The Green Transformation Technologies Inventory (GXTI), released by the JPO shows how various GX technologies can be categorized, and how patent documents related to each category of GX technology can be searched. GXTI helps enterprises and others to objectively explain their GX efforts. GXTI categorizes GX technologies and searches for patent documents pertinent to the five respective GX technology categories: energy supply; energy saving; electrification; demand-supply flexibility; batteries; energy storage; CO2 reduction in the non-energy sector; and capture, storage, utilization, and removal of greenhouse gas.\n\nOn the other hand, patents are the most common method in the automotive industry to protect intellectual property (Borgstedt et al., 2017), and patent analysis has been used to evaluate the competitiveness of firms, develop technology plans, prioritize research and development (R&D) investment, and monitor technological change in firms (Yoon and Park, 2004). Japanese respondents also reported patents as being as effective as other mechanisms for protecting product innovation. Furthermore, patents are the most important channel of information flow in Japan (Cohen et al., 2002). Although Jiang et al. (2022) have searched for “green” patents in the vehicle powertrains field, and Jiang et al. (2023) collected cited information about them, there have not been reports of research on GX patents, because of a delay in the development of a database, which is a void that we are trying to fill. We generated this dataset for GX patent applications of Japanese corporations and published GX patents in Mendeley Data, which is available to everyone. The full dataset may be used to conduct further searches, such as natural language analysis and machine learning, on patent description documents as well as statistical data analysis for empirical economics. This dataset may also be merged with many other databases such as the EPO’s PATSTAT database and the Corporate Social Responsibility Database of Toyo Keizai Inc. We expect our dataset to be meaningful for forecasting the development of new technologies and encouraging environmental innovation.\n\n\nMethods\n\nWe generated this dataset by searching for GX patent applications of Japanese corporations on the Japan Platform for Patent Information (J-PlatPat). The search formulas are published at https://www.jpo.go.jp/e/resources/statistics/gxti.html and use a combined search strategy of International Patent Classification (IPC) codes and keywords. Applications of similar methods that have been previously reported include those of Jiang et al. (2022), the authors proposed a method of combining IPC and keywords to define “green” patents in vehicle powertrain systems, based on data of patent applications to the Japan Patent Office as recorded in EPO’s PATSTAT.1 Borgstedt et al. (2017) proposed a search strategy using IPC-classes and keywords is introduced that reveals all relevant patents and clearly differentiated four vehicle powertrain technologies. And Mirzadeh Phirouzabadi et al. (2020) introduced a database using a combined search strategy of keywords and IPC codes.\n\nFrom the present search, we obtained 37,476 patent applications by 298 corporations during the period 1999–2022. When analyzing patents, it is necessary to consider the social situation of each country, including language background (Jiang et al., 2022). Thus, since the names of Japanese corporates are written in both kanji and katakana, when we searched for one corporate’s patents, we searched in both kanji and katakana.2 The name list of corporations and their industry sectors was supplied by Toyo Keizai Inc., a leading business publisher in Japan, with the most well-known comprehensive database of Japanese companies. Most companies are listed in the first section of the Tokyo Stock Exchange Market (Sueyoshi and Goto, 2019). Figure 1 aggregates the sampled patents by the industry sector.\n\nFrom this figure, we can see that most GX patents were from the transportation equipment sector, there are 20,385 patents, account for 54%, and second-most common sector of GX patents was the electrical appliances sector, there are 6,290 patents, account for 17%. The number of GX patents from the metal products, Glass & Stone products, non-ferrous metals, and chemistry sectors was also over 1000. There are comparatively few GX patents from the retail, banking, securities, and commodity futures sectors.\n\nFigure 2 shows the yearly number of GX patent applications for the period 1999–2022. As shown, the number increased every year until peaking in 2012, after which it remained relatively stable for several years and then decreased from 2019 because of a delay in opening in J-PlatPat.\n\nTable 1 lists the top 10 companies in terms of the number of patents owned. As shown, in our sample, Toyota Motor Corporation owns the most GX patents (11,514), followed by Mitsubishi Electric Corporation (4,443), Honda Motor Co., Ltd. (4,011), and Nissan Motor Corporation (3,256), who also had numerous GX patents.\n\nThe limitation of this dataset is that it focuses almost exclusively on large publicly traded corporations, as little is known about small and medium-size enterprises (SMEs). Further research on SMEs is needed.\n\nNot applicable.", "appendix": "Data availability\n\nFigshare: Japanese GX patents with English titles. https://doi.org/10.6084/m9.figshare.25434724.v3 (Jiang, 2024).\n\nThis project contains the following underlying data:\n\n• Japanese GX patents with English titles\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nNot applicable.\n\n\nReferences\n\nBorgstedt P, Bastian N, Schewe G: Paving the Road to Electric Vehicles —A Patent Analysis of the Automotive Supply Industry. J. Clean. Prod. 2017; 167: 75–87. Publisher Full Text\n\nCohen W, Goto A, Nagata A, et al.: R&D spillovers, patents, and the incentives to innovate in Japan and the United States. Res. Policy. 2002; 31(8-9): 1349–1367. Publisher Full Text\n\nJiang J: Japanese GX patents.xlsx. [Dataset]. figshare. 2024. Publisher Full Text\n\nJiang J, Baba K, Zhao Y, et al.: Dataset of Japanese patents and patents holding firms in the field of green vehicle powertrains. Data Br. 2022; 44: 108524. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJiang J, Zhao Y: Technology Trend Analysis of Japanese Green Vehicle Powertrains Technology Using Patent Citation Data. Energies. 2023; 16(5): 2221. Publisher Full Text\n\nMirzadeh Phirouzabadi A, Savage D, Blackmore K, et al.: Global patent dataset on the vehicle powertrains of ICEV, HEV, and BEV. Data Br. 2020; 32: 106042. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSueyoshi T, Goto M: DEA Non-Radial Approach for Resource Allocation and Energy Usage to Enhance Corporate Sustainability in Japanese Manufacturing Industries. Energies. 2019; 12(9): 1785. Publisher Full Text\n\nYoon B, Park Y: A text-mining-based patent network: Analytical tool for high-technology trend. J. High Technol. Manag. 2004; 15: 37–50. Publisher Full Text\n\n\nFootnotes\n\n1 See https://www.epo.org/en/searching-for-patents/business/patstat\n\n2 For example, the ホンダ can also be written in 本田; the トヨタ sometimes is written in 豊田." }	[ { "id": "296596", "date": "12 Jul 2024", "name": "Yang Pingjian", "expertise": [ "Reviewer Expertise environmental policy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAs mentioned in the article, green transition (GX) technologies are crucial to the achievement of carbon neutrality goals. Enterprises, especially large ones, can not only lead to the improvement of green technology level in their industries, but also achieve the green transformation of the whole society. Although the authors have good ideas, the amount of work done by the authors is inadequate, both in terms of literature review, methodology presentation, and sample selection.\n1.The end of the first paragraph of the introduction seems to be 8 categories of green transformation technologies, please check it.\n\n2.The authors are requested to add a section which should describe which IPC codes and which keywords the authors used in their search.\n3. Sample size issues. The authors need to explain the following issues or add appropriate content to the article. i) Why were only 298 large enterprises selected? ii) What are the conditions on which the 298 large enterprises were selected? iii) Most of the top ten companies are \"transport equipment\" companies. This leads to the suspicion that the reason for this result is related to the sample selection. Therefore, the authors need to add more details about the sample selection. iv) In addition, what are the limitations in sample selection?\n4. Data description issues. i) Too few descriptive statistics for the data. ii) It is recommended to add the description of data such as annual mean, annual standard deviation, and maximum and minimum values of each industry in order to have a more intuitive insight into the development trend of each industry. iii) Figure 1 and Figure 2 are not suitable.\nWe suggest the authors to dig further into the data content. For example: 1. the level of spatial distribution of the number of patents; 2. whether there is a spillover effect of technological innovation; 3. the level of green transformation in each industry, etc.\n\nIs the rationale for creating the dataset(s) clearly described? Partly\n\nAre the protocols appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and materials provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-288
https://f1000research.com/articles/13-284/v1	17 Apr 24	{ "type": "Systematic Review", "title": "Understanding rapid oral health deterioration and its associated factors among older adults: A scoping review", "authors": [ "Radhika Ranjith", "Ramya Shenoy", "Parul Dasson Bajaj", "Ashwini Rao", "Mithun Pai", "Praveen Jodalli", "Avinash BR", "Harsh Priya", "Navya Shinaj", "Violet D'Souza", "Radhika Ranjith", "Parul Dasson Bajaj", "Ashwini Rao", "Mithun Pai", "Praveen Jodalli", "Avinash BR", "Harsh Priya", "Navya Shinaj", "Violet D'Souza" ], "abstract": "Background Understanding the pivotal interplay between systemic and oral health is paramount to ensuring holistic care, particularly among the aging demographic. Therefore, this review article aims to explore the emerging concept of Rapid Oral Health Deterioration (ROHD) by reviewing the current knowledge base among older adults and identifying knowledge gaps in this area of research.\n\nMethods This scoping review was conducted in line with Arksey and O’Malley’s framework between December 2023 and March 2024 and reported while adhering to the PRISMA-ScR guidelines. A systematic database search was performed across three databases i.e. PubMed, Scopus, and EMBASE to collate the existing literature published in English between January 2013 and February 2024 addressing ROHD among older adults. After data charting, a critical appraisal of the selected studies was followed by qualitative thematic analysis.\n\nResults Among the 12 papers in this scoping review, 10 were cross-sectional studies, with one each of retrospective cohort and case-control studies. The qualitative thematic analysis of the selected articles resulted in the emergence of four main themes: risk factors for ROHD, attributes related to ROHD, challenges encountered in the management of ROHD, and management approaches for ROHD among older adults.\n\nConclusions This scoping review provides an overview of the rapid deterioration of oral health among older adults. Age-related dental disease harms the quality of life and overall health. To avoid dental disorders and to maintain and improve oral health in older adults, an integrated and multidisciplinary approach is essential. If ROHD is not treated, it may lead to poor health, a lower quality of life, and in severe cases, systemic infections that increase hospitalizations and possibly cause death.", "keywords": [ "Health and wellbeing", "clinical deterioration", "Oral health deterioration", "Aged", "Older adults" ], "content": "Introduction\n\nThe aging demographic is an enduring worldwide phenomenon, with projections indicating that by 2050, one out of every six individuals globally will be aged 65 or above, compared to one in ten in 2021.1 As individuals age, they become more vulnerable to a variety of systemic illnesses, with the older adults exhibiting a significantly higher prevalence of chronic and non-communicable diseases compared to the younger demographic.2 It is often suggested that the condition of the oral cavity reflects a person’s general health.3,4 Oral diseases, particularly periodontal disease, have been linked to various non-communicable conditions like diabetes, cardiovascular diseases, cancer, cognitive decline, among others.5,6 Therefore, recognizing the vital relationship between overall health and oral health is essential for safeguarding an individual’s overall well-being, as general health status significantly influences oral health outcomes.3\n\nAlthough the complete loss of teeth may be declining, gradual tooth loss remains a significant indicator of poor oral health in older adults with dental caries continuing to be the most prevalent oral condition among older individuals.5,6 Hence, early detection and treatment of oral health issues in older adult patients can mitigate oral health complications, particularly in those with chronic illnesses, and contribute to enhancing overall Oral Health-Related Quality of Life.7\n\nThe care needs of older individuals are diverse and intricate, which is highlighted by the emergence of medical and dental specializations that prioritize patient-centered care. Programs in geriatric dentistry specifically aim to understand the interplay between oral health conditions, socioeconomic factors, and systemic health issues in this demographic.8 Common chronic systemic disorders diagnosed in older individuals include arthritis, hypertension, diabetes, depression, neurodegenerative conditions, dementia, and stroke. Recognizing potential interactions between oral health factors and these systemic health events is crucial for addressing the poor oral health encountered in this age-group. This serves as the foundational premise of the systematic framework outlined in the Rapid Oral Health Deterioration (ROHD) concept, aiding dental professionals in assessing the probability of progressive oral health deterioration among older adult patients.6,9\n\nUnderstanding the potential the concept of ROHD holds in alleviating the oral disease burden among older adults, the aim of this scoping review was to explore the existing literature on ROHD in older adults, an area that has received relatively limited attention in research. The objective was to compile and analyze the literature while also pinpointing and comprehending the existing knowledge gaps in this realm of research.\n\n\nMethods\n\nThe time frame for this scoping review ranged between December 2023 and March 2024 following the framework outlined by Arksey and O’Malley,10 to address the research question “What is known about rapid oral health deterioration among older adults in the existing literature?” A review protocol was not registered for this scoping review, and the findings are presented in accordance with the PRISMA-ScR checklist.11\n\nThis scoping review included articles focusing on one or more facets of oral health deterioration in older adults, published in English between January 2013 and February 2024 reflecting on the heightened awareness around oral health needs of the geriatric population. Review articles, letters to editors, and other papers with missing full-text formats, such as conference proceedings, were excluded from this scoping review.\n\nA systematic search was conducted across three databases i.e. PubMed, Scopus, EMBASE, where the last search was performed in February 2024. The search strategy involved using key terms such as ‘older adults’, ‘older adults’, ‘aged’, ‘clinical deterioration’ and ‘rapid oral health deterioration’, along with Boolean operators ‘OR’ and ‘AND’. The detailed search strategy across the databases has been provided in Table 1.\n\nThe initial database search was conducted by one author (RR) using the search strategy, followed by the removal of duplicates. Title and abstract screening were independently performed by two investigators (RR and RS), with each article categorized as “Yes”, “No”, or “Maybe”. Subsequently, the articles selected during title and abstract screening underwent full-text review by the two investigators independently. Disagreements were resolved through discussion at each stage, leading to consensus. The articles which fulfilled the eligibility criteria were included in this scoping review for data extraction and critical appraisal.\n\nOne author (RR) charted the data from the selected full-text articles using a predetermined format, which was followed by random verification by another author (RS). The predetermined format encompassed the following headings: title of the study and the authors, year of publication, purpose of theoretical and conceptual orientation, research questions and/or hypothesis, sample description, methods and analysis, key measures, main findings or results, author(s) stated limitations of the study, additional limitations of the study, strength and importance of the study.\n\nThe Crowe Critical Appraisal Tool (CCAT)12 was employed to assess the quality of the available evidence and accurately identify the research gaps in the literature. CCAT enables the critical assessment of various research methodologies and evaluates each article in eight categories i.e. preliminaries, introduction, design, sampling, data collection, ethical issues, results and discussion. Each category is scored between from 0-5 and with a possibility of the maximum total score of 40. Based on the CCAT scores, articles with a score of 35 or more were labelled as high quality, scores from 25 to 34 were deemed medium quality while articles with scores less than 25 were considered as low quality.13 The critical appraisal was executed by one author (RR), with a subset of articles randomly selected for reassessment by another author (RS) to ensure accuracy.\n\nThe findings of this scoping review were synthesized through qualitative thematic analysis of each selected article. Two authors (RR and PDB) independently conducted the coding process for thematic analysis, where the appropriate segments of the selected articles pertaining to the research question on rapid oral health deterioration among older adults were identified and initially coded using Atlas.ti Mac14 (Version 23.2.1). Subsequently, both authors deliberated on the initial codes to arrive at the final codes and at this juncture, a third author (RS) joined the discussion for further refinement of the codes and through comprehensive discussion, the main themes emerging from the selected articles addressing the research question were identified and organized into main themes and subthemes for enhanced clarity and comprehension.\n\n\nResults\n\nA total of 86 articles were selected after the initial search based on title screening, of which 27 duplicates were eliminated. Subsequently, this was followed by a title and abstract screening of the remaining 59 articles, of which 39 were considered for a comprehensive full-text review. Based on the eligibility criteria, finally 12 articles were deemed suitable for inclusion in this scoping review. The selection process of the articles is illustrated in Figure 1 with a PRISMA flow diagram.15\n\nAmong the 12 papers included in this scoping review, ten were cross-sectional studies, with one each of retrospective cohort and case-control studies. These papers were mostly published within the last ten years, as per the eligibility criteria which included articles from 2013 onwards. Table 2 offers a comprehensive overview of the characteristics of the articles selected for this scoping review, along with the data extracted from these sources.\n\nCCAT was used to conduct a quality appraisal of the selected sources of evidence, and the detailed scores for each paper across all domains are presented in Table 3. According to the CCAT scores, eleven papers included in the review were deemed as medium quality, while one was labelled as low quality based on the CCAT scores.\n\nThe qualitative thematic analysis of the selected articles resulted in the emergence of four main themes namely: risk factors for ROHD, attributes related to ROHD, challenges encountered in managing ROHD and management approaches for ROHD among older adults. The details of the main and sub-themes are provided in Table 4.\n\nRisk factors for ROHD included systemic, socioeconomic factors and oral factors. Systemic factors included a wide array of systemic conditions mainly dementia, schizophrenia, and cardiovascular disorders among others. Oral factors included oral conditions such as xerostomia, hyposalivation, microbiota as well as level of oral self-care and oral frailty. Attributes related to ROHD comprised of frailty, malnutrition, oral frailty and oral conditions encountered. These attributes depicted a close linkage with one another as well as with the living conditions such as oral hygiene habits, institutionalization, edentulism, and oral health related quality of life (OHRQoL).\n\nThe next two themes were related to the challenges encountered in the management of ROHD and the potential solutions which could be implemented in the management of ROHD among older adults.\n\n\nDiscussion\n\nThis scoping review intended to examine the available evidence on the rapid deterioration of oral health in the older population, with a special emphasis on identifying the research gaps. Additionally, the findings relating to the qualitative thematic analysis shed light on potentially promising approaches which could be imbibed into everyday interprofessional medical practices to better manage ROHD among older adults, thereby enhancing OHRQoL.\n\nThere is a strong relationship between oral diseases and systemic diseases, with research demonstrating a robust connection between dental health and noncommunicable diseases such as cancer, neurodegenerative disorders, diabetes, heart disease, depression, inflammatory bowel disease, rheumatic diseases, obesity, stomach helicobacter pylori, and asthma.7 It is important to note that the prevalence of several chronic medical disorders rises with age.8\n\nDementia emerged as an important condition affecting the oral health condition among older adults in this scoping review. Poor oral hygiene in older people with dementia is caused by a number of variables, including behavioural issues, deteriorating cognitive function, degree of dementia and insufficient dental staff nursing education.19,22 Similarly, neuropsychatric disorders like schizophrenia have a significant negative effect on people’s health. These patients have poor dental hygiene, which lowers their quality of life and raises their risk of systemic illnesses.24\n\nSystemic health and oral health share a bi-directional relationship with each other as can be observed in the available evidence, where oral health also tends to adversely affect the general health of individuals. The importance of regular dental check-ups in preventing acute hospitalization occurring due to diseases like pneumonia, cerebrovascular disease and urinary tract infections, has been highlighted by a retrospective study conducted in Japan on older adults included in this review.26 The studies on diabetes and oral health has been always focused on the periodontal tissues and maintenance of glycemic control.28 This is in line with evidence which suggests that early detection and treatment of oral health issues could avert poor oral health and a reduction in OHRQoL particularly in older adult patients with chronic illnesses.7\n\nThere is a reciprocal and dynamic relationship between dental health and nutrition. Poor dental health may increase an older adult person’s risk of malnourishment or malnutrition, particularly if they are institutionalized.21,23 This further magnifies the importance of including oral health indicators in geriatric examinations.21 Evidence suggests that a risk of nutritional deficiency was substantially correlated with a negative self-perception of oral status; however, this correlation vanished when socioeconomic level, neurosensory impairments, and chronic illnesses were taken into account.18\n\nReduced stress tolerance, elevated susceptibility, and compromised functioning are all considered indicators of frailty. It raises the possibility of hospitalization, disability, falls, and death. Oral Frailty (OFr), which is defined in the literature as “weakness and fatigue of the oral muscles,” contains elements including poor oral health, impaired muscle performance, the possibility of weight loss, issues with chewing and swallowing, changes in the food’s composition, trouble speaking, and tongue or tooth pain. One of the included studies suggested that protection against OFr may come from maintaining one’s natural teeth, maintaining good oral health throughout one’s life, and preventing oral illnesses.27\n\nInstitutionalized older adults need assistance in doing oral hygiene activities17 and usage of various oral hygiene aids such as adaptive toothbrush handles, collis-curve brushes, triple-headed toothbrushes, water flossers, interdental brushes of different diameters, floss holders/single-use floss picks, and other oral hygiene products like electric toothbrushes help these people remove plaque more effectively and help with physical adaptations.6,9\n\nAmong other potential approaches to manage ROHD in older adults, the need for specific dental protocols to be followed in residential care institutions along with training for nursing staff to cater to oral health maintenance and empowering caregivers in identifying oral pain-related signs were highlighted in the included articles. In particular, attention to nutritional needs in orally frail individuals as well as providing adequate dental care against periodontal disease emerged as important approaches. Another study discussed a simple yet effective teaching tool for dental students to provide care to the geriatric population and people with special needs.20\n\nThe findings of the present review warrant more high quality research in this important area with rising geriatric population worldwide. This research also lays down potentially promising approaches, which can be researched as well as implemented with regards to the management of ROHD among aging adults.\n\n\nConclusion\n\nAge-related dental disease has a negative effect on overall health and quality of life. In order to avoid dental disorders and to maintain and improve oral health in older adults, an integrated and multidisciplinary approach is essential. If ROHD is not treated, it may lead to poor health, a lower quality of life, and in severe cases, systemic infections that increase hospitalizations and possibly cause death.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: PRISMA ScR guidelines checklist Shenoy, R. Understanding Rapid Oral Health Deterioration and its associated factors among Older Adults-A Scoping Review. figshare. Dataset. 2024 https://doi.org/10.6084/m9.figshare.25360291.v5. 29\n\n\nReferences\n\nWilmoth JR, Bas D, Mukherjee S, et al.: World social report 2023: Leaving no one behind in an ageing world. UN; 2023.\n\nPoudel P, Paudel G, Acharya R, et al.: Oral health and healthy ageing: a scoping review. BMC Geriatr. 2024 Jan 8; 24(1): 33. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMüller F, Shimazaki Y, Kahabuka F, et al.: Oral health for an ageing population: the importance of a natural dentition in older adults. Int. Dent. J. 2017 Oct; 67: 7–13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBotelho J, Mascarenhas P, Viana J, et al.: An umbrella review of the evidence linking oral health and systemic noncommunicable diseases. Nat. Commun. 2022 Dec 9; 13(1): 7614. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMurray TW: Epidemiology of oral health conditions in older people. Gerodontology. 2014 Feb; 31: 9–16. Publisher Full Text\n\nDesai JP, Nair RU: Oral health factors related to rapid oral health deterioration among older adults: a narrative review. J. Clin. Med. 2023 Apr 29; 12(9): 3202. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nvan der Putten G-J , de Baat C : An Overview of Systemic Health Factors Related to Rapid Oral Health Deterioration among Older People. J. Clin. Med. 2023; 12(13). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarchini L, Ettinger RL: The Prevention, Diagnosis, and Treatment of Rapid Oral Health Deterioration (ROHD) among Older Adults. J. Clin. Med. 2023; 12(7). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSlack-Smith L, Arena G, See L: Rapid Oral Health Deterioration in Older People—A Narrative Review from a Socio-Economic Perspective. J. Clin. Med. 2023; 12(6). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArksey H, O’Malley L: Scoping studies: towards a methodological framework. Int. J. Soc. Res. Methodol. 2005; 8(1): 19–32. Publisher Full Text\n\nPRISMA: PRISMA-ScR: Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews.2018. [Accessed on 22 January 2024]. Reference Source\n\nCrowe M, Sheppard L, Campbell A: Reliability analysis for a proposed critical appraisal tool demonstrated value for diverse research designs. J. Clin. Epidemiol. 2012; 65(4): 375–383. PubMed Abstract \| Publisher Full Text\n\nDasson Bajaj P, Shenoy R, Davda LS, et al.: A scoping review exploring oral health inequalities in India: a call for action to reform policy, practice and research. Int. J. Equity Health. 2023 Nov 21; 22(1): 242. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nATLAS: ti Scientific Software Development GmbH. ATLAS.ti Mac. V. 23.2.1. ATLAS.ti Scientific Software Development GmbH. Mac.2023.\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. Int. J. Surg. 2021; 372: 105906. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen X, Clark JJ, Preisser JS, et al.: Dental caries in older adults in the last year of life. J. Am. Geriatr. Soc. 2013 Aug; 61(8): 1345–1350. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaarela RK, Soini H, Muurinen S, et al.: Oral hygiene and associated factors among frail older assisted living residents. Spec. Care Dentist. 2013 Mar; 33(2): 56–61. PubMed Abstract \| Publisher Full Text\n\nEl Hélou M, Boulos C, Adib SM, et al.: Relationship between oral health and nutritional status in the older adults: A pilot study in Lebanon. J. Clin. Gerontol. Geriatr. 2014 Sep 1; 5(3): 91–95. Publisher Full Text\n\nLauritano D, Moreo G, Carinci F, et al.: Aging and oral care: an observational study of characteristics and prevalence of oral diseases in an Italian cohort. Int. J. Environ. Res. Public Health. 2019 Oct; 16(19): 3763. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCraig T, Johnsen DC, Hartshorn JE, et al.: Teaching rapid oral health deterioration risk assessment: A 5-year report. J. Dent. Educ. 2020 Oct; 84(10): 1159–1165. PubMed Abstract \| Publisher Full Text\n\nHakeem FF, Bernabé E, Sabbah W: Association between oral health and frailty among American older adults. J. Am. Med. Dir. Assoc. 2021 Mar 1; 22(3): 559–563.e2. PubMed Abstract \| Publisher Full Text\n\nLopez-Jornet P, Zamora Lavella C, Pons-Fuster Lopez E, et al.: Oral health status in older people with dementia: A case-control study. J. Clin. Med. 2021 Jan 27; 10(3): 477. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmalz G, Denkler CR, Kottmann T, et al.: Oral health-related quality of life, oral conditions, and risk of malnutrition in older German people in need of care—A cross-sectional study. J. Clin. Med. 2021 Jan 22; 10(3): 426. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang M, Li Q, Deng C, et al.: Prevalence and clinical correlation of decayed, missing, and filled teeth in older adults inpatients with schizophrenia. Front. Psych. 2021 Sep 14; 12: 728971. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDevika AB, Shenoy R, Avinash BR, et al.: Oral health and nutritional assessment among older adults -An explorative study. Scope. 2023 Jun 2; 13(2): 417–425.\n\nMitsutake S, Ishizaki T, Edahiro A, et al.: The effects of dental visits on the occurrence of acute hospitalization for systemic diseases among patients aged 75 years or older: A propensity score-matched study. Arch. Gerontol. Geriatr. 2023 Apr 1; 107: 104876. PubMed Abstract \| Publisher Full Text\n\nJulkunen L, Saarela R, Roitto HM, et al.: Oral frailty among dentate and edentate older adults in long-term care. BMC Geriatr. 2024 Jan 11; 24(1): 48. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLin BP, Taylor GW, Allen DJ, et al.: Dental caries in older adults with diabetes mellitus. Special care in dentistry: official publication of the American Association of Hospital Dentists, the Academy of Dentistry for the Handicapped, and the American Society for Geriatric Dentistry. 1999 Jan 1; 19(1): 8–14. Publisher Full Text\n\nShenoy R: Understanding Rapid Oral Health Deterioration and its associated factors among Older Adults-A Scoping Review. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "271999", "date": "28 May 2024", "name": "Tarakant Bhagat", "expertise": [ "Reviewer Expertise Dentistry", "oral health", "geriatric health", "dental caries", "oral cancer" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study explores a compelling case of sharp decline in oral health in geriatric populations because of the complex interplay between systemic and oral health. Congratulations to the authors for their intriguing work! We feel there are few facets in this research that can be framed in a finer way.\nOne of the objective is to identify knowledge gaps in research. This could have been discussed further in the report. Under information sources and search strategy in the Methods section, it appears as if keywords have been repeated. ( ‘older adults’, ‘older adults’) Specifying the limitations of the scoping review process may be considered.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [] }, { "id": "272000", "date": "31 May 2024", "name": "Rohit Nair", "expertise": [ "Reviewer Expertise Geriatric Dentistry", "Dentistry for Adults with Special Health Care Needs" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAs a clinical concept, Rapid Oral Health Deterioration (ROHD) is tangible but difficult to define. What constitutes \"deterioration\" and the time frame for such change can vary from person to person but it can be agreed that oral disease negatively impacts the frail older adult's quality of life. It is imperative to address dental caries, periodontal disease as needs arise to avoid undesired sequelae. In this article, Ranjith and colleagues provide a detailed review of emerging thought about oral health deterioration seen in medically frail older adults. Their approach seems to be methodologically robust and reproducible, and care has been taken at every step to ensure inclusion of the best available literature that pertains to their specific topic of interest. Table 4 neatly summarizes the key themes that one might encounter when dealing with patients who are either at risk for, are experiencing or have experienced ROHD.\nAlthough we may accept a general association between oral and systemic disease as proposed here, the issue is a rather complex one. As suggested by Philstrom et al, it is sufficient to promote good oral health as a benefit in and of itself rather than because it carries a specific systemic health benefit [Ref-1]. The current article might present a more balanced view if it referenced controversies in this area and the limitations inherent in studying associations between oral and systemic health.\n\nOverall, a very good report .\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-284
https://f1000research.com/articles/13-283/v1	17 Apr 24	{ "type": "Review", "title": "Theranostics-enabling high-tech centers: the value of centralizing resources in countries in development", "authors": [ "Pascal Kahlem", "Pau Berenger-Molins", "Hakan Akbulut", "Pau Berenger-Molins", "Hakan Akbulut" ], "abstract": "Theranostics is a rapidly advancing field that is driving significant advancements in the healthcare industry by providing individualized medical solutions. Demand for theranostics is increasing over time and has led to the creation of theranostics-enabling high-tech technological centers. This review investigated the potential advantages and drawbacks of consolidating theranostics resources within technologically advanced facilities, particularly in developing nations, and led to three main observations: 1) The centralization of theranostics resources can lead to improved research, cost efficiency, and quality of healthcare services; 2) Developing countries may encounter hurdles such as resource allocation, infrastructure development, and skill acquisition, but these risks can be mitigated; 3) High-tech centers can play a major role in fostering innovation and advancing theranostics industry in these countries. In conclusion, this paper provides insights into the potential of high-tech centers as a pivotal point in the evolution of healthcare in developing countries. It calls for more funding support, in-depth research and collaborative efforts to overcome the challenges and harness the full potential of theranostics, as it has already occurred in some countries.", "keywords": [ "Theranostics", "healthcare", "personalized medicine", "diagnostics", "therapeutics", "high-tech centers" ], "content": "1. Theranostics: rapprochement of diagnostics and therapeutics for personalized medicine\n\nThroughout history, the approach to medicine has been typically generalized. However, with the advent of theranostics, healthcare has ventured into an era of personalized medicine that caters to the unique needs of every individual. This shift in medical philosophy and practice has been gradual and guided by several key developments (Table 1).\n\n1. Primitive medicine: The earliest form of healthcare was largely symptom-based and generalized, with rudimentary treatments applied broadly to all patients exhibiting similar symptoms.\n\n2. Emergence of diagnostics: The advent of diagnostic tools and technologies allowed for the identification and differentiation of diseases, making a case for more specific treatment approaches.\n\n3. Biological understanding: As our understanding of human biology improved through discoveries such as DNA, genes, and the human genome, scientists and physicians began to appreciate the vast biological variations between individuals. This fueled the drive toward personalized medicine.\n\n4. Theranostics: The fusion of diagnostics and therapeutics into an integrated approach, known as theranostics, is the latest milestone in this evolution. It allows to tailor treatments for individual patients based on their unique biological characteristics, paving the way for personalized medicine. The advent and subsequent generalization of the use of artificial intelligence (AI) will certainly accelerate the implementation and advancement of theranostics.\n\nThe shift towards personalized medicine, powered by theranostics, is not just an evolution in healthcare but a revolution. It is a paradigm shift that promises to transform the way we diagnose and treat diseases, ultimately leading to better patient outcomes and a healthier world.\n\nWith its traditional meaning, the term theranostics pairs diagnostic biomarkers with therapeutic agents to diagnose and treat cancer. The most common use of the term covers only the application of radiopharmaceuticals in diagnosing and treating cancer patients. However, in the modern era of cancer treatment, this definition could encompass much more than this traditional definition. Especially in the era of targeted therapy for cancer, the personalized approach has gained significant importance about improving both the clinical efficacy and cost-effectiveness of the treatments and decreasing the side effects. Therefore, the combination of diagnostic approaches providing predictive and prognostic value with therapeutic strategies could be included within the scope of theranostics. Accordingly, theranostics could be further expanded to include developing diagnostic tools and treatment strategies under the same production roof. The term theranostics can be defined as the development and use of therapeutic agents based on diagnostic tools (Choudhury & Gupta, 2018; Herrmann et al., 2022; Seifert et al., 2021; Yin et al., 2022; Zahiri et al., 2021).\n\nAt its core, theranostics is guided by the fundamental idea that each patient’s disease profile is distinct, demanding a targeted and customized approach. The primary components of theranostics include (Figure 1):\n\n1. Diagnostics: The diagnostic aspect of theranostics involves identifying biomarkers, molecular signatures, and other indicators that can provide insights into a patient’s disease condition. These markers can be detected using advanced imaging techniques, molecular profiling, genetic analysis, and other diagnostic tools.\n\n2. Patient stratification/Personalized Medicine: The overarching goal of theranostics is to achieve personalized medicine, an approach that recognizes the uniqueness of each patient’s medical condition. By applying theranostic principles, medical practitioners can avoid a “one-size-fits-all” approach and, instead, offer interventions optimized for the patient’s genetic makeup, disease progression, and treatment responses. By comprehensively analyzing a patient’s biological characteristics, healthcare providers gain a deeper understanding of the underlying disease processes and stratify patients accordingly.\n\n3. Specific Therapeutics: Based on the diagnostic information, therapeutics encompass treatment strategies that are precisely tailored to the individual patient. This involves selecting the most suitable therapeutic agents for patient groups or individuals, drug delivery methods, and treatment regimens based on the patient’s disease characteristics. Theranostics enables the administration of targeted therapies that are more effective with fewer side effects by exploiting the information obtained through diagnostics.\n\nThe figure illustrates the main components of theranostics, including: 1) diagnostic, which focuses on the identification of biomarkers, molecular signatures and other indicators using advanced tools that provide crucial insights into the patient’s disease; 2) patient stratification and personalized medicine through the previous diagnostics, allowing interventions tailored to the patient’s genetic makeup, disease progression and treatment response; and 3) specific therapeutics for individual patients or groups drawn from diagnostics information, which includes selecting suitable agents and delivery methods, and designing specific treatment regimes, minimizing side effects.\n\nTheranostics has yielded remarkable advances in various medical domains, including oncology, cardiovascular diseases, neurology, and infectious diseases. In oncology, for instance, theranostics enables the identification of specific tumor markers that guide the selection of targeted therapies and monitor treatment response (Altena et al., 2023; Buck et al., 2022; Lecocq et al., 2019). Similarly, in cardiovascular diseases, molecular imaging techniques assist in detecting early-stage arterial plaques, enabling timely intervention and treatment (Zan et al., 2023).\n\nNotably, both medical practitioners and patients are experiencing remarkable outcomes with the application of theranostics in the context of prostate cancer (O’Dwyer et al., 2021; Plichta et al., 2021). This form of cancer poses significant challenges when diagnosed at an advanced stage, contributing to an annual toll of over 1.4 million lives, according to the World Health Organisation. Furthermore, theranostics extends its benefits to various clinical scenarios, encompassing the management of bone metastases originating from prostate cancer, neuroendocrine tumors, non-Hodgkin lymphoma, and adrenergic tumors (Ballinger, 2018). Moreover, its well-established role in addressing hyperthyroidism and thyroid cancer (Gomes Marin et al., 2020) underscores its versatility. Besides the above-mentioned traditional examples of theranostics, genomics, and molecular-based diagnostics, they have also fueled targeted drugs such as tyrosine kinase inhibitors and immunotherapeutic agents (Smidova et al., 2021; Xu et al., 2022). While the potential for theranostics to expand into novel realms of care is substantial in the near future, the extent of this expansion will inevitably hinge on the pace of drug development and the necessary regulatory clearances (Perera & Morris, 2022).\n\nIntegrating theranostics into infectious disease management, especially in the context of viral infections, is an evolving area of research and practice. There are indications that theranostics could offer valuable insights into managing viral infections (Gholami et al., 2023), with a notable emphasis on viral outbreaks (Itani et al., 2020).\n\nOne of the most prominent examples lies in the realm of antiviral therapies. Consider the case of Hepatitis C, a viral infection that affects millions globally, according to the World Health Organisation. Theranostics has been explored to guide treatment decisions by identifying specific genetic markers within the virus. This information helps tailoring antiviral therapies to the patient’s viral strain, thereby increasing treatment efficacy while minimizing side effects (Coppola et al., 2015).\n\nIn addition, the application of systems medicine within theranostics offers a unique avenue for understanding the complex interactions between viruses and their host organisms. In the face of viral outbreaks, such as the Zika virus, systems medicine takes a holistic approach, considering not only the virus itself but also the individual’s immune response, genetic factors, and environmental influences (Ferraris et al., 2021; Fuller et al., 2017; Giraldo et al., 2023). By integrating vast amounts of data, this approach can predict disease progression, identify potential treatment targets, and ultimately contribute to more effective interventions (Abrams et al., 2017; Alam et al., 2021).\n\nHowever, it is essential to acknowledge the challenges and uncertainties of applying theranostics to viral infections. Viruses are notorious for their rapid mutation rates, which can impact the accuracy of diagnostic markers and the effectiveness of targeted therapies (Pawlotsky, 2014; Thompson & McHutchison, 2009). As such, the use of theranostics in this context requires ongoing research and adaptation to keep up with evolving viral strains.\n\nFurthermore, regulatory considerations and the pace of drug development play a crucial role in determining the extent to which theranostics can be integrated into viral infection management. Regulatory agencies need to evaluate the safety and efficacy of theranostics-based approaches before they can be widely adopted (Herrmann et al., 2022; Perera & Morris, 2022).\n\nIn conclusion, while there are instances where theranostics has shown promise in managing viral infections, its full integration into this field is a complex and evolving process. The success of such endeavors requires a multidisciplinary approach, collaboration between researchers and healthcare practitioners, and a continuous effort to adapt to the dynamic nature of viral infections.\n\nOverall, theranostics represents a paradigm shift in medicine, departing from generalized treatment approaches toward personalized care. It capitalizes on the synergy between diagnostics and therapeutics, providing medical professionals with a comprehensive toolkit to combat diseases more effectively while minimizing adverse effects. As technologies continue to evolve, theranostics holds the promise of transforming healthcare by offering patients treatments tailored to their individual needs, fostering better patient outcomes, and enhancing the quality of life.\n\n\n2. Demand for theranostics-enabling high-tech technological infrastructures\n\nThe healthcare sector is currently witnessing an important increase in demand for both theranostics infrastructures, according to the Society of Nuclear Medicine & Molecular Imaging and best practices (Herrmann et al., 2022).\n\nThe establishment of high-tech technological infrastructures dedicated to offering biotechnological services for Small and Medium Enterprises (SMEs) to develop products in the realm of theranostics marks a significant advancement at the intersection of biotechnology, healthcare, and entrepreneurship. These specialized infrastructures serve as pivotal hubs where innovation, scientific expertise, and collaborative efforts converge to drive the development of cutting-edge theranostics solutions.\n\nAs SMEs play an increasingly vital role in technological advancements, these centers provide an environment tailored to their needs, fostering growth and innovation in the field of theranostics. By offering access to state-of-the-art infrastructure, expertise from multidisciplinary teams, and a platform for collaboration, these centers empower SMEs to bring their ideas from concept to market reality.\n\nBenefits of such high-tech infrastructures include:\n\n1. Collaboration and Networking: SMEs can collaborate with experts, researchers, and other businesses in a conducive environment, leading to cross-pollination of ideas and innovative solutions.\n\n2. Access to high-tech Infrastructure: Many SMEs might not have advanced equipment and facilities. High-tech centers provide access to state-of-the-art biotechnology infrastructures for research and development.\n\n3. Reduced Costs and Risks: Developing theranostics products can be expensive and risky. Centers can help SMEs navigate regulatory hurdles, reduce costs through shared resources, and accelerate product development.\n\n4. Expertise and Support: Centers often have a team of experienced scientists, clinicians and entrepreneurs who can offer SMEs guidance, mentorship, and technical support. Accordingly, along with the experts, the high-tech infrastructure might serve as R&D partners of the pharma industry. Likewise, these centers’ accredited lab services might accelerate the local recruitment of patients to the clinical trials of investigational new drugs.\n\n5. Accelerated Innovation: The collaborative and focused environment of these centers can lead to quicker innovation and product commercialization.\n\n\n3. Examples of theranostics-enabling infrastructures in high-income countries\n\nIn recent years, a remarkable trend has been shaping the landscape of healthcare innovation across the globe – the emergence of theranostics-enabling high-tech technological centers. These centers represent a convergence of cutting-edge technology, medical expertise, and innovative thinking, all aimed at revolutionizing the way diseases are diagnosed and treated. Here, we delve into four successful examples of centers, showcasing their impact on healthcare and their contribution to advancing the field of theranostics. These centers demonstrate a range of resource management strategies, with some focusing on resource centralization within their premises while others emphasize collaboration locally and internationally. The combination of these approaches contributes to the advancement of theranostics, propelling the field of personalized medicine forward.\n\nSituated within the renowned Johns Hopkins University, the Theranostics Center is a prime example of resource centralization that offers personalized cancer diagnostics and therapies. This center boasts state-of-the-art imaging facilities, molecular analysis laboratories, and a comprehensive clinical setup. By centralizing these resources, it facilitates seamless interaction between researchers, clinicians, and engineers. The center’s multidisciplinary approach fosters collaboration, allowing experts from various fields to collectively develop and refine theranostics-based solutions. This center has propelled groundbreaking research in precision medicine, with teams of experts collaborating to develop targeted therapies based on individual patients’ molecular profiles. By utilizing state-of-the-art imaging technologies and advanced treatment modalities, they have achieved remarkable outcomes in cancer treatment - especially prostate cancer - and neurodegenerative disorders (Beik et al., 2021; Solnes et al., 2020; Zhang et al., 2005).\n\nSweden’s Karolinska Institute, known for awarding the Nobel Prize in Physiology or Medicine, has established the Karolinska Theranostics Center as a beacon of innovation. Within the Karolinska Institute, collaboration between clinicians, researchers, and industry partners is paramount. While the center centralizes advanced imaging technologies, it also thrives on collaborations with neighboring research institutions and hospitals. This approach capitalizes on each entity’s strengths, enabling the center to tackle complex challenges through shared expertise and resources. This center focuses on leveraging nanotechnology and molecular imaging to enable early disease detection and personalized treatment plans. Their successful endeavors include developing nanoparticle-based drug delivery systems for cancer therapy and non-invasive imaging techniques for neurological disorders (Altena et al., 2023; Porsch et al., 2013).\n\nGustave Roussy Cancer Campus exemplifies a collaborative theranostics ecosystem centered around patient care. As Europe’s largest cancer center, it unites diverse medical disciplines, researchers, and technology experts. By centralizing expertise and integrating patient data, the campus creates a collaborative environment that tailors theranostics solutions to individual needs. This approach showcases how resource centralization and interdisciplinary collaboration can synergize for better patient outcomes, specifically in cancer treatment (Petranović Ovčariček et al., 2023; Seban et al., 2019).\n\nSeoul National University Theranostics Center underscores the pivotal role that international collaboration plays in advancing healthcare. This center brings together experts from diverse fields, including medicine, engineering, and material science, to develop innovative theranostics solutions. While it centralizes facilities, its strength lies in global partnerships. Collaborations with research institutions, industries, and academic entities worldwide foster a dynamic ecosystem where knowledge exchange and shared resources drive theranostics breakthroughs. Their achievements range from early cancer detection using molecular imaging to the creation of smart nanoparticles for precision drug delivery (Jung et al., 2022; Oh et al., 2023).\n\nThese examples underscore the global momentum behind theranostics-enabling high-tech technological centers. By fostering interdisciplinary collaboration, investing in cutting-edge technologies, and prioritizing personalized approaches to healthcare, these centers are paving the way for a future where diseases are detected earlier, treatments are more effective, and patient outcomes are improved. As they continue to push the boundaries of innovation, their collective efforts promise to reshape the landscape of modern medicine and offer new hope to patients worldwide.\n\n\n4. Establishing theranostics-enabling high-tech centers in countries undergoing development\n\nAs one navigates the complex landscape of development in many parts of the world, it is imperative to recognize the numerous challenges these countries face. The spectrum of issues is vast, encompassing economic, social, and technological dimensions, according to United Nations (United Nations, 2018). In particular, developing countries face a plethora of challenges when it comes to accessing quality health care. These issues revolve around infrastructure, quality of health services, expertise availability, affordability, and geographical reach. Let’s explore these challenges and how the centralization of resources can significantly mitigate them.\n\nInfrastructure\n\nLack of adequate infrastructure in these countries often inhibits efficient healthcare delivery concerning personalized medicine. Essential facilities like well-equipped hospitals are often lacking, and the existing ones need to be improved to handle the needs of the population.\n\n• Mitigation strategy: By centralizing resources into high-tech centers, countries can optimize resource utilization. The establishment of such centers ensures the availability of state-of-the-art infrastructure necessary for advanced health care delivery.\n\nQuality of health services\n\nThe quality of health services often suffers in developing countries given the constraints such as the lack of appropriate equipment, the lack of standardization in services, and the reduced availability of specialized care.\n\n• Mitigation strategy: Centralizing resources in high-tech centers can lead to standardization and interoperation of healthcare services, access to advanced diagnostic and treatment options, and evidence-based patient care management. This approach helps to elevate the quality of healthcare services provided.\n\nExpertise availability\n\nA significant impediment to healthcare in developing countries is the shortage of skilled healthcare professionals and experts in various medical disciplines.\n\n• Mitigation strategy: The centralized centers can attract rare expert personnel from around the world. These professionals bring with them their extensive knowledge and expertise which significantly enhances the quality of care provided in these centers.\n\nAffordability\n\nHigh costs related to health services are a major deterrent for many individuals in developing countries.\n\n• Mitigation strategy: Centralization of resources can lead to cost optimization, ensuring affordability of medical services for a larger part of the population. High-tech centers can achieve economies of scale by serving large volumes of patients.\n\nGeographical reach\n\nIn many developing countries, healthcare facilities are often concentrated in urban areas, rendering it inaccessible to a significant portion of the population residing in remote and rural areas.\n\n• Mitigation strategy: Centralized, high-tech healthcare facilities can function as hubs in a hub-and-spoke model of healthcare delivery. Using telemedicine and mobile clinics, they could extend their services to remote or rural areas, thus increasing their geographical reach.\n\nIn summary, centralizing resources into high-tech centers addresses several key challenges in healthcare delivery in developing countries, making advanced and quality care more accessible and affordable for their population. The benefits of centralizing resources at the national level range from enhancing healthcare delivery to fostering research and development. Here are some of the many benefits:\n\n• Economic growth: Centralizing resources can stimulate the economy by creating job opportunities and increasing the country’s GDP.\n\n• Research and development: High-tech centers can foster an environment conducive to innovative research and development, leading to the creation of novel diagnostic and therapeutic products.\n\n• Improved healthcare: With the development of advanced theranostics products, the quality of healthcare services can significantly improve.\n\n• International recognition: Centralization can put the developing country on the global map as a hub for theranostics development.\n\nFigure 2 provides a visual representation of the impact of implementing resource centralization for the availability of theranostics in developing countries.\n\nIn this graphical abstract, a sequence of consecutive steps is presented on the left, with their immediate short and long-term impact depicted on the right. These steps encompass: 1) identify resources for the creation of a resource allocation plan in the short-term and for the improvement of resource management in the long-term; 2) invest in high-tech centers, which in the short-term leads to job creation and economy stimulation, and in the long-term provides a sustainable economic growth; 3) foster research and development drive innovation in theranostics products in the short-term and improves the healthcare delivery in the long-term; and 4) establish international collaborators results in gaining global recognition in the short-term and increasing the international investments in the long-term.\n\nWhile the centralization of resources in countries in development can indeed pose certain challenges, it is important to understand that these potential risks are far outweighed by the numerous benefits. A major concern often voiced revolves around the potential for unequal distribution of resources. However, these risks can be mitigated through thoughtful planning and effective management.\n\nIn the context of centralizing resources, it is crucial to ensure that the benefits are evenly distributed and accessible to all regions within the given country. Without careful oversight, there is a risk that certain areas may be left underserved. This could potentially exacerbate existing inequalities, with more affluent or urban regions having better access to these high-tech centers than rural or impoverished areas.\n\nWhile centralizing resources does have its advantages, it is also vital for policymakers and decision-makers to address the potential pitfalls to effectively streamline the development of theranostics technologies. Here, we share several strategies that can be implemented to mitigate the associated risks.\n\n1. Risk diversification: Centralizing resources in underdeveloped countries can be an innovative approach to diversifying risk. By investing in the development of diagnostic and therapeutic products in such areas, nations can not only boost their healthcare capacities, but also strengthen economic resilience. This shift in focus can help to mitigate the impacts of geographical and economic instabilities, contributing to the overall fortification of global healthcare systems.\n\n2. Regulatory oversight and transparency: In the context of theranostics, centralizing resources in countries under development necessitates a requisite level of regulatory oversight and transparency. This is essential not only to uphold the ethical integrity of the healthcare sector but also to ensure that the funding and resources allocated to these high-tech centers attain their intended objectives. While regulatory frameworks may differ across regions, harmonizing these systems can facilitate the sharing of resources and knowledge to yield benefits that surpass geographical boundaries. Unified regulations not only contribute to the better coordination of resources, but they also foster a climate of accountability and transparency. The nurturing of such an environment lies at the very heart of the successful implementation of theranostics in any healthcare system. Hence, it is crucial for decision-makers to recognize the inherent value of regulatory oversight and assign due importance to transparency when centralizing resources within their countries.\n\n3. Strong infrastructure and logistics: Crucial for successful theranostics-based centers, they include advanced research and production labs, training institutes, supply chains and distribution networks. Centralizing these can improve efficiency, reduce costs, and spur innovation. It can also increase the accessibility of theranostics to all citizens, fostering equality in healthcare. Centralized infrastructure and logistics are key to furthering theranostics, especially in developing countries. Legislators should consider centralization as it holds potential for significant healthcare growth. Its scalability, accessibility and quality can have extensive global health impacts.\n\n4. Capacity building: Ensuring successful implementation of theranostics heavily relies on targeted and comprehensive training and development. Promoting the centralization of resources allows for a significantly condensed and effective training program. By congregating all necessary assets within a single location, the required skill set for developing advanced therapeutic and diagnostic products can be disseminated more efficiently. A well-trained team is the true backbone of any high-tech center.\n\n5. Mitigation plans: Mitigation plans must comprise holistic measures that ensure the centralization of resources for theranostics in countries under development. The key to this is establishing partnerships with global health organizations, local governments, and private sector stakeholders. These alliances can facilitate the transfer of technology, skill-building, and the creation of conducive market environments for diagnostic and therapeutic product development.\n\nIn conclusion, centralizing resources in developing countries for theranostics development can bring significant economic and health advantages. Over and above these points, centralization also presents an opportunity for capacity building within developing countries. High-tech centers can serve as hubs of innovation and learning, fostering the growth of local talent and driving economic development. It is an opportunity that developing nations should seize to foster growth and improve the quality of life for their citizens.\n\nThe establishment of high-tech centers aimed at enabling theranostics in developing nations offers crucial benefits that extend beyond the realm of technological advancement. The potential of theranostics is vast, promising not only significant healthcare enhancements but also substantial societal and economic gains. Below are ten reasons why these centers warrant serious consideration:\n\n1. Technological advancement: The creation of high-tech centers fosters an environment conducive to the adoption and further development of cutting-edge technologies. This can pave the way for breakthroughs in medical devices, diagnostic tools, imaging methods, and treatment avenues, thereby catalyzing the evolution of the healthcare sector.\n\n2. Economic growth: SMEs act as pillars of economic growth and job creation in numerous countries. By directing their focus towards theranostics, these centers can invigorate economic movements, attract investment interest, and create job opportunities, resulting in an uptick in regional prosperity.\n\n3. Healthcare improvement: The advent of theranostics products could herald a healthcare revolution through the enablement of personalized medicine. This approach allows treatments to be custom-fit to individual patients, leading to more targeted and effective therapies, reduction in side effects, and improvement in patient outcomes.\n\n4. Disease management: By amalgamating diagnostics and therapeutics, early disease detection and monitoring can become a reality. This is an essential factor for effective disease management, particularly in regions where healthcare infrastructure might be lacking. Theranostics centers can aid in identifying health issues at an early stage, allowing for prompt interventions.\n\n5. Research and innovation: High-tech centers can cultivate a collaborative atmosphere that stimulates research and innovation. By providing a platform for SMEs, researchers, and academic institutions to work in harmony, these centers can drive the creation of groundbreaking solutions, propelling scientific advancements and placing the country firmly on the global innovation stage.\n\n6. Capacity building: The development of theranostics expertise necessitates the acquisition of specialized skills and knowledge. As such, these centers can double as educational hubs, offering opportunities for education and skill development to the local talent pool. This not only aids the expansion of the healthcare sector but also addresses the issue of unemployment by creating a highly skilled workforce.\n\n7. Healthcare access: Access to advanced medical treatments and diagnostics is often limited in many developing countries. The establishment of theranostics-focused centers can bridge this gap by promoting the creation of cost-effective, locally produced solutions, thereby making quality healthcare more accessible to a wider demographic.\n\n8. Global competitiveness: A developing country can establish itself as a global contender in healthcare innovation by investing in high-tech theranostics centers. This can catalyze international collaborations, create opportunities for exports, and enhance the country’s standing within the international scientific and medical community.\n\n9. Reduced dependence on imports: Many developing countries depend heavily on the import of advanced medical technologies. By establishing local capabilities for the development of theranostics products, this dependence on imports can be reduced, leading to cost savings and increased control over the healthcare infrastructure.\n\n10. Public health impact: The integration of diagnostics and therapy can lead to improved disease management and prevention strategies. This has a direct impact on public health, lessening the burden of diseases, and improving overall wellbeing.\n\nIn sum, the establishment of high-tech technological centers for SMEs to develop theranostics products in developing countries can catalyze economic growth, healthcare advancement, and innovation. These efforts align with broader goals of enhancing healthcare access, boosting local economies, and positioning the country as a frontrunner in scientific and medical innovation leader.\n\nAs decision-makers, it is crucial to understand the immense potential that centralizing resources in developing countries brings. This strategy can not only boost the economy but also enhance the infrastructure for the development of diagnostic and therapeutic products, known as Theranostics.\n\nThe Theranostics Revolution in India\n\nIndia stands as a shining example of how resource centralization has magnified their capabilities in the theranostics sector. In the past decade, India has made remarkable strides in the field of theranostics, courtesy of their concerted efforts towards centralizing resources.\n\nIndia’s Biotech Consortium India Limited (BCIL) is a prime example of this model. BCIL was established by the government as an entity to aid in the centralization of resources and to foster collaboration among various stakeholders. This initiative has enabled the development and production of diagnostic and therapeutic products at a fraction of the time and cost.\n\nWith resource centralization, we have been able to pool our best minds, cutting-edge technology, and financial resources together. This collective effort has helped us make significant advancements in theranostics, bringing better healthcare solutions to our people.\n\n- CEO, Biotech Consortium India Limited\n\nThe Chilean model of centralized innovation\n\nChile has been at the forefront of technological innovation in South America, thanks to its robust policy of pooling resources.\n\nThe government’s establishment of The Chilean Economic Development Agency (CORFO) has played a pivotal role in this success story. CORFO has been aiding in the consolidation and distribution of resources to high-tech centers, paving the way for cutting-edge theranostics solutions.\n\nAs a result, Chile has seen a surge in its innovation and technological prowess, significantly improving its healthcare system and making strides in achieving sustainable development goals.\n\nSouth Africa’s Leap into theranostics\n\nSouth Africa sets a precedent with its successful implementation of centralized resources in the theranostics sector. The country’s Department of Science and Innovation (DSI) has been instrumental in this regard.\n\nDSI, through its National System of Innovation (NSI), has fostered the centralization of resources, enabling the development and implementation of theranostics solutions. This move has not only led to significant advancements in healthcare but has also created numerous job opportunities, bolstering the country’s economy.\n\nThese three examples serve to underline the fact that resource centralization is no longer a luxury but a necessity for developing countries aiming to make significant strides in the theranostics sector. It’s a blueprint for success that can empower nations to transform their healthcare systems and significantly enhance their global standing in the high-tech industry.\n\n\n5. Conclusion: A call to action for policymakers and decision makers\n\nIt is crucial to underscore the pressing need for the implementation of centralization policies for resources, particularly in the sphere of theranostics. Harnessing the potential of theranostics in developing countries requires an intricate process that involves financial, structural, and educational components.\n\nFor this reason, we call upon policymakers and decision-makers, to take decisive action. With their commitment, the vision of transforming healthcare systems and uplifting economies in developing countries can be actualized. The process may be challenging, but the potential rewards are enormous.\n\n• Financial commitment: Governmental bodies must invest significantly in infrastructural development, such as state-of-the-art theranostics centers. This calls for strategic budgeting and the allocation of resources.\n\n• Structural development: The establishment of theranostics centers requires careful planning and execution. This includes site selection, construction, equipment procurement, and the training of skilled personnel.\n\n• Legal incentives: Governments should provide supportive legal incentives, especially for the industry and SMEs to cluster around these theranostics centers.\n\n• Educational initiatives: There is a need for comprehensive educational programs to generate a workforce that is proficient in theranostics. This involves collaborations with universities, hospitals, and research institutions.\n\nAs demonstrated by the success stories of India, Chile, and South Africa, the centralization of resources can catapult a nation on the path of progress. By investing in theranostics, countries can improve the quality of life for their citizens and concurrently stimulate economic growth. The role of theranostics in healthcare cannot be underestimated - its potential to revolutionize diagnostics and treatment is unparalleled.\n\nTherefore, we can no longer afford to sidestep this pressing issue. The successful integration of theranostics into the healthcare system of developing countries hinges on the decisive actions of policymakers and decision-makers. Let us not shirk this responsibility, rather, let us embrace it with determination and courage. By attacking the root of the problem - the lack of resources - we can unlock the full potential of theranostics in these nations.\n\nIn conclusion, we urge policymakers and decision-makers to consider the overwhelming evidence presented in this discourse. The centralization of resources for theranostics in developing countries is not just an option - it is a necessity. By taking action now, we can shape a future where health inequities are a thing of the past and every citizen has access to cutting-edge medical treatments.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAbrams RPM, Solis J, Nath A: Therapeutic Approaches for Zika Virus Infection of the Nervous System. Neurotherapeutics. 2017; 14(4): 1027–1048. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlam MA, Hasan MR, Anzar N, et al.: Diagnostic approaches for the rapid detection of Zika virus–A review. Process Biochem. 2021; 101: 156–168. Publisher Full Text\n\nAltena R, Tzortzakakis A, Af Burén S, et al.: Current status of contemporary diagnostic radiotracers in the management of breast cancer: First steps toward theranostic applications. EJNMMI Res. 2023; 13: 43. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBallinger JR: Theranostic radiopharmaceuticals: Established agents in current use. Br. J. Radiol. 2018; 91(1091): 20170969. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeik J, Alamzadeh Z, Mirrahimi M, et al.: Multifunctional Theranostic Graphene Oxide Nanoflakes as MR Imaging Agents with Enhanced Photothermal and Radiosensitizing Properties. ACS Appl. Bio Mater. 2021; 4(5): 4280–4291. PubMed Abstract \| Publisher Full Text\n\nBuck AK, Serfling SE, Lindner T, et al.: CXCR4-targeted theranostics in oncology. Eur. J. Nucl. Med. Mol. Imaging. 2022; 49(12): 4133–4144. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChoudhury PS, Gupta M: Differentiated thyroid cancer theranostics: Radioiodine and beyond. Br. J. Radiol. 2018; 91(1091): 20180136. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCoppola N, Pisaturo M, Zampino R, et al.: Hepatitis C virus markers in infection by hepatitis C virus: In the era of directly acting antivirals. World J Gastroenterol: WJG. 2015; 21(38): 10749–10759. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFerraris P, Wichit S, Cordel N, et al.: Human host genetics and susceptibility to ZIKV infection. Infect. Genet. Evol. 2021; 95: 105066. PubMed Abstract \| Publisher Full Text\n\nFuller TL, Calvet G, Genaro Estevam C, et al.: Behavioral, climatic, and environmental risk factors for Zika and Chikungunya virus infections in Rio de Janeiro, Brazil, 2015-16. PLoS One. 2017; 12(11): e0188002. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGholami A, Mousavi SM, Masoumzadeh R, et al.: Advanced Theranostic Strategies for Viral Hepatitis Using Carbon Nanostructures. Micromachines. 2023; 14(6): 1185. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGiraldo MI, Gonzalez-Orozco M, Rajsbaum R: Pathogenesis of Zika Virus Infection. Annu. Rev. Pathol. 2023; 18(1): 181–203. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGomes Marin JF, Nunes RF, Coutinho AM, et al.: Theranostics in Nuclear Medicine: Emerging and Re-emerging Integrated Imaging and Therapies in the Era of Precision Oncology. RadioGraphics. 2020; 40(6): 1715–1740. PubMed Abstract \| Publisher Full Text\n\nHerrmann K, Giovanella L, Santos A, et al.: Joint EANM, SNMMI and IAEA enabling guide: How to set up a theranostics centre. Eur. J. Nucl. Med. Mol. Imaging. 2022; 49(7): 2300–2309. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nItani R, Tobaiqy M, Al Faraj A: Optimizing use of theranostic nanoparticles as a life-saving strategy for treating COVID-19 patients. Theranostics. 2020; 10(13): 5932–5942. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJung HN, Lee S-Y, Lee S, et al.: Lipid nanoparticles for delivery of RNA therapeutics: Current status and the role of in vivo imaging. Theranostics. 2022; 12(17): 7509–7531. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLecocq Q, De Vlaeminck Y, Hanssens H, et al.: Theranostics in immuno-oncology using nanobody derivatives. Theranostics. 2019; 9(25): 7772–7791. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nO’Dwyer E, Bodei L, Morris MJ: The Role of Theranostics in Prostate Cancer. Semin. Radiat. Oncol. 2021; 31(1): 71–82. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOh C, Lee W, Park J, et al.: Development of Spleen Targeting H2S Donor Loaded Liposome for the Effective Systemic Immunomodulation and Treatment of Inflammatory Bowel Disease. ACS Nano. 2023; 17(5): 4327–4345. PubMed Abstract \| Publisher Full Text\n\nPawlotsky J-M: New Hepatitis C Therapies: The Toolbox, Strategies, and Challenges. Gastroenterology. 2014; 146(5): 1176–1192. PubMed Abstract \| Publisher Full Text\n\nPerera M, Morris MJ: From Concept to Regulatory Drug Approval: Lessons for Theranostics. J. Nucl. Med. 2022; 63(12): 1793–1801. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPetranović Ovčariček P, Campenni A, de Keizer B , et al.: Molecular Theranostics in Radioiodine-Refractory Differentiated Thyroid Cancer. Cancers. 2023; 15(17): 4290. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPlichta KA, Graves SA, Buatti JM: Prostate-Specific Membrane Antigen (PSMA) Theranostics for Treatment of Oligometastatic Prostate Cancer. Int. J. Mol. Sci. 2021; 22(22): 12095. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPorsch C, Zhang Y, Östlund Å, et al.: In Vitro Evaluation of Non-Protein Adsorbing Breast Cancer Theranostics Based on 19F-Polymer Containing Nanoparticles. Part. Part. Syst. Charact. 2013; 30(4): 381–390. Publisher Full Text\n\nSeban R-D, Nemer JS, Marabelle A, et al.: Prognostic and theranostic 18F-FDG PET biomarkers for anti-PD1 immunotherapy in metastatic melanoma: Association with outcome and transcriptomics. Eur. J. Nucl. Med. Mol. Imaging. 2019; 46(11): 2298–2310. PubMed Abstract \| Publisher Full Text\n\nSeifert R, Alberts IL, Afshar-Oromieh A, et al.: Prostate Cancer Theranostics: PSMA Targeted Therapy. PET Clinics. 2021; 16(3): 391–396. Publisher Full Text\n\nSmidova V, Michalek P, Goliasova Z, et al.: Nanomedicine of tyrosine kinase inhibitors. Theranostics. 2021; 11(4): 1546–1567. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSolnes LB, Werner RA, Jones KM, et al.: Theranostics: Leveraging Molecular Imaging and Therapy to Impact Patient Management and Secure the Future of Nuclear Medicine. J. Nucl. Med. 2020; 61(3): 311–318. PubMed Abstract \| Publisher Full Text\n\nThompson AJV, McHutchison JG: Antiviral resistance and specifically targeted therapy for HCV (STAT-C). J. Viral Hepat. 2009; 16(6): 377–387. PubMed Abstract \| Publisher Full Text\n\nUnited Nations: Handbook on the Least Developed Country Category. United Nations; 2018. Reference Source\n\nXu W, Ye C, Qing X, et al.: Multi-target tyrosine kinase inhibitor nanoparticle delivery systems for cancer therapy. Materials Today Bio. 2022; 16: 100358. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYin B, Ni J, Witherel CE, et al.: Harnessing Tissue-derived Extracellular Vesicles for Osteoarthritis Theranostics. Theranostics. 2022; 12(1): 207–231. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZahiri M, Taghavi S, Abnous K, et al.: Theranostic nanobubbles towards smart nanomedicines. J. Control. Release. 2021; 339: 164–194. PubMed Abstract \| Publisher Full Text\n\nZan C, An J, Wu Z, et al.: Engineering molecular nanoprobes to target early atherosclerosis: Precise diagnostic tools and promising therapeutic carriers. Nanotheranostics. 2023; 7(3): 327–344. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang L, Shimoji M, Thomas B, et al.: Mitochondrial localization of the Parkinson’s disease related protein DJ-1: Implications for pathogenesis. Hum. Mol. Genet. 2005; 14(14): 2063–2073. PubMed Abstract \| Publisher Full Text" }	[ { "id": "275020", "date": "14 Sep 2024", "name": "Zijian Zhou", "expertise": [ "Reviewer Expertise Molecular Imaging", "Theranostics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis work centers the topic of Theranostics-enabling high-tech centers in developing countries. This topic is interesting to both scientific communities related and also the policy makers. Theranostics is an important emerging trend in current medical research, not only because the combination of two most important aspects of diagnosis and therapy, but also the merits in revolutionizing our way and ability to treat diseases. Delineating the demands and the gaps on the development of theranostics-enabling high-tech centers in developing countries is certainly helpful to the global spread of science. I have several points on this manuscript:\nThe following literature are recommended to include in the discussion of the term of Theranostics, e.g., Theranostics 2011; 1: 1-2. Chen XS (2011 [Ref - 1]); Nature Reviews Materials 2 (7), 1-18 Chen H et al. (2017 [Ref - 2]). When talking about ‘theranostics’, one of the most important and elegant approaches of achieving theranostics is nuclear medicine, which matches well with the aim of theranostics. This part should be elaborated. The authors believes that “Theranostics…., allows to tailor treatments for individual patients based on their unique biological characteristics, paving the way for personalized medicine”. I do not doubt about the goal of ‘personalized medicine’, however, it is somewhat far from the current understanding of ‘Theranostics’.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] }, { "id": "313741", "date": "16 Sep 2024", "name": "Nisha Rani", "expertise": [ "Reviewer Expertise Nuclear medicine imaging", "PET-Pharmacokinetic Modeling", "Multimodality Neuroimaging (PET/MRI/SPECT) and Image processing", "Alzheimer’s research", "MCI research", "Cognitive Neuroscience", "Epigenetic", "Neuro-Oncology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article aimed comprehensive examination of theragnostic-enabling high-tech centers, with a particular focus on the advantages of centralizing resources in developing countries. The paper is well-organized and clearly structured, making the argument easy for readers to follow. Given the increasing interest in personalized medicine and the need to strengthen healthcare infrastructure in developing countries, the topic is timely and significant. While the article presents centralized high-tech centers as a promising solution, there are several areas that could be improved:\n1. Although the article provides a strong theoretical framework, it could benefit from the inclusion of more empirical data to support the claims made. For example, the discussion on cost savings and improved healthcare outcomes from centralized high-tech centers would be more convincing if supported by specific data or case studies that quantify these benefits. Additionally, the article could benefit from including comparative data showing the impact of such centers in both developed and developing countries.\n2. The paper highlights the benefits of high-tech centers but does not fully address the potential technological challenges. Critical issues, such as the availability of skilled personnel or the logistical challenges of maintaining cutting-edge technology in remote areas are, are not sufficiently explored. Including a discussion on these challenges would offer a more balanced and comprehensive assessment of the feasibility of implementing such centers.\n\n3. While the article covers various developing countries, it sometimes generalizes the challenges and solutions for developing countries. Please add a more nuanced discussion that considers the specific economic, social, and political contexts of different regions would add depth to the analysis. For example, the healthcare infrastructure and regulatory environment in developing countries with limited theragnostic resources and high patient load which might differ significantly from that in a smaller, less developed countries. A more nuanced discussion that considers these regional differences and tailors the proposed solutions accordingly would add depth to the analysis and make the recommendations more actionable.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-283
https://f1000research.com/articles/12-1511/v1	27 Nov 23	{ "type": "Systematic Review", "title": "Comparison between staged laparoscopic technique in children with high intra-abdominal undescended testis: a systematic review and meta-analysis", "authors": [ "Safendra Siregar", "Jupiter Sibarani", "Zola Wijayanti", "Albert Ciam", "Safendra Siregar", "Jupiter Sibarani", "Zola Wijayanti" ], "abstract": "Background: This study performed a systematic review and meta-analysis to compare the outcomes of the staged laparoscopic Fowler-Stephens Laparoscopic Orchiopexy (FSLO) and Staged Laparoscopic Traction Orchiopexy (SLTO) in patients with intra-abdominal testes (IAT).\nMethods: This study reviewed literature published from 2016 to 2023. A systematic literature search was conducted on three databases: PubMed, ScienceDirect, and Google Scholar, using keywords (High intra abdominal testis) AND ((\"Fowler Stephens laparoscopic orchiopexy\" OR (FSLO)) OR (Staged Laparoscopic traction orchiopexy OR (SLTO)). Non-randomized trials and observational studies comparing staged laparoscopic FSLO and SLTO, without any time range restriction are included. Studies without FLSO orchidopexy as a control, case reports, case studies, duplicate publication, no full text and non-English studies are excluded. This study used the PRISMA protocol, the Jadad Scale, and the Newcastle Ottawa Scale (NOS) to evaluate the included studies. To analyze statistical data, the Review Manager (RevMan) software was used. The Chi-squared test was used to calculate statistical heterogeneity in the meta-analysis.\nResults: This study included four studies of 151 patients (72 SLTO group and 79 FSLO group). There was no significant difference between the two groups in terms of testicular descent (p=0.08), and there was no testicular atrophy in the SLTO group compared to the FSLO group (p=0.04). Statistical analysis revealed a significantly shorter first-stage operation time in the FSLO group (p 0.0001), whereas the SLTO group reported a significantly shorter second-stage operation time (p = 0.04).\nConclusions: In terms of testicular descent, the SLTO technique yields similar results to the FSLO technique. The SLTO position is preferable to the FSLO position. Both techniques have advantages and disadvantages, and we recommend SLTO as the first choice in children with a high IAT of 4 cm.\nPROSPERO registration: CRD42023412407", "keywords": [ "Staged laparoscopic technique", "intra-abdominal undescended testes", "surgery", "systematic review", "meta-analysis." ], "content": "Introduction\n\nCryptorchidism is one of the most frequent congenital deformities of male neonates, also known as undescended testis (UDT). The incidence varies according to gestational age, affecting 1.0–4.6% of full-term infants and 1.1–45% of preterm infants.1 Undescended testis (UDT), also known as cryptorchidism, is a condition in which the testicles are not ordinarily found at the bottom of the scrotum.2 For clinical reasons, UDT is usually classified between palpable and non-palpable. The management of UDT is determined by the location and presence of the testes. About 20% of UDT are non-palpable, and about 10-50% of these impalpable testes either vanished or atrophied.3\n\nUDT diagnosis is established by clinical examination, and its diagnosis is supplemented by imaging techniques, for example, B-ultrasound and magnetic resonance imaging; however, laparoscopic exploration remains the gold standard for unpalpable UDT.4–6 Undescended intra-abdominal testis (IAT) is a type of non-palpable UDT that occur in 40% of laparoscopy findings.1 Short gonadal arteries typically make it difficult to successfully mobilize the testis to the scrotum without strain, making IAT a technical surgical challenge for pediatric urologists.7 Usually, a High IAT that lies more than 2 cm superior to the internal inguinal ring will probably not reach the scrotum and requires a staged procedure.1\n\nThe most effective and safest procedure for highly impalpable IAT is laparoscopic staged orchiopexy.8 Several techniques have been described for laparoscopic orchidopexy. After spermatic vascular transection, single-stage testicular descent fixing was carried out, as Fowler and Stephens first described in 1959.9 The Fowler-Stephens laparoscopic orchiopexy (FSLO) procedure describes proximal cutting and transection of the testicular vessels with preservation of the collateral arterial blood supply through the deferential artery and cremasteric vessels to gain sufficient length, which helps mobilize and relocate the testis into the scrotum.1,5,6,9 Due to the nature of these procedures, the testicles may be in jeopardy of hypotrophy or atrophy if the collateral blood supply is lacking.1 In one-stage FSLO, the testicular survival rate ranges between 50 and 65%, while in second-stage FSLO, it is 90%.1\n\nShehata et al.10 proposed a preliminary study with the preservation of a vascular technique called SLTO (staged laparoscopic traction orchiopexy) to overcome these problems. This technique does not divide the testicular vessels, which spares the major testicular blood supply. The strategy is based on tissue expansion of the testicular vasculature to expand the distended veins to the opposing anterosuperior part of the iliac spine without tearing them apart.10\n\nHowever, it is still debated whether SLTO techniques have more advantages than FSLO.11 Currently, few studies compare head-to-head measures between FSLO and SLTO with small sample sizes. The best approach and schedule for the treatment of undescended testes have been a matter of debate for decades,12 and recent studies showed sub-optimal results in managing high IAT. In the scientific community, coming to a consensus is difficult, particularly in the medical domain, where one needs to have a long enough follow-up in a randomized controlled study with a big enough size and standardized patient groups.11 In this study, we executed a systematic review and meta-analysis to compare the staged laparoscopic FSLO and SLTO outcomes in patients with intra-abdominal testes.\n\n\nMethods\n\nA systematic literature search was performed in electronic databases, including PUBMED, ScienceDirect, and Google Scholar, from 2016 to 2023. The following keywords used are as follows: (High intra abdominal testis) AND ((“Fowler Stephens laparoscopic orchiopexy” OR (FSLO)) OR (Staged Laparoscopic traction orchiopexy OR (SLTO)). References and reviews were also applied to broaden the search.\n\nThe reporting is written based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.28 The International Prospective Register of Systematic Review (PROSPERO) study’s Registration Number CRD42023412407 on 8th April 2023,\n\nIn our systematic review and meta-analysis, three reviewers screened title and abstracts independently. Non-randomized trials and observational studies comparing staged laparoscopic FSLO and SLTO, without any time range restriction are included. Studies without FLSO orchidopexy as a control, case reports, case studies, duplicate publication, no full text and non-English studies are excluded.\n\nThree reviewers independently screened each eligible study and each report retrieved to decide whether a study met the inclusion criteria of the review and in the case of a deadlocked vote, a fourth reviewer was asked to make the final decision. The variables obtained from the articles including the first author’s name, year of publication, type of study, sample size, the definition of IAT, mean age, testicular descent, testicular atrophy, mean operation time, time of follow-up, slippage, number of operators, additional finding and period waiting time from stage 1 to stage 2 from each indicvidual study will be displayed in table. Study intervention characteristics and comparing against the planned groups will be tabulated for each synthesis. The main outcome measures of our analysis were to assess the successful descent defined by testicular descent and testicular atrophy. Secondary outcome measures included the duration of the operation. Any missing data will be discarded, and only available data will be analyzed.\n\nWe evaluated the quality of the meta-analysis studies using the Jadad Composite Scale and Newcastle Ottawa Scale (NOS) (Table 1). The results showed a good quality four-point scale in Jadad Composite Scale in a prospective randomised study and eight points in NOS for three retrospective studies.\n\nReview Manager (RevMan) version 5.3 were used to analyze the data. We computed mean differences (MDs) with 95% confidence intervals for continuous data (CIs). Relative Risk (RR) was shown for dichotomous data. Algebraic manipulation to convert reported statistic to required statistic or effect estimate may be performed if needed. The Chi-squared test with significance set at P<0.05 was used to determine the statistical heterogeneity in the meta-analysis, and the I2 statistic was used to determine the heterogeneity. With significant heterogeneity I2, a random-effect model was used. Otherwise, the fixed-effect model was used.\n\nSubgroup and sensitivity analyses will be conducted to explore possible causes of heterogeneity among study results assess robustness of the synthesized results when needed.\n\n\nResults\n\nAfter article screening and applying exclusion criteria, 161 articles were identified from the three databases. A total of 147 studies were examined after duplicates were eliminated. Fourteen of these papers with reviewed full texts were determined to be relevant based on their titles and abstracts. A total of four papers were finally included in the qualitative and quantitative analysis (Figure 1).\n\nWe identified 161 studies, and the PRISMA protocol was implemented. After removing duplicates and excluding studies with irrelevant subjects, irrelevant intervention, and studies not evaluating our outcome of interest, we yielded four studies from which 151 patients (72 SLTO group and 79 FSLO group) with IAT met all inclusion requirements and were included in this meta-analysis and systematic review. One RCT that was appraised using the Jadad scale had good quality. Nonetheless, the remaining three studies were cohort studies and had a fair quality score on the Newcastle-Ottawa scale (Table 1). Study characteristics, including the first author’s name, year of publication, type of study, sample size, the definition of IAT, mean age, testicular descent, testicular atrophy, mean operation time, time of follow-up, slippage, number of operators, additional finding and period waiting time from stage 1 to stage 2 are shown in Table 2.\n\nTesticular descend\n\nThe testicular ascend success rate for both FSLO and STLO was reported in all four studies. The testicular growth rate between the STLO and FSLO groups had low heterogeneity and was not statistically significant, according to a meta-analysis of these trials (RR: 1.14; 95% CI: 0.99 – 1.31; p<0.000) (Figure 2).\n\nTesticular atrophy\n\nThe testicular atrophy rate for both FSLO and STLO was recorded in all four studies. A meta-analysis of these studies revealed that the FSLO group had statistically significant testicular atrophy rates (RR: 0.21; 95% CI: 0.05 – 0.95; p 0.04), and there was a low heterogeneity (I2: 0%) (Figure 3).\n\nOperation time in the first stage\n\nThe FSLO group had significantly shorter operation times (Mean Difference: 9.31; 95% CI: 7.08 – 11.55; p<0.0001), and there was considerable heterogeneity, according to a meta-analysis of these studies (Figure 4).\n\nOperation time in the second stage\n\nAll four studies reported the mean second-stage operation time of both FSLO and STLO. The SLTO group had a statistically significant decreased operation time (Mean Difference: -4.05; 95% CI: -7.99 – 0.12; p<0.04), and there was considerable heterogeneity, according to a meta-analysis of these investigations (Figure 5).\n\nEvaluation for publication bias\n\nDue to the small number of research, a funnel plot was not generated. Tests for funnel plot asymmetry should generally only be conducted when there are at least ten study groups. The power of the test is insufficient to distinguish between chance and actual asymmetry because of the small number of included studies examining the results of the staged laparoscopic FSLO and SLTO in patients with intra abdominal testes.13\n\n\nDiscussion\n\nPediatric surgeons continue to face many difficulties when doing surgery for the abdominal testis. Although numerous surgical techniques have been documented to address this issue, none have emerged as the clinical paradigm’s gold standard. The lack of an optimal surgical method or imaging technologies and an inadequate understanding of the interactions between the genetic, physiological, and hormonal pathways involved in testicular descent are the main causes of the unavailability of an international agreement on a management plan.14–17 The most typical method of exploring unpalpable testicles is by minimally invasive laparoscopy. An orchiopexy, or the surgical transfer of the testis into the scrotum, can be carried out if the testicle is visible. The absent or vanishing testis is diagnosed if the spermatic arteries have blind endings. In this way, both the diagnosis and treatment can be performed in a single setting by laparoscopic.14\n\nThere is still no consensus regarding the criteria for high IAT; however, the latest Ains shams classification type 4 (Figure 2) can be used to categorize high IAT for similar criteria with several studies that define high intra-abdominal testis if the testis is more than 2 cm from ipsilateral side of the inner ring.18–20 These studies also have taught us that the IAT less than 2 cm away from the inner ring can be lowered and attached securely to the scrotum. Other studies like Bawazir and Bagga et al. defined high intra-abdominal testis if the testis is >1 cm from the ipsilateral inner ring.15,16 Whereas Esposito et al. claimed that the standard distance is 3 cm.17 However, Agrawal et al. believed that the appropriate distance is 2.5 cm.18 Multi-center studies with large samples and long-term follow-up are needed for selection criteria that could be properly used as a consensus.19\n\nSince the advancement of minimally invasive surgery, there have been several methods for laparoscopic procedures in managing IAT. In this study, we compared two surgical methods (SLTO and FSLO) for the management of High IAT. As an alternative, testes can be repositioned in the scrotum and the distal testicular vessels (TVs) and can be anastomosed with the inferior epigastric vessels through the division of the proximal TVs. This procedure is known as microvascular testicular auto-transplantation.22,24,25 Unfortunately, there are several issues in the supporting data for this technique.22–25 It is labor-intensive (median time: 4.5 hours), time-consuming, and has a variable success rate (84–97%).24\n\nAfter spermatic vascular transection, single-stage testicular descent fixing was carried out, as Fowler and Stephens first described in 1959. Since then, though with only unsatisfactory outcomes, Fowler-Stephens staged orchidopexy has dominated surgical procedures.9 A single or two stages procedure to lower the testis into the scrotum is necessary and is dependent on collateral blood flow from the deferential and external spermatic arteries. To provide more direct access to the scrotum, the testis can also be passed medially to the inferior epigastric arteries via the Prentiss maneuver, which involves opening the transversalis fascia. However, this approach has been linked to testicular atrophy. A phased surgery has considerably decreased the rate of testicular atrophy, which is quite common in the initial stages of the F-S technique.26 By using the test for testicular ischemia, prevention has been made to ensure testicular collateral circulation.27 Testicular ischemia test was done by blocking the blood vessels of the spermatic cord with some silk thread and holding them for 10 minutes. When making a knot, it should be assured that the knot can be loosened when necessary, and then see if there are visible changes in the blood supply of testicles before and after the test. It is considered appropriate for F-S surgery if there is no visible ischemic change in the testis following spermatic vascular blockage. It means that the collateral blood supply of the testicles is plentiful, and the gubernaculum’s blood supply is adequate.27 However, since the impact of the testicular ischemia test on the phenomena of testicular atrophy has not been researched, everything depends heavily on the surgeon’s practices.19\n\nShehata proposed a pilot research with encouraging findings from gradually controlled traction facilitated by laparoscopic surgery in 2008.10 This method was revised and reposted later in 2016, confirming its efficacy and safety.20 Similar to the Fowler Stephen group, this procedure used a comparable anesthetic technique, operation posture, and trocar position for the puncture.9 An inch superior and medial to the contralateral side of the anterior superior iliac spine (ASIS) in the abdomen, the testis is secured with a round needle to the fixation location. After three months, a second-stage laparoscopic-assisted orchiopexy was scheduled. The testicles are lowered to the scrotum and secured by incision from the scrotum on the affected side in the second stage of both surgical procedures, which are both assisted by laparoscopy.23 Because the internal spermatic artery, vas deferens artery, and veins were intact throughout the procedure, the Shehata approach efficiently secured the blood supply of the testis. The spermatic cord is pushed backward and downward by the gut, and the testis is stabilized in the rightful location during the first stage. The primary advantage of this approach is the ability to progressively enlarge the spermatic cord blood vessels without causing testicular ischemia, which is achieved by either chronic intestinal compression or continual respiratory movement.23 This may be explained by the SLTO technique of non-transection of the testicular vasculature and the vascular pedicle’s progressive, gentle elongation.\n\nThe successful outcome of the orchiopexy is the study’s main objective. The right testicular location in the scrotum without atrophy or ascent was considered successful. A testis in the bottom or middle of the scrotal cavity without tension was referred to as being in the scrotal position. A testis located at the neck of the scrotum was not considered a successful example since it did not meet the criteria of the scrotal location. A testicle relocation outside the scrotal cavity is referred to as testicular ascension. Based on physical examination by clinicians and the data from ultrasonography measurements, postoperative testicular atrophy was defined as the presence of a nubbin or more than 50% testicular volume loss or a postoperative testicular volume of 25% of the volume of the contralateral testis, with no detectable blood flow as evidenced by color Doppler ultrasound in comparison to the normal contralateral side.\n\nAccording to our research, both groups’ testicular descent rates are equivalent. Regarding the fixed position of the scrotum in the case of High IAT, both staged laparoscopic methods showed a similar success rate.26 However, because the testicular artery was disrupted during this treatment, the FSLO group has a greater rate of testicular atrophy. We believe that keeping the testicular arteries intact may result in superior outcomes and reduce the chance of testicular atrophy. When excessive tension was not applied from the beginning in the case of testicular veins that are too short, the testicular ascent would occur and could not accomplish adequate elongation necessary for free testis mobilization into the scrotum.21 However, according to Aljubaibi et al., the success rate of the SLTO group was 93% for <2 cm; 78% for 2-4 cm; nil for >4 cm, respectively. Hence, they advocated the FSLO procedure be conducted to testes more than 4 cm from the IIR.22\n\nThe secondary outcomes of our study are mean operation time between the first and second stages of both procedures. Although it is shown that the first stage favoured the FSLO procedure, the limited number of the study showed high heterogenicity. Further comparisons are needed to conclude since SLTO is still a new technique, and a learning period is still needed for surgeons to adapt to this technique. Testicular ischemia test in FSLO also can be considered for extra 10 minutes of procedure, making both results similar is conducted. According to our review, FSLO and SLTO shared similar results in the second procedure. This may contribute to similar procedures in both techniques. This outcome is crucial so that the surgeons may safely choose the position based on their knowledge and the comorbidities of the patient.\n\nThe success rate of the SLTO procedure for aged less than two years or distances less than 4 cm was higher than FSLO. The limitation of Shehata is that when it is applied on patients over two years, and the distance is over 4 cm, the failure rate of the Shehata increases as older age results in a longer pull distance. To measure the length gain indirectly, Shehata et al., introduced a Meryland and allowed it to extend the testicular pedicle under its weight. They then measured the length from the pedicle to the anterior abdominal wall in the midline and found a mean gain of 4.7 cm.20 But Aljunaibi et al. found a mean gain of 3.4 cm using a more objective and trustworthy method because it is connected to and evaluated against the scrotal distance.22\n\nAnother benefit was that SLTO only required three months to go from stage one to stage two, while FSLO took at least six months. Following Fowler Stephen’s recommendation, Shehata and his coauthors established a 12-week gap between the two stages. This gap is essential to facilitate neovascularization between the artery of the vas and the distal testicular arteries, which provides an alternative blood supply to the testis. Still, a recent study by Aljunaibi showed that traction orchiopexy should adhere to the same time intervals as other traction and stretching procedures used in other pathologies, such as tissue expanders and long-gap esophageal atresia.9,20,22 Both approaches follow a 1-week break; then, a reevaluation was done to see if further stretching to a new stretch point is necessary after tissue remodeling has gone into effect and the preceding stretch point is no longer effective.22\n\nA shorter time between the two stages reduces the risk of internal hernia or suture slippage. It also lessens the probability that the testicles would adhere to the abdominal wall and helps to mobilize them if they do so because they are fibrinous adhesions rather than fibrous ones. By the time of follow-up, all patients had achieved the previously defined success. None of them experienced a hernia or a wound infection within proximity of the port.22\n\nFrom this study, we proposed an algorithm regarding the management of IAT. We hope that with the existing algorithm, we can minimize the number of unwanted side effects and maximize the existing procedures, one of which is for future research to assess the level of fertility after the procedure is carried out (Figure 6).\n\nUDT: Undescended testis, IAT: Intra-abdominal testis, VILO: Vessel-intact laparoscopic orchiopexy, FSLO: Fowler-stephens laparoscopic orchiopexy, SLTO: Staged laparoscopic traction orchiopexy.\n\nThe small sample size and the excessive heterogeneities in the mean operation time variables are the study’s drawbacks. Consequently, the writers believe that a more extensive study should be carried out in urology centers with a larger sample size and with surgeons who specialise in both FSLO and SLTO in the management of High IAT. Because the method was published in 2016, it is also impossible to know the fertility results for the SLTO group. So, at this time, it is impossible to compare the long-term outcomes of the two types of surgery.\n\nIn conclusion, the SLTO showed a similar result to the FSLO technique in terms of testicular descent. However, in terms of testicular atrophy, SLTO offered a better option than the FSLO position. There is a difference in mean operation time in the first stage; however, further study is needed to conclude. The mean operation time in the second stage is shorter. Therefore, it could be inferred that the SLTO technique has superiority in terms of complication and waiting time between procedures. Both techniques have their respective advantages and disadvantages; however, we recommend SLTO as the first choice in children with high IAT < 4 cm.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: PRISMA checklist for ‘Comparison between staged laparoscopic technique in children with high intra abdominal undescended testis: a systematic review and meta-analysis. 10.6084/m9.figshare.24197760.v1. 28\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nRiedmiller H, Androulakakis P, Beurton D, et al.: EAU guidelines on paediatric urology. Eur. Urol. 2022; 40(5): 589–599. Publisher Full Text\n\nVirtanen HE, Bjerknes R, Cortes D, et al.: Cryptorchidism: Classification, prevalence and long-term consequences. Acta Pediatr, Int J Pediatr. 2007; Vol. 96: p. 611–6. Publisher Full Text\n\nVikraman J, Hutson JM, Li R, et al.: The undescended testis: Clinical management and scientific advances. Semin. Pediatr. Surg. 2016 Aug 1; 25(4): 241–248. PubMed Abstract \| Publisher Full Text\n\nKim JK, Chua ME, Ming JM, et al.: A critical review of recent clinical practice guidelines on management of cryptorchidism. J. Pediatr. Surg. 2018; 53: 2041–2047. W.B. Saunders. PubMed Abstract \| Publisher Full Text\n\nMoursy EE, Gamal W, Hussein MM: Laparoscopic orchiopexy for non-palpable testes: Outcome of two techniques. J. Pediatr. Urol. 2011 Apr; 7(2): 178–181. PubMed Abstract \| Publisher Full Text\n\nSingh RR, Rajimwale A, Nour S: Laparoscopic management of impalpable testes: Comparison of different techniques. Pediatr. Surg. Int. 2011 Dec; 27(12): 1327–1330. Publisher Full Text\n\nWayne C, Chan E, Nasr A: What is the ideal surgical approach for intra-abdominal testes? a systematic review. Pediatr. Surg. Int. 2015; 31: 327–338. Springer Verlag. Publisher Full Text\n\nAbouzeid AA, Safoury HS, Hay SA: Laparoscopic classification of the impalpable testis: An update. Ann. Pediatr. Surg. 2012 Oct; 8(4): 116–122. Publisher Full Text\n\nFowler R, Stephens F: the Role of Testicular Vascular Anatomy in the Salvage of High Undescended Testes. Aust. N. Z. J. Surg. 1959; 29: 92–106. Publisher Full Text\n\nShehata SM: Laparoscopically assisted gradual controlled traction on the testicular vessels: A new concept in the management of abdominal testis. A preliminary report. Eur. J. Pediatr. Surg. 2008 Dec; 18(6): 402–406.\n\nMartin Ritzén E, Bergh A, Bjerknes R, et al.: Nordic consensus on treatment of undescended testes. Acta Pediatr. 2007; 96: 638–643. PubMed Abstract \| Publisher Full Text\n\nElder JS: Surgical Management of the Undescended Testis: Recent Advances and Controversies.Eur. J. Pediatr. Surg [Internet].2016 Oct 1 [cited 2023 Feb 12];26(5): 418–426. PubMed Abstract \| Publisher Full Text\n\nIrwig L, Macaskill P, Berry G, et al.: Bias in meta-analysis detected by a simple, graphical test. Graphical test is itself biased. BMJ (Clinical Research Ed.). 2013; 316(7129).\n\nKurz D, Tasian G: Current Management of Undescended Testes. Curr Treat Options Pediatr. 2016 Mar; 2(1): 43–51. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBagga D, Prasad A, Grover SB, et al.: Evaluation of two-staged Fowler–Stephens laparoscopic orchidopexy (FSLO) for intra-abdominal testes (IAT). Pediatr. Surg. Int. 2018; 34(1): 97–103. PubMed Abstract \| Publisher Full Text\n\nBawazir OA, Maghrabi AM: A comparative study between two techniques of laparoscopic orchiopexy for intra-abdominal testis. Indian J Urol. 2021 Jul 1; 37(3): 261–266. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEsposito C, Vallone G, Savanelli A, et al.: Long-Term Outcome of Laparoscopic Fowler-Stephens Orchiopexy in Boys With Intra-Abdominal Testis. J. Urol. 2009; 181(4): 1851–1856. PubMed Abstract \| Publisher Full Text\n\nAgrawal A, Joshi M, Mishra P, et al.: Laparoscopic stephen-fowler stage procedure: Appropriate management for high intra-abdominal testes. J. Laparoendosc. Adv. Surg. Tech. A. 2010; 20(2): 183–185. PubMed Abstract \| Publisher Full Text\n\nLiu J, Tang R, Wang X, et al.: Comparison of Two Types of Staged Laparoscopic Orchiopexy for High Intra-Abdominal Testes in Children: A Retrospective Study From a Single Center. Front. Pediatr. 2021 Jun 17; 9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShehata S, Shalaby R, Ismail M, et al.: Staged laparoscopic traction-orchiopexy for intraabdominal testis (Shehata technique) Stretching the limits for preservation of testicular vasculature. J. Pediatr. Surg. 2016; 51: 211–215. W.B. Saunders. PubMed Abstract \| Publisher Full Text\n\nDawood W, Youssif M, Badawy H, et al.: Laparoscopic staged management of high intrabdominal testis: A prospective randomized study. J. Pediatr. Surg. 2021 Dec 1; 56(12): 2385–2391. PubMed Abstract \| Publisher Full Text\n\nAljunaibi A, Alsaid A, Hobeldin M, et al.: Modified Traction Technique for Intraabdominal Testes With Short Vessels. Urology. 2022; 165: 351–355. PubMed Abstract \| Publisher Full Text\n\nTackett LD, Wacksman J, Billmire D, et al.: The High Intra-Abdominal Testis: Technique and Long-Term Success of Laparoscopic Testicular Autotransplantation. J. Endourol. 2002; 16: 359–361. PubMed Abstract \| Publisher Full Text\n\nFrey P, Bianchi A: Microvascular autotransplantation of intra-abdominal testes.Prog. Pediatr. Surg [Internet].1989 [cited 2023 Feb 12]; 23: 115–125. PubMed Abstract\n\nBukowski TP, Wacksman J, Billmire DA, et al.: Testicular autotransplantation for the intra-abdominal testis.Microsurgery [Internet].1995 [cited 2023 Feb 12]; 16(5): 290–295. PubMed Abstract\n\nKelley BP, Higuera S, Cisek LJ, et al.: Combined laparoscopic and microsurgical techniques for testicular autotransplantation: is this still an evolving technique?J. Reconstr. Microsurg [Internet].2010 [cited 2023 Feb 12];26(8): 555–558. PubMed Abstract\n\nBraga LH, Farrokhyar F, McGrath M, et al.: Gubernaculum Testis and Cremasteric Vessel Preservation during Laparoscopic Orchiopexy for Intra-Abdominal Testes: Effect on Testicular Atrophy Rates.J. Urol [Internet].2019 Feb 1 [cited 2023 Feb 12]; 201(2): 378–385. PubMed Abstract\n\nUro F: PRISMA_2020_checklist CM.docx. figshare. Figure. 2023. Publisher Full Text" }	[ { "id": "241655", "date": "09 Feb 2024", "name": "Ferdinando Agresta", "expertise": [ "Reviewer Expertise Laparoscopy", "emergency", "abdominal wall" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nwell done and interesting paper to read and to know about. The analysis is well done, as is the research. The topic is interesting and important and the conclusion of the paper seems in according with and light of the actual evidence. Again: well done systemic review and meta analysis\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] }, { "id": "241648", "date": "20 Feb 2024", "name": "Valeska Bidault-Jourdainne", "expertise": [ "Reviewer Expertise Pediatric Urology", "uro-genital surgery", "testicular surgery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article presents a systematic review of clinical studies comparing Fowlers Stephens laparoscopic two stage orchiopexy (FSLO) and Shehata laparoscopic traction staged orchiopexy (STLO), between 2016 and 2023. FSLO is the most commonly used technique for high intra-abdominal testis (IAT), but since 2008, Shehata introduced a new technique (STLO), without division of the spermatic vessels. 4 articles were included and analysed in the review: one prospective and 3 retrospective comparative studies, with a total of 151 patients. The primary outcome analysed in the review was the testicular descend success rate, which was similar with both FSLO and STLO. Testicular atrophy was significantly lower in the STLO group (p=0.04), and completed the primary outcomes of the review. Operation times were in favour of FSLO for first stage of orchiopexy (p<0.0001), and in favour of STLO during second stage (p<0.04). This systematic review has a good rationale, since no consensus exists on the best technique for high IAT orchiopexy, and FSLO does not provide complete satisfaction with at least 10% testicular atrophy described in the literature. The objectives are also well exposed, although one may object that duration of each stage for orchiopexy should not be considered, if one technique is superior to the other in terms of testicular descend and atrophy. Methods for selection of articles and statistical analysis are well defined and adapted to the goal of this review. However, the small number of patients in each study included weakens the conclusion of this study. For example, only 11 patients with high IAT had STLO in Bawazir and Maghrabi's study. Thus, the conclusion with recommendations for IAT management is criticisable and lacks power. It would be more valuable to open on a larger study needed for high IAT (published recently in JPU 2024).\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly", "responses": [ { "c_id": "11327", "date": "16 Apr 2024", "name": "Albert -", "role": "Author Response", "response": "We would like to express our gratitude for your time and efforts in reviewing our manuscript. We have carefully considered all the comments provided by the editor and reviewers. After several discussion and updates in our research data, here is our responses regarding dr Valeska comments in 2 separate points ”However, the small number of patients in each study included weakens the conclusion of this study. For example, only 11 patients with high IAT had STLO in Bawazir and Maghrabi's study. Thus, the conclusion with recommendations for IAT management is criticisable and lacks power. It would be more valuable to open on a larger study needed for high IAT (published recently in JPU 2024).” Thank you for your guidance, We have included one additional article for analysis, bringing the total to five studies involving 240 patients to strengthen our conclusion in this study and updated our pool data. Our meta-analysis revealed that there was minimal variation and no statistically significant difference in the rate of testicular growth between the STLO and FSLO groups (RR: 1.08; 95% CI: 0.96 – 1.23; p<0.20). Similarly, the rate of testicular atrophy between the STLO and FSLO groups showed low variation and lacked statistical significance (RR: 0.45; 95% CI: 0.19 – 1.09; p<0.08), with low heterogeneity (I2: 0%). In summary, the SLTO technique demonstrated comparable outcomes to the FSLO technique in terms of testicular descent and atrophy. This finding showed the importance for surgeons to make informed decisions based on patient characteristics and their own expertise, as neither technique appears significantly superior regarding testicular descent and atrophy. “The objectives are also well exposed, although one may object that duration of each stage for orchiopexy should not be considered, if one technique is superior to the other in terms of testicular descend and atrophy.” Since the result of our study show that there are no significant differences between both techniques in terms of testicular descent and testicular atrophy, we can conlude that there are no superiority in both techniques. we still need more data regarding the operation time in each stages of procedure to draw conclusion since our result show high heterogenicity mean operation time. Thank you" } ] }, { "id": "241646", "date": "08 May 2024", "name": "Jie Liu", "expertise": [ "Reviewer Expertise pediatric surgery" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study on high intra-abdominal undescended testis, and the authors conclude: In terms of testicular descent, the SLTO technique yields similar results to the FSLO technique. The SLTO position is preferable to the FSLO position. Both techniques have advantages and disadvantages, and we recommend SLTO as the first choice in children with a high IAT of 4 cm. The conclusions of this study are basically the same as our actual observations, which is an interesting study. The discussion section is also well written and worth reading for researchers.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1511
https://f1000research.com/articles/12-1007/v1	21 Aug 23	{ "type": "Research Article", "title": "Sentiment analysis of Indonesian tweets on COVID-19 and COVID-19 vaccinations", "authors": [ "Viskasari Pintoko Kalanjati", "Nurina Hasanatuludhhiyah", "Annette d'Arqom", "Danial H. Arsyi", "Ancah Caesarina Novi Marchianti", "Azlin Muhammad", "Diana Purwitasari", "Annette d'Arqom", "Danial H. Arsyi", "Ancah Caesarina Novi Marchianti", "Azlin Muhammad", "Diana Purwitasari" ], "abstract": "Background: Sentiments and opinions regarding COVID-19 and the COVID-19 vaccination on Indonesian-language Twitter are scarcely reported in one comprehensive study, and thus were aimed at our study. We also analyzed fake news and facts, and Twitter engagement to understand people’s perceptions and beliefs that determine public health literacy.\nMethods: We collected 3,489,367 tweets data from January 2020 to August 2021. We analyzed factual and fake news using the string comparison method. The difflib library was used to measure similarity. The user's engagement was analyzed by averaging the engagement metrics of tweets, retweets, favorites, replies, and posts shared with sentiments and opinions regarding COVID-19 and COVID-19 vaccination.\nResult: Positive sentiments on COVID-19 and COVID-19 vaccination dominated, however, the negative sentiments increased during the beginning of the implementation of restrictions on community activities (PPKM). The tweets were dominated by the importance of health protocols (washing hands, keeping distance, and wearing masks). Several types of vaccines were on top of the word count in the vaccine subtopic. Acceptance of the vaccination increased during the studied period, and the fake news was overweighed by the facts. The tweets were dynamic and showed that the engaged topics were changed from the nature of COVID-19 to the vaccination and virus mutation which peaked in the early and middle terms of 2021. The public sentiment and engagement were shifted from hesitancy to anxiety towards the safety and effectiveness of the vaccines, whilst changed again into wariness on an uprising of the delta variant.\nConclusion: Understanding public sentiment and opinion can help policymakers to plan the best strategy to cope with the pandemic. Positive sentiments and fact-based opinions on COVID-19, and COVID-19 vaccination had been shown predominantly. However, sufficient health literacy levels could yet be predicted and sought for further study.", "keywords": [ "COVID-19", "COVID-19 vaccination", "Tweets", "Sentiment analysis", "Vaccine", "social media" ], "content": "Introduction\n\nSince first named as a global pandemic by the World Health Organization (WHO) in March 2020, COVID-19 has been the utmost issue challenging all aspects of human life worldwide.1,2 Whilst, at the beginning of the crisis, little had been known about the pathogen, its detection, and its management; the disease began to increase the morbidity and mortality rate steeply and thus overwhelming the health care system in many countries, especially during the pre-vaccination period.3\n\nOne of the keys to controlling the morbidity and mortality rate increase is vaccination allied with the implementation of WHO-recommended efforts for reducing transmission, together with strong epidemiology surveillance.4 These are called for public literacy and engagement on COVID-19 and COVID-19 vaccination, which sentiments represent public opinion and beliefs toward the issues could be read on various platforms of social media including Twitter and might affect public acceptance toward the vaccine and vaccination program.3,4 Although robust evidence has supported the efficacy and safety of various types of COVID-19 vaccines, public skepticism concerning vaccine effectiveness and side-effectd has become a significant shortcoming in achieving wide-vaccination coverage.5\n\nAnaylsis of social media content is a reliable way of mining for peoples opinions and beliefs, including toward COVID-19, COVID-19 vaccines, and vaccination; thus might help decision-makers to develop policies related to COVID-19 and COVID-19 vaccination.6 The use of social media has been rising drastically and the analysis of public opinion uploaded on social media can be an effective means to capture real-time public sentiment.7 Previous studies have been conducted on public opinion regarding COVID-19 vaccines and vaccinations in various countries; it was reported that the surge in COVID-19 positive cases was not necessarily associated with the levels of vaccinations.8,9\n\nIn Indonesia, hesitancy towards the vaccine and low literacy levels affect the acceptance of COVID-19 vaccination or certain vaccine brands.10 An early survey on vaccine acceptance from 1359 Indonesian respondents conducted from the end of March to April 2020, showed the acceptance rate as high as 95% for the free vaccine with reported efficacy of approximately 95%. However, the acceptance level dropped to 67% if the reported efficacy of COVID-19 vaccine was only 50%.11 The Ministry of Health of the Republic of Indonesia stated that a survey on vaccination by the COVID-19 Symptom Survey conducted by the University of Maryland Joint Survey Methodology Program in partnership with Facebook showed several factors cause doubts about vaccination acceptance amongst Indonesian people e.g. concern about the side effects, and the comorbidity that may affect the post-vaccination health state.12 Although Indonesia has the fourth-highest number of social network users worldwide,13 studies on social media data to identify public sentiments and engagement towards COVID-19 and COVID-19 vaccination have still been limited, and thus is the aim of the current study.\n\n\nMethod\n\nThis study received approval from the Health Research Ethics Committee (KEPK), Faculty of Medicine, Universitas Airlangga, Indonesia (approval no. 145/EC/KEPK/FKUA/2021).\n\nSeveral stages were carried out in this study to identify and analyze public opinion (Figure 1). The preprocessing started with data preparation which included determining searching terms for COVID-19 and COVID-19 vaccinations, then crawling the Indonesian-language tweets data based on the meta-tagging language stored on Twitter (https://twitter.com/?lang=en-id) during the period of 1st January 2020 to 31st August 2021.\n\nThe searching terms are listed in Table 1. After the preprocessing stage, subsequently, the data was cleaned from several elements such as emoticons, hashtags, non-alphanumeric characters, and URLs. The lower-text was used to convert all Twitter text to the lowercases, then we removed the punctuation in the Tweet text. The cleaned data that had gone through these stages were then labeled manually. The data was labeled into classifications, namely COVID-19, COVID-19 types and brands of vaccine, vaccine effectiveness, vaccine side effect, and vaccination (program). The labeling was then carried out into several classes, which were tweet exposure and engagement analysis, differentiating the fake and the fact tweets, also sentiment and public opinion analysis (Figure 1).\n\nBefore data classifying according to a predetermined class, each topic was developed using the clustering method. The clustering method used was IndoBERT model by IndoNLU. After the clustering process was complete, the resulted data were visualized using exploratory data analysis (EDA) to find out the insight about the data, to discover patterns, to spot anomalies, to test hypothesis and to check assumptions with the help of summary statistics and graphical representations.14 Detailed visualizations included pie charts, line charts, bar charts, tweet average engagement rate, and word cloud. Data visualization was employed to evaluate public opinion and sentiments. The test results will be analyzed in several stages, namely as follows:\n\n1. Analysis of tweet exposure and engagement, this involved measurement of the metadata accompanying posts, including engagement measures such as the number of times each tweet was shared (retweeted), liked (favorite), people responded (replied), and retweeted with a comment (quote). Summary of engagement metrics calculated on average, including retweets, favorites, replies, and shares of posts with positive, negative or neutral sentiments. We continued with the data visualization and data analysis based on trends using python visualization.15\n\n2. Determination of the fact or fake news on the tweets, the string comparison method was used to assess fact or fake tweets. This method compared tweets with a list of fake tweets in the list of fake tweets dictionary issued by Turn Back Hoax.16 The difflib library was used to obtain the similarity value between tweets. In determining fake news labeled tweets, it is necessary to have an additional parameter in the form of threshold to tolerate the similarity between a tweet that can be considered a fake tweet and a tweet that is still considered factual. The range of similarity values was determined based on a sample test by taking into account the data results with a range of 0 – 1, where the closer the value to 1 means the more appropriate the word is in the list of incorrect tweets dictionary. After observing the tweet data, the threshold value was determined to be 0.7. The tweets with a similarity value above 0.7 would be categorized as fake tweets (Table 2).\n\nAnalysis of public opinion and sentiment, datasets from public and private accounts that had gone through the preprocessing stage were labeled as positive, negative, and neutral, as well as knowing the pattern of agreement on vaccination program data that have been marked as positive (pro-vaccination), negative (anti- and doubtful toward the vaccination) and Neutral which refers to the study.17 Pro vaccines are categorized for tweets with a positive tendency towards vaccination. Tweets show that the public can well accept the existence of vaccines and invitations to participate in vaccinations, even when giving an opinion about their condition after the vaccination process, commonly known as adverse event following immunization (AEFI). Anti-Vaccine is given in tweets that reject vaccination, accompanied by arguments against it. Doubt is given to tweets that tend to be confused about the purpose of vaccination or still doubt the effectiveness of certain vaccine brands, such as wanting only Pfizer vaccines and disparaging other brands of vaccines. Neutral category tweets were usually dominated by news accounts and only inform facts or narratives without expressing an opinion that says whether the statement is negative or positive towards vaccination.5,6,11 A total of 3000 data were taken randomly from the dataset to be used as training data using the IndoBert model,18 with an accuracy rate of 75%. After the process was successfully carried out, we continued with data visualization and data analysis stages based on trends using Python visualization.15\n\n\nResults and discussion\n\nA total of 3,489,367 Indonesian tweets data were collected from 1st January 2020 to 31st August 2021. The total dataset obtained was 324,358 data; consisting of 24,579 data related with COVID-19 and the rests were related with COVID-19 vaccine and vaccination.\n\nFigure 2 showed the peak counts of tweets were seen in three parts during this period of time. In June 2020; in January 2021 and again in July 2021. The word-cloud of these tweets were seen in this figure, e.g. corona virus, health protocol, COVID-19 spread, preventing COVID-19, PPKM (abbreviation of Indonesian government program to control COVID-19), hand washing and physical distancing. Several keywords i.e. PCR (polymerase-chain reaction), antigen swab and transportation protocols dominated the tweets.\n\nDuring 2020 when the vaccine and vaccination programs had yet known, the trending keywords were more into the COVID-19 virus and how to take a preventive step i.e. PPKM (pemberlakuan pembatasan kegiatan masyarakat)/restrictions towards community activity), and working from home/wfh (Figure 3). The word count graph shows many Twitter users discussed the COVID-19 virus along with tweets containing education to prevent exposure to the virus. During that period, the topic of discussion was still about education to suppress the spread of COVID-19. Preventive actions still being promoted, such as staying at home, avoiding direct contact with other people, avoiding non-essential travel, social distancing, frequent hand washing, and so on19,20 remain hot topics among the public. Meanwhile, the word count shows a hot topic among the people after implementing PPKM. After the government established and implemented the PPKM policy, Twitter users discussed correlated issues such as working from home.21–23 PPKM is intended as a form of response to the increase in COVID-19 cases, so the problem of the virus is still quite busy being discussed on Twitter. Implementing PPKM levels 1-4 by the government, which has brought pros and cons to the community, has also become a topic of discussion. Even so, this policy is considered effective in suppressing the surge in the increase in COVID-19 cases.21\n\nIn general, retweets dominate engagement, followed by replies (Figure 4). This supports evidence that the public is more focused on sharing information such as the rise or fall of cases as well as information on education and preventive measures implemented by the government to suppress the spread of COVID-19.22\n\nOn the other hand, the tweets count on COVID-19 and COVID-19 vaccination was highest at July 2021 (Table 3), arguably due to the rise of SARS-CoV-2 delta variant that significantly increased the morbidity and mortality rate, thus called for more definitive prevention act.22–24\n\nThe engagement on COVID-19 vaccine was topped by the likes during 2020-2021, followed by retweets and reply (Figure 5). In Indonesia, several brands that have gone through safe and halal tests that adapt to the conditions of Indonesia, being a country with one of the largest Muslim population in the world, are exciting topics to be discussed by the public.23 For example, the most popular brand in Indonesia is Sinovac.24 This is because Sinovac is the fastest vaccine brand to enter Indonesia.25 It can be seen from the data that has been successfully presented that Sinovac continues to dominate, especially at the end of 2020 and early 2021, when the Sinovac vaccine has entered Indonesia. The Moderna vaccine also experienced an increase in the number of tweets because, during this period, many of these vaccines were distributed in Indonesia.26 Moderna vaccine produces more side effects than other vaccines,27 thus becoming increasingly discussed on Twitter. The AstraZeneca vaccine also carries more frequent side effects when compared to the Sinovac vaccine (Figure 5).28\n\nThe side effect of COVID-19 vaccine was seen as the engagement topic topped by likes, retweets and reply which were higher in December, 2020; in March, 2021 and in July, 2021 compared to other months during this period. Whereas the type of vaccine engagement showed higher in February 2021; in May 2021 and in July 2021 compared to other months (Figure 6).\n\nThe graphs and word cloud show that of the vaccine side effects subtopics recorded, the word most frequently discussed in tweets was COVID-19 vaccine and its side effect (Figure 7).\n\nOn the other hand, the trending keywords on the vaccine effectiveness was topped by trending keywords of the disease transmission, management guidelines, virus variance e.g. delta variant also with the immune system, prevention and health system (Figure 8).\n\nFrom Figure 9, we can see that the paid vs. free vaccination programs became the trending keywords along with the vaccination program of the government and herd immunity. People were cautious on the paid vaccination, when in reality the vaccination program was held nationally since February 2021 by the government with primary target of healthy people aged 18-59 years old, and also prioritized for the health providers to instigate the herd immunity that was discussed as the ideal condition after vaccination coverage was achieved widely.22–24\n\nBased on the analysis using similarity value, 15 tweets were indicated as fake tweets with misleading content. Some of them include the worldwide approval of a dendritic cell-based vaccine candidate developed by a group of Indonesian researchers, which in fact had not even been authorized into phase 2 clinical trial by the Indonesian authoritative body. There was also content about the affiliation of several vaccine manufacturers to certain companies. Another topic was that up to 21% of vaccine trial participants experienced adverse effects after receiving the Moderna vaccine. The fake tweets of vaccine manufacturing companies presumed to have been developing COVID vaccines even before the COVID-19 pandemic started was also found to be misleading content. From the entire dataset, it can be concluded that there was extremely low tweet activity of spreading fake news with a negative context, such as finding supporters for fake news from tweets that are replied.\n\nThe sentiment referred to in the discussion includes users agreeing and understanding the conditions for COVID-19. The debate regarding the support for preventive actions by the government is also a topic that is still hotly discussed. In addition, Twitter users continue to carry out their activities as usual and provide education on how to prevent exposure to the virus, increasing positive sentiment about the issue. In the second period, the trend of positive sentiment led to discussions around the expressions of Twitter users to express their response to the increasing number of COVID-19 cases in Indonesia, accompanied by campaigns from all parties to carry out vaccinations aggressively. However, there was an increase in negative sentiment in the second period compared to the first period. This period was when the government begins to issue PPKM policies that reap the pros and cons of the community. PPKM, which has a level of 1-4, was arguably considered to harm the community’s economy because of the limited activities of the community at work. During PPKM 3-4 part of rules was closing the purchasing center at 20.00 GMT+7, and making the visitor capacity a maximum of 50%.29 Thus, many parties have complained about the condition of the policy. The sentiment distribution every monthis presented as shown in Figure 10.\n\nSentiment analysis was conducted to find out the positive and negative sentiments of the public towards the vaccination program in 2020, shows that positive tweet sentiment dominates all existing sentiments. Analysis of the dataset indicates that generally, tweets come from news accounts where tweets originating from these accounts are classified as neutral tweets. While the period of 2021, shows that although the number of tweets is more dominant than in the first period, it shows that public opinion has a positive sentiment tendency. This might be due to the public rise of awareness of the importance of vaccination to help reducing the spread of the COVID-19 virus. However, negative sentiment is still a significant problem because people expect only certain types of vaccines would work, and/or are still doubtful and do not believe in vaccination programs to tackle the pandemic (Figure 11).\n\nFigure 12 shows that both in 2020 and 2021, positive sentiment tends to dominate above 50%. The proportion of positive sentiment decreases considerably while negative sentiment only slightly decreases in 2021. The percentage of neutral sentiment doubles in 2021 compared to 2020. Negative sentiment can happen because, in 2020, the existing vaccine research is still in the development stage by scientists, while during the first midterm of 2021, COVID-19 vaccines are still being rolled out to limited people in Indonesia.\n\nIn 2021, various vaccine products have gone through stages of trials and study results of their efficacies and side effects have been released to public by vaccine manufacturers. Due to the increasing clarity of reports regarding the effect of vaccine in stimulating the body’s immunity against virus, the public has more confidence in the role of vaccines in accelerating recovery from the pandemic. It is reflected by slightly increased positive sentiment of vaccination program in 2021 (Figure 11). However, fear toward vaccine’s side effect yet exists, possibly contribute to the decrease of positive sentiment in 2021 (Figure 12).\n\nAt Figure 13, the sentiment of the vaccination program in Indonesia was mostly positive (59.1%); whilst the analysis sentiment of various types of vaccines for COVID-19 that were available was predominated by positive opinions in general, during both years (approximately five times higher than the negative sentiments). We compared sentiment polarities toward vaccines in 2020 and 2021 and found increases in both positive and negative sentiments in 2021 after the vaccination program had started. Although positive sentiments showed a greater increase, the negative sentiments, which remained at 15.2%, deserve attention, as they may reflect a proportion of individuals with vaccine hesitancy and/or rejection.\n\nSocial media studies have been used over the past decade to identify public opinion and sentiment toward particular health issues, for instance, the 2009 H1N1 outbreak.30 The vaccination issue has been a matter of importance to be analyzed using this approach since the individual decision on vaccine uptake is modulated by opinions from social networks.31 Disinformation narratives spread on social media that are sometimes hostile, causing anxiety, fear, and distrust toward vaccination could largely contribute to vaccine hesitancy and refusal.32 The rapid and vast dissemination of disinformation should be addressed appropriately by effective strategies for vaccine promotion. The surveillance of real-time social media information flow could be a remarkable source of timely data updates for adjusting those strategies.31 Interestingly, a strong correlation was shown between online-expressed sentiments and estimated vaccination rates.33\n\n\nConclusions\n\nRecent studies have confirmed evidence of vaccination impacts on several public health parameters, which give promise for its role in achieving herd immunity and further ending pandemic. Vaccination has remarkably reduced COVID-19 cases and hospitalizations.34 COVID-19 related morbidity and mortality,35 and incidence due to variants of concern.36 Additionally, rapid vaccine roll-out is believed to boost economic recovery.37 Therefore, accelerating the vaccination pace is imperative for countries worldwide.34 Efforts to lower vaccine hesitancy should be prioritized as it is the greatest threat to achieving high vaccine coverage.38 Social media is perceived to be a major source of misinformation and is able to amplify and disseminate it without temporal and spatial limits, fostering vaccine hesitancy and lowering vaccine uptake.39 Our study identified a number of vaccine-related misinformation circulating on social media that were categorized as fake tweets. Our finding is in accordance with a study by Islam et al., that analyzed rumors and conspiracy theories related to COVID-19 vaccine on variable online platforms. They encountered that the majority of these contents were false and/or misleading. They also reported that Indonesia was among the countries with a high number of online rumors related to COVID-19 vaccine.40 Our study found 15 vaccine-related fake tweets. Even though they were quite low in number considering the dataset collected was within 20 months, their impact on vaccine hesitancy shouldn’t be undermined.41 We found fake tweets about the adverse effect of Moderna vaccine that was said to affect 21% of trial participants. This exaggerated misinformation certainly may raise public concern about vaccine safety, which may lead to vaccine hesitancy.42 Another fake tweets issue was that vaccine manufacturers had been developing COVID-19 vaccines long before the pandemic emerged. This issue appeared to arise due to doubt about the fast pace of vaccine development. Some individuals may furtherly link it to the conspiracy theory that COVID-19 is a bioweapon designed by particular countries or parties. Meanwhile, belief in conspiracy theories is a driving factor for an individual to reject vaccination.43,44 Actually, Twitter has set policies and conducted efforts to counteract any types of misinformation. It has launched detailed criteria and examples of false or misleading information about COVID-19 vaccine posted by users. Some actions taken to violations include content removal, tweet labeling, and adding corrective information. Twitter may also disable retweets, quoting, or any other ways of engagement to those false tweets, in case they pose potential harm to the public. The user’s account may be temporarily locked or permanently suspended.45 It is very likely that Twitter has effectively cleansed any circulating misinformation. In addition, the ministry of health and the ministry of communication and informatics have provided platforms to continuously inform the public about the identified fake news or hoax and cooperate with social media to monitor misinformation related-contents and provide authoritative information as valuable trusted sources.46 However, social media remains a battleground where the anti-vaccine movement is difficult to combat.47\n\nWe confirmed the usefulness of social media studies to provide insights into the public’s attention, discussion, concerns, and sentiments about COVID-19 vaccination.48 We demonstrated the dynamically changing public attention over time, where it peaked in July 2021, during the second surge of COVID-19 cases. It can be extrapolated that the public well responded to the government campaign of accelerating vaccine rollout as a means to curb the disease.49 The top trend discussion topics may reflect a public concern, for instance, “paid vaccination. Even though we did not perform sentiment analysis on this specific topic, it can be proposed that the public highly disagreed with this policy.\n\nWe deep-dived user-generated Twitter posts to elaborate on factors associated with vaccine hesitancy. Other than the spread of misinformation through social media, we discovered the public’s perceptions and concerns about vaccines effectiveness and side effects. The negative sentiment toward these topics may be associated with the public’s doubt regarding the vaccine as an effective and secure means to manage the pandemic. Our result was in line with a study on medical students reporting most of the participants had concerns regarding vaccines adverse effects and ineffectiveness.50 We identified a potential misconception regarding the side effects of the vaccine that it may indeed cause COVID-19 infection. This was actually one of the false myths identified and clarified by health authorities, yet still remains to be popular according to our findings. In this study, we found that people’s opinion showed on this particular social media is arguably correlated with their literacy on the issue.51 It might be affected by the ambience of social environment and information percepted at a certain period.", "appendix": "Data availability\n\nThe underlying data to this research cannot be shared due to the ethical and copyright restrictions surrounding social media data. The Methods section contains detailed information to allow replication of the study. Any queries about the methodology should be directed to the corresponding author.\n\n\nAcknowledgements\n\nThank you to the Faculty of Medicine, Universitas Airlangga, Surabaya Indonesia for their support.\n\n\nReferences\n\nChou W-YS, Budenz A: Considering emotion in COVID-19 vaccine communication: Addressing vaccine hesitancy and fostering vaccine confidence. Health Commun. 2020 Dec 5; 35(14): 1718–1722. PubMed Abstract \| Publisher Full Text\n\nEl Keshky MES, Basyouni SS, Al Sabban AM: Getting through COVID-19: The pandemic’s impact on the psychology of sustainability, quality of life, and the global economy – A systematic review. Front. Psychol. 2020 Nov 12; 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTangcharoensathien V, Bassett MT, Meng Q, et al.: Are overwhelmed health systems an inevitable consequence of COVID-19? Experiences from China, Thailand, and New York State. BMJ. 2021 Jan 22; 372: n83. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan Kerkhove MD: COVID-19 in 2022: controlling the pandemic is within our grasp. Nat. Med. 2021 Dec 14; 27(12): 2070–2070. Publisher Full Text Reference Source\n\nTroiano G, Nardi A: Vaccine hesitancy in the era of COVID-19. Public Health. 2021 May; 194: 245–251. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nHan X, Wang J, Zhang M, et al.: Using social media to mine and analyze public opinion related to COVID-19 in China. Int. J. Environ. Res. Public Health. 2020 Apr 17; 17(8): 2788. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nSinnenberg L, Buttenheim AM, Padrez K, et al.: Twitter as a tool for health research: A systematic review. Am. J. Public Health. 2017 Jan; 107(1): e1–e8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSubramanian SV, Kumar A: Increases in COVID-19 are unrelated to levels of vaccination across 68 countries and 2947 counties in the United States. Eur. J. Epidemiol. 2021 Dec 30; 36(12): 1237–1240. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVelavan TP, Meyer CG: The COVID-19 epidemic. Trop. Med. Int. Heal. 2020 Mar 16; 25(3): 278–280. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGerretsen P, Kim J, Caravaggio F, et al.: Individual determinants of COVID-19 vaccine hesitancy. PLoS One. 2021 Nov 17; 16(11): e0258462. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarapan H, Wagner AL, Yufika A, et al.: Acceptance of a COVID-19 vaccine in Southeast Asia: A cross-sectional study in Indonesia. Front Public Heal. 2020 Jul 14; 8. Publisher Full Text\n\nThe Ministry of Health of Republic of Indonesia: 80,8% orang Indonesia bersedia menerima vaksin COVID-19. Kementerian Kesehatan Republik Indonesia.2021. Reference Source\n\nStatistae: Number of social network users in selected countries in 2021 and 2026. Statista; 2021. Reference Source\n\nPatil P: What is exploratory data analysis? Towards Data Science.2018. Reference Source\n\nNantasenamat C: How to build a machine learning model.2020. Reference Source\n\nSatyawati NP, Utari P, Hastjarjo S: Fact checking of hoaxes by masyarakat antifitnah Indonesia. Int. J. Multicult. Multireligious Underst. 2019; 6(6). Reference Source\n\nYousefinaghani S, Dara R, Mubareka S, et al.: An analysis of COVID-19 vaccine sentiments and opinions on Twitter. Int. J. Infect. Dis. 2021 Jul; 108: 256–262. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nSaadah S, Auditama KM, Fattahila AA, et al.: Implementation of BERT, IndoBERT, and CNN-LSTM in classifying public opinion about COVID-19 vaccine in Indonesia. J. RESTI (Rekayasa Sist dan Teknol Informasi). 2022 Aug 30; 6(4): 648–655. Publisher Full Text Reference Source\n\nLotfi M, Hamblin MR, Rezaei N: COVID-19: Transmission, prevention, and potential therapeutic opportunities. Clin. Chim. Acta. 2020 Sep; 508: 254–266. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nTfi MR, Hamblin MR, Rezaei N: COVID-19: Transmission, prevention, and potential therapeutic opportunities. Clin. Chim. Acta. 2020; 508(January): 254–266.\n\nSaraswati I, Muzdalifah A, Herawati AR, et al.: Implementation of restrictiuons on community activities (PPKM) policy analysis level 1-4 in dealing with the covid-19 outbreak in Indonesia. Int. J. Soc. Serv. Res. 2021 Nov 14; 1(3): 203–210. Publisher Full Text Reference Source\n\nHasanah NA, Suciati N, Purwitasari D: Identifying degree-of-concern on COVID-19 topics with text classification of twitters. Regist. J. Ilm. Teknol. Sist. Inf. 2021 Feb 16; 7(1): 50. Publisher Full Text Reference Source\n\nPristiyono RM, Al Ihsan MA , Anjar A, et al.: Sentiment analysis of COVID-19 vaccine in Indonesia using Naïve Bayes Algorithm. IOP Conf. Ser. Mater. Sci. Eng. 2021 Feb 1; 1088(1): 012045. Publisher Full Text\n\nNurdeni DA, Budi I, Santoso AB: Sentiment analysis on Covid19 vaccines in Indonesia: From the perspective of sinovac and pfizer. 2021 3rd East Indonesia Conference on Computer and Information Technology (EIConCIT). IEEE. 2021; pp. 122–127. Reference Source\n\nYeremia AE, Raditio KH: Indonesia-China Vaccine Cooperation and South China Sea Diplomacy. ISEAS Yusof Ishak Inst.; 2021; p. 55. Reference Source\n\nU.S. Embassy & Consulates in Indonesia: United States provides 4 million moderna COVID-19 vaccine doses to Indonesia through COVAX 2021.Reference Source\n\nMeo SA, Bukhari IA, Akram J, et al.: COVID-19 vaccines: comparison of biological, pharmacological characteristics and adverse effects of Pfizer/BioNTech and Moderna Vaccines. Eur. Rev. Med. Pharmacol. Sci. 2021 Feb; 25(3): 1663–1669. PubMed Abstract \| Publisher Full Text\n\nBralianti PD, Akbar FN: Covid-19 vaccines and its Adverse Events Following Immunization(AEFI). Avicenna Med. J. 2021 Jul 15; 2(1): 19–28. Publisher Full Text Reference Source\n\nMiharja M, Salim E, Nachrawi G, et al.: Implementation of emergency public activity restrictions (PPKM) in accordance with human rights and Pancasila principles. BIRCI-Journal. 2021; 15: 6855–6866.\n\nChew C, Eysenbach G: Pandemics in the age of twitter: Content analysis of tweets during the 2009 H1N1 uutbreak. Sampson M, editor. PLoS One. 2010 Nov 29; 5(11): e14118. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDu J, Xu J, Song H-Y, et al.: Leveraging machine learning-based approaches to assess human papillomavirus vaccination sentiment trends with Twitter data. BMC Med. Inform. Decis. Mak. 2017 Jul 5; 17(S2): 69. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPulido C, Ruiz-Eugenio L, Redondo-Sama G, et al.: A new application of social impact in social media for overcoming fake news in health. Int. J. Environ. Res. Public Health. 2020 Apr 3; 17(7): 2430. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nSalathé M, Khandelwal S: Assessing vaccination sentiments with online social media: Implications for infectious disease dynamics and control. Meyers LA, editor. PLoS Comput. Biol. 2011 Oct 13; 7(10): e1002199. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen X, Huang H, Ju J, et al.: Impact of vaccination on the COVID-19 pandemic in U.S. states. Sci. Rep. 2022 Jan 28; 12(1): 1554. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nMoghadas SM, Vilches TN, Zhang K, et al.: The impact of vaccination on coronavirus disease 2019 (COVID-19) outbreaks in the United States. Clin. Infect. Dis. 2021 Dec 16; 73(12): 2257–2264. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nSuthar AB, Wang J, Seffren V, et al.: Public health impact of covid-19 vaccines in the US: observational study. BMJ. 2022 Apr 27; 377: e069317. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoediono L: Indonesia: Rapid mass vaccination, effective pandemic control and strong fiscal and monetary support are critical to boost the economic recovery. The World Bank; 2021. Reference Source\n\nNossier SA: Vaccine hesitancy: the greatest threat to COVID-19 vaccination programs. J. Egypt. Public Health Assoc. 2021 Dec 5; 96(1): 18. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWilson SL, Wiysonge C: Social media and vaccine hesitancy. BMJ Glob. Heal. 2020 Oct; 5(10): e004206. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIslam MS, Kamal A-HM, Kabir A, et al.: COVID-19 vaccine rumors and conspiracy theories: The need for cognitive inoculation against misinformation to improve vaccine adherence. Lavorgna L, editor. PLoS One. 2021 May 12; 16(5): e0251605. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPierri F, Perry BL, DeVerna MR, et al.: Online misinformation is linked to early COVID-19 vaccination hesitancy and refusal. Sci. Rep. 2022 Apr 26; 12(1): 5966. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nWagner AL, Huang Z, Ren J, et al.: Vaccine hesitancy and concerns about vaccine safety and effectiveness in Shanghai, China. Am. J. Prev. Med. 2021 Jan; 60(1): S77–S86. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nBertin P, Nera K, Delouvée S: Conspiracy beliefs, rejection of vaccination, and support for hydroxychloroquine: A conceptual replication-extension in the COVID-19 pandemic context. Front. Psychol. 2020 Sep 18; 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDouglas KM: COVID-19 conspiracy theories. Gr. Process Intergr. Relations. 2021 Feb 4; 24(2): 270–275. Publisher Full Text\n\nTwitter help centre: COVID-19 misleading information policy. Twitter.Reference Source\n\nMinistry of Communication and Informatics of Republic of Indonesia: Pers release No. 116/HM/KOMINFO/09/2020. Pemerintah RI nyatakan komitmen tangani Infodemic.\n\nGermani F, Biller-Andorno N: The anti-vaccination infodemic on social media: A behavioral analysis. PLoS One. 2021 Mar 3; 16(3): e0247642. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen J, Wang Y: Social media use for health purposes: Systematic review. J. Med. Internet Res. 2021 May 12; 23(5): e17917. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nNugraha RR, Miranda AV, Ahmadi A, et al.: Accelerating Indonesian COVID-19 vaccination rollout: a critical task amid the second wave. Trop. Med. Health. 2021 Dec 22; 49(1): 76. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaied SM, Saied EM, Kabbash IA, et al.: Vaccine hesitancy: Beliefs and barriers associated with COVID-19 vaccination among Egyptian medical students. J. Med. Virol. 2021 Jul 25; 93(7): 4280–4291. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKalanjati VP, Hasanatuludhhiyah N, d’Arqom A, et al.: Health literacy on COVID-19 and COVID-19 vaccinations in Indonesia [version 2; peer review: 2 approved]. F1000Research. 2022; 11: 1296. Publisher Full Text" }	[ { "id": "219774", "date": "15 Nov 2023", "name": "Giuseppe Porro", "expertise": [ "Reviewer Expertise sentiment analysis", "subjective well-being evaluation", "statistical methods for causal inference" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper offers a sentiment and opinion analysis about the reactions to Covid-19 pandemic, vaccination strategies and measures of social restrictions in Indonesia. The data source is a collection of Twitter messages posted between January 2020 and August 2021.\nThe topic is interesting, its relevance is well argued and the results are properly presented and discussed.\nMy main remarks concern the opportunity of providing more detailed information about the methodology the Authors apply in the study.\n\nThe unavailability of the data (due to privacy constraints) makes it necessary to be clear about the analytical procedures illustrated in Fig.1, in order to ensure the replicability of the study, albeit with different data and to avoid, as far as possible, any \"black box\" effect.\nIn particular:\na) I assume that the data were labeled into the categories indicated in Table 1 in the downloading stage. Then they were further classified into \"classes, which were tweet exposure and engagement analysis\" (p.3): how was this classification stage performed?\nb) before classifying data, a cluster analysis was applied using IndoBERT model. What is the role of cluster analysis in the study? Is there any relationship between cluster analysis and classification stages? Or, alternatively, is cluster analysis only aimed at visual inspection of data (in this case, it should be described before the classification stage, in order to avoid misunderstanding)?\n\nc) please, provide details on how the sentiment analysis is performed: how is a tweet evaluated as positive, negative or neutral? At p.5 (point 2) the manual classification of a 3000-texts-size random sample is described and indicated as a training set for the IndoBERT model. How does the IndoBERT model work? Is the 75% accuracy rate the result of a test by the Authors themselves?\nd) p.2, point 2: the description of the content of positive, negative and neutral tweets is accompanied by a sort of opinion analysis: is it the result of a reading of the training sample or has an opinion analysis been actually extended to the whole dataset?\ne) despite the low incidence of fake tweets, the Authors invite not to undervalue the impact of fake news. Is there any way for identifying a fake news diffusion pattern, following retweets, replies and \"like\"s, as these seem to be available pieces of information (see p.6)?\nIn order not to move the focus of the paper from a public health to an artificial intelligence one, going into a more detailed description of the methodology may require a methodological appendix, where some examples could also be provided.\nMinor remarks:\n- as usual, when a sentiment or opinion analysis is performed via social network sites data, some words should be spent to comment the lack of representativeness of these data with respect to the whole country population.\n\n- Table 1: I'm assuming possible overlap between the \"Covid-19\" and the \"Covid-19 Vaccine and Vaccination\" subsets. This, of course, does not undermine the validity of the analysis in any sense, but it should be pointed out to the reader.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10602", "date": "29 Nov 2023", "name": "Viskasari Kalanjati", "role": "Author Response", "response": "The paper offers a sentiment and opinion analysis about the reactions to Covid-19 pandemic, vaccination strategies and measures of social restrictions in Indonesia. The data source is a collection of Twitter messages posted between January 2020 and August 2021. The topic is interesting, its relevance is well argued and the results are properly presented and discussed. Answer: We highly appreciate your comment. My main remarks concern the opportunity of providing more detailed information about the methodology the Authors apply in the study. The unavailability of the data (due to privacy constraints) makes it necessary to be clear about the analytical procedures illustrated in Fig.1, in order to ensure the replicability of the study, albeit with different data and to avoid, as far as possible, any \"black box\" effect. In particular: a) I assume that the data were labeled into the categories indicated in Table 1 in the downloading stage. Then they were further classified into \"classes, which were tweet exposure and engagement analysis\" (p.3): how was this classification stage performed? — Answer: Thank you for the question. We try to clarify the explanation of the stages of analysis in the manuscript. Please find it in the revised manuscript, in the method chapter. b) before classifying data, a cluster analysis was applied using IndoBERT model. What is the role of cluster analysis in the study? Is there any relationship between cluster analysis and classification stages? Or, alternatively, is cluster analysis only aimed at visual inspection of data (in this case, it should be described before the classification stage, in order to avoid misunderstanding)? — Answer: We highly appreciate your question. We have clarified the explanation of the method. Please find it in the revised manuscript. We reworded the term of cluster analysis. We used IndoBERT model to label all cleaned data within the categories of positive, neutral, and negative sentiments. IndoBERT (Bidirectional Encoder Representations from Transformers) constitutes a self-contained Deep Learning model designed for Natural Language Processing (NLP), inspired by the Transformer model. Each output element in this model is intricately connected to every input element, with dynamically computed weights based on inter-element relationships. BERT is formulated to aid computers in comprehending the ambiguous meaning of language within a text by utilizing the surrounding text to establish context. IndoBERT represents the Indonesian iteration of the BERT model, a Deep Learning model tailored for Natural Language Processing (NLP). This model is trained using over 220 million words in the Indonesian language. BERT is engineered to assist computers in understanding the ambiguous meaning of language within a text by leveraging the surrounding text to construct context, thereby obtaining improved word weighting values. In this study, IndoBERT is employed for the tokenization process of words before engaging in the classification task. Following the successful tokenization of the Indonesian language by IndoBERT, the data proceeds directly to the classifier layer to discern patterns in word tendencies, classifying them into three categories: positive, neutral, and negative. c) please, provide details on how the sentiment analysis is performed: how is a tweet evaluated as positive, negative or neutral? At p.5 (point 2) the manual classification of a 3000-texts-size random sample is described and indicated as a training set for the IndoBERT model. How does the IndoBERT model work? Is the 75% accuracy rate the result of a test by the Authors themselves? Answer: Thank you for the question. The training and testing processes within the IndoBERT model depend on a dataset prepared by the researcher, comprising 3000 randomly selected text data. The entirety of this process involves the researcher labeling the data into three classes. Upon completion of the labeling process, the data is subsequently partitioned into training and testing sets at an 80%:20% ratio. The training data is utilized by the IndoBERT model to discern patterns within words indicative of their tendency to fall into one of three categories: positive, neutral, or negative. After the model completes its training process, the subsequent step involves testing the data. Specifically, the model attempts to predict text data using the test data and compares these predictions with the labels assigned by the researcher. This comparative analysis aims to demonstrate the model's performance in classifying text sentiment. The results of this testing reveal an accuracy value of 75%, evaluated against the labels predicted by the model and those designated by the researcher. This accuracy value signifies the model's successful acquisition of patterns in the Indonesian language and its proficient performance in sentiment classification. d) p.2, point 2: the description of the content of positive, negative and neutral tweets is accompanied by a sort of opinion analysis: is it the result of a reading of the training sample or has an opinion analysis been actually extended to the whole dataset? — Answer: Thank you for the question, The opinion analysis has been applied to the whole dataset. e) despite the low incidence of fake tweets, the Authors invite not to undervalue the impact of fake news. Is there any way for identifying a fake news diffusion pattern, following retweets, replies and \"like\"s, as these seem to be available pieces of information (see p.6)? — Answer: Thank you for the question. This is an interesting topic to learn more about the diffusion pattern of circulating fake news, that necessarily will be useful for combating the spread of fake news. For further research, the idea is to capture all the metadata of users who interacted with the main post that the model has predicted as fake news by crawling all replies, likes, and retweets. This enables us to track how far the influences of the first posts are. It is also interesting for further study about the development of automated reply that notifies the main post audience that this Tweet has been classified as fake news, and provides a valid source of information In order not to move the focus of the paper from a public health to an artificial intelligence one, going into a more detailed description of the methodology may require a methodological appendix, where some examples could also be provided. Answer: Thank you for the suggestion. We highly appreciate it. Since this journal applies an open review system whereby all readers can access the communication between authors and reviewers, details of the methods can easily be found through this communication. Therefore, we do not add the appendix. Minor remarks: - as usual, when a sentiment or opinion analysis is performed via social network sites data, some words should be spent to comment the lack of representativeness of these data with respect to the whole country population. Answer: Thank you for the suggestion. We are pleased to accommodate it. - Table 1: I'm assuming possible overlap between the \"Covid-19\" and the \"Covid-19 Vaccine and Vaccination\" subsets. This, of course, does not undermine the validity of the analysis in any sense, but it should be pointed out to the reader. Answer: Thank you for the suggestion. We are pleased to accommodate it." } ] }, { "id": "206421", "date": "27 Feb 2024", "name": "Annisa Ristya Rahmanti", "expertise": [ "Reviewer Expertise health informatics", "NLP", "social media data analytics", "AI" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe work presents a clear and structured overview of the study, which focuses on analyzing sentiments regarding COVID-19 and vaccinations expressed in Indonesian-language tweets. However, while the author briefly mentions previous studies, the current research would benefit from a more comprehensive literature review. This would better contextualize the research within the broader scope of existing findings, particularly those focusing on studies conducted in similar contexts or regions. The study design employs relevant tools such as the IndoBERT model for clustering and the difflib library for string comparison. However, the technical soundness is difficult to fully assess without more detail on the validation of these methods and their appropriateness for the analysis of Indonesian-language tweets. Could you provide the performance model? Although the results were presented using pie charts to illustrate sentiment trends, a time series analysis would provide a more accurate representation of how sentiments have evolved over time. Time series analysis can capture the dynamic nature of public opinion affected by fake news or government actions, allowing for a clearer understanding of trends and patterns that may not be immediately apparent in static visual representations such as pie charts. It would be pertinent to adjust the conclusion to acknowledge the methodological limitations and suggest more robust analytical methods, like time series analysis, for future studies. Additionally, addressing the ethical considerations involved in using social media data is also crucial.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11218", "date": "13 Apr 2024", "name": "Viskasari Kalanjati", "role": "Author Response", "response": "Comment and suggestion: The work presents a clear and structured overview of the study, which focuses on analyzing sentiments regarding COVID-19 and vaccinations expressed in Indonesian-language tweets. However, while the author briefly mentions previous studies, the current research would benefit from a more comprehensive literature review. This would better contextualize the research within the broader scope of existing findings, particularly those focusing on studies conducted in similar contexts or regions. Answer: Thank you for the insightful comment. We have added an explanation of our result in comparison with other studies in Indonesia. Please find it in the result and discussion chapter. The study design employs relevant tools such as the IndoBERT model for clustering and the difflib library for string comparison. However, the technical soundness is difficult to fully assess without more detail on the validation of these methods and their appropriateness for the analysis of Indonesian-language tweets. Could you provide the performance model? Answer: Thank you for the suggestion. We have added an explanation about the validation of IndoBert Model, and cited previous studies that have shown good performance and validity of IndoBERT model. Difflib is an established method of string comparison that is often used to examine the similarity of text. Please find further explanation at https://docs.python.org/3/library/difflib.html . Although the results were presented using pie charts to illustrate sentiment trends, a time series analysis would provide a more accurate representation of how sentiments have evolved over time. Time series analysis can capture the dynamic nature of public opinion affected by fake news or government actions, allowing for a clearer understanding of trends and patterns that may not be immediately apparent in static visual representations such as pie charts. Answer: Thank you for the suggestion. We highly appreciate it. We recognize it as one of the limitations of our study and put it in a suggestion for future studies. It would be pertinent to adjust the conclusion to acknowledge the methodological limitations and suggest more robust analytical methods, like time series analysis, for future studies. Additionally, addressing the ethical considerations involved in using social media data is also crucial. Answer: Thank you for the suggestion. We have made revisions accordingly. Please find it in the paragraph about the limitations of our study and also in the conclusion." } ] } ]	1	https://f1000research.com/articles/12-1007
https://f1000research.com/articles/12-208/v1	23 Feb 23	{ "type": "Research Article", "title": "Impact of an educational flyer and sensitization on performance-enhancement attitudes of bodybuilders in United Arab Emirates", "authors": [ "Dixon Thomas", "Adhnan Abdul Shabeek", "Hala Ahmed", "Malak Mohammed", "Marina Kawaguchi-Suzuki", "Ashley Anderson", "Aji Gopakumar", "Reema Alhosani", "Sherief Khalifa", "David Mottram", "Adhnan Abdul Shabeek", "Hala Ahmed", "Malak Mohammed", "Marina Kawaguchi-Suzuki", "Ashley Anderson", "Aji Gopakumar", "Reema Alhosani", "Sherief Khalifa", "David Mottram" ], "abstract": "Background: A high proportion of bodybuilders use supplements to improve performance, with some turning to prohibited substances and methods. The attitudes of bodybuilders towards performance enhancement may be gauged through surveys such as the Performance Enhancement Attitude Scales (PEAS). Educational interventions are recommended as part of anti-doping measures. The objective of this project was to assess the impact of a pharmacy-led intervention using an antidoping educational flyer and the performance enhancement attitude scale to measure the attitude of bodybuilders in the United Arab Emirates (UAE). Methods: The PEAS eight-item short form questionnaire was administered to male bodybuilders in the UAE. The PEAS was conducted before and after administration of an educational flyer concerning the problems associated with supplement use among bodybuilders. The Wilcoxon Signed-Rank and Kruskal Wallis tests were used for data analysis. Results: A total of 218 bodybuilders, who reported taking dietary supplements, filled out the survey both pre and post viewing the antidoping educational flyer. A difference was observed between the full-time professional bodybuilders, students, and part-time bodybuilders with other primary occupations (p-value <0.05). In addition, PEAS score decreased among the study population for all eight PEAS items (p-value <0.05). Conclusions: The pharmacy-led intervention using an antidoping educational flyer and sensitization by PEAS achieved more favorable scores, suggesting a significant shift of opinion toward avoiding use of performance enhancing substances among the bodybuilder study population. More research is required on sustaining the attitude and demonstrating the impact on doping behavior.", "keywords": [ "Bodybuilders", "performance enhancement", "doping", "educational intervention" ], "content": "Introduction\n\nExercise in gymnasiums is a feasible way to be physically active in the United Arab Emirates (UAE). Chronic diseases pose significant public health issues among the UAE population.1 In particular, attitudes about obesity management need improvement.2 There is a lack of public awareness of the importance of engaging in physical activity in the UAE, resulting in high levels of sedentary behavior among young adults.3 Promotion of the benefits of physical activity are therefore required among the UAE population.4\n\nIt is acknowledged, however, that gymnasium use may progress from simple exercise regimens to a desire for image enhancement that leads some to bodybuilding.5 Among gymnasium users in the UAE, bodybuilding, either for non-competitive (recreational) or competitive purposes, is a popular sport. The motivation for bodybuilding is manifold and ranges from the improvement of body image and well-being through to participation in competitive sport.6\n\nMany gymnasium-users take supplements to improve their performance or image enhancement. In a study in Sharjah, it was shown that about half of the men exercising in gyms were using dietary supplements.7 In another study, in Dubai, it was reported that people who were consuming dietary supplements had a high level of knowledge about the supplements that they used and consequently, adverse events were infrequent.8\n\nDietary supplements are used widely among bodybuilders. However, in addition, some bodybuilders may use hormonal products, which pose a potential health risk9 and may lead to illegal doping in the competitive areas of bodybuilding.10,11 Some bodybuilders in the Gulf region reportedly use anabolic steroids,12 reflecting an increased prevalence of anabolic-androgenic steroid (AAS) use generally across the Eastern Mediterranean Region.13\n\nMany factors contribute to performance enhancement by bodybuilders and its progressive normalization.14 There is a growing body of evidence which suggests that anabolic androgenic steroids are used globally by a diverse population, with varying motivations, including bodybuilders.15 As the trend of bodybuilding is transforming to create a well-defined and moderately muscular body, it is speculated that fitness doping is becoming increasingly common.16 However, the boundary between natural performance enhancement and doping might be blurred for the bodybuilders. Considering the potential adverse effects of AAS use on health, it is important to consider intervention strategies to prevent misuse, both in sport and in the general population.17 Such strategies include targeted education and a greater understanding on doping attitudes through tools such as the Performance Enhancement Attitude Scale (PEAS).18\n\nPharmacists are well-placed and highly accessible resources of drug information for the public. The opportunity exists to increase pharmacy-led initiatives that support the antidoping movement.\n\nAntidoping assessments and education raise awareness of doping. It is suspected that bodybuilders might be sensitized to the problems of performance enhancement attitude just by filling out the pre-intervention survey. This awareness of perceptions associated with doping, in addition to the educational flyer developed for antidoping education for bodybuilders, was expected to influence attitudes toward higher concern for the risk of performance enhancement substances among bodybuilders in the study population.\n\nThe aim of this project was to assess the impact on local bodybuilders’ views of using substances for performance enhancement before and after a pharmacy led intervention using an antidoping educational flyer, as measured by the PEAS.\n\n\nMethods\n\nThe study used a pre-post intervention design. Attitudinal data were collected using a PEAS. An antidoping educational flyer was designed by a sports pharmacy team with a simple infographic design and clear messaging on the risk of doping. Sports pharmacy team members then administered the intervention by presenting the educational flyer to bodybuilders enrolled in the study. The educational flyer is included as Figure 1. The educational flyer was provided to bodybuilders prior to the post-intervention survey. The second PEAS survey was administered approximately one month after the first administration of the PEAS survey among the study population.\n\nThe study population included self-described bodybuilders in the UAE. The study did not use any brand name or manufacturer names of any performance enhancement substance. Being a male bodybuilder who uses nutritional supplements and consenting to participate in the study were the inclusion criteria. Any level of bodybuilders, including recreational, amateur, or professional athletes, were recruited. Bodybuilders who were not regularly practicing in their gym, could not read English, or were not living in the UAE were excluded from the study population. Background data was collected from the bodybuilders on their level of involvement in bodybuilding and nutritional supplements used.\n\nThe sample size was calculated using a formula that considers the population size, margin of error, and sampling confidence level. Survey Monkey's sample size calculator accounts for the three factors mentioned above. The bodybuilder population in UAE is approximately 500,000, based on data from Dubai World Trade Centre. Using a 95% confidence interval and margin of error of eight, the calculated sample size was 151 bodybuilders. The sampling strategy included distributing a pre-intervention survey to registered study participants through email and WhatsApp. A post-intervention survey following the educational intervention was sent only to those who completed the pre-intervention survey. Each survey was conducted using Google Forms and paper-based by member of the sports pharmacy team visiting local gyms. The total duration of the study was one year.\n\nA modified version of the PEAS, known as the eight-item short form, was used as the survey instrument.18,19 For each item a six-point Likert scale of strongly disagree (1), disagree (2), slightly disagree (3), slightly agree (4), agree (5), and strongly agree (6) was used. The PEAS is an internationally validated instrument. Only in required items, the word “bodybuilding” was added to connect to the athletes of this study population. The meaning of doping was added in parenthesis when it appeared for the first time on the survey. In addition to some background enquiries, the pre- and post-survey questionnaire included the following eight-items.\n\n1. Legalizing performance enhancements would be beneficial for sports or bodybuilding (competitive or non-competitive).\n\n2. Doping (consuming prohibited substances) is necessary to be competitive.\n\n3. The risks related to doping (consuming prohibited substances) are exaggerated.\n\n4. Bodybuilders should not feel guilty about breaking the rules and taking performance-enhancing drugs.\n\n5. Doping is an unavoidable part of competitive sport/bodybuilding.\n\n6. Doping is not cheating since everyone does it.\n\n7. Only the quality of performance should matter, not the way bodybuilders achieve it.\n\n8. There is no difference between drugs and dietary supplements that are all used to enhance performance.\n\nA higher number for the final score of the PEAS suggests agreement with the statements that support use of performance enhancing substances or the doping culture.\n\nEthical approval to conduct the research was granted by the Institutional Review Board of the Gulf Medical University (IRB/COP/STD/73/Oct-2021). Written informed consent was obtained for participating in the study. No personal identifiers of study participants were collected except email and phone numbers for sending the post-intervention survey. Such contact details were kept confidential. No brand names of bodybuilding supplements or medications were mentioned in the study. All confidential information was maintained by the authors from Gulf Medical University and not shared with the authors from other organizations in this study.\n\nDescriptive and analytical statistical tools were used to compare the attitudes of bodybuilders before and after the pharmacy-led educational intervention. Wilcoxon Signed-Rank test was used to assess performance enhancement attitude (PEA) scores before and after the intervention. Kruskal Wallis tests were used to find the statistical significance of the pre-post intervention among different groups. SPSS version 26 (Armonk) was used for all the analyses.\n\n\nResults\n\nOf the 322 bodybuilders who filled out the pre-intervention survey, 254 completed the post-intervention surveys (79% response rate).29 For the analysis, 22 respondents were removed due to the lack of matching email or mobile numbers used as identifiers in the pre-survey to post-survey tracking. Other respondents were excluded from the study by not being located in the UAE or reporting they were not consuming dietary supplements. A final total of 218 respondents were used for the data analysis. The majority (98.2%) of study participants found the antidoping educational flyer to be informative, while four (1.8%) participants responded that it was not informative enough.\n\nThe study population constituted of 80 bodybuilders of non-sports employment, 16 full-time bodybuilders, 111 university students, and 11 school students. All were male. The Kruskal Wallis test showed a significant difference in the post-intervention (p-value 0.002) but not in pre-intervention (p-value 0.07) among the four subgroups of this study population.\n\nWhen the average score is compared among the four groups by the median test, the median (average) of the overall pre-score varied across the groups (p-value <0.001), but the average of the overall pre-score is almost the same between the groups (p-value 0.07). It implies that the post score changed significantly when compared with the average pre-score, but the average attitude level became stable and is matched among different types of participants.\n\nWith the intervention of the educational flyer and sensitization, the PEA was changed favorably towards recognition of concerns associated with doping among the participants. Agreement to pro-doping statements in the PEAS survey decreased, meaning disagreement increased with the intervention as shown in Table 1. For tabulation, “strongly agree” and “agree” were combined; likewise, responses of “slightly agree” and “slightly disagree,” and “disagree” and “strongly disagree” were combined.\n\nAs per the Wilcoxon sign rank test, the average performance enhancement attitude levels before and after were significantly different in the study sample. The distribution of attitude scores were reduced from before to after the intervention with statistical significance in addition to median of agreement decreased for 7 out of 8 items (Table 2).\n\nThe median score for the pre-intervention survey was 24, and for the post-intervention survey was 14. The decrease in median score demonstrated a movement away from supporting use of performance enhancement substances and toward an anti-doping awareness.\n\n\nDiscussion\n\nThe aim of this study was to assess any changes in the attitude of bodybuilders in the UAE about the use of supplements and doping, following the introduction of an antidoping educational flyer. The major finding was that there were significant changes in the attitudes of the study population to performance enhancement through supplement use and doping practices following pharmacy-led education with introduction of an antidoping flyer. Analysis of the responses to the eight-item PEAS survey revealed significantly different scores between pre- and post-intervention, suggesting less support for the use of performance enhancement substance among study participants. Using median, statistical tests proved the significance of the decrease in all eight survey items. Educational interventions and sensitization of sports people have shown similar results in the following studies.\n\nIt was found that doping susceptibility perceptions can be immediately reduced with educational interventions. The face-to-face intervention was observed to be more sustainable than online interventions among high-level athletes.20 Nevertheless, a mobile application was found to be a practical method for disseminating anti-doping education. The application improved knowledge and decreased favorable doping attitudes among coaches. The mobile application had educational modules on nutritional supplements, substances, rules, leadership, and fair play.21 Practical strength training advice provided in addition to anti-doping education to youth athletes was found beneficial in decreasing PEA.22 PEA was found in many studies among gym users and athletes. Such studies proposed educational interventions to decrease PEA.7,8,23\n\nSensitizing those who have potential for doping needs to start early, even in schools. Students who were professionally involved in sports perceived performance enhancement as more acceptable than other students.24 Body image, nutritional supplement use, and weight change behaviors influence adolescents' PEA.25 Media literacy interventions were effective to decrease doping behaviors of adolescent students.26 It is accepted that attitudes and knowledge about doping are influenced by educational activity.27,28 In addition, it is also possible that the studies itself had sensitized participants against PEA as assumed in our study.\n\n\nConclusion\n\nThis study showed that the PEAS short-form survey, along with the introduction of an antidoping educational flyer provided by a sports pharmacy team, resulted in decreasing PEA among bodybuilding populations in the UAE. The decline of PEA was significant for all eight items of the PEAS. Bodybuilders, regardless of level of profession in the sport or level of competition, showed reduction in their attitude scores in the post-intervention survey. This study shows the potential for pharmacy-led educational interventions for bodybuilder athletes to influence favorable PEA, in support of the antidoping movement.\n\nA limitation of the study was that, even though the UAE is a multicultural society, with English and Arabic being common languages, the survey was only conducted in English; therefore, the study population might not have fully represented the UAE population.", "appendix": "Data availability\n\nOSF: Drug Use, https://doi.org/10.17605/OSF.IO/AUQX2. 29\n\nThis project contains the following underlying data:\n\n• Bodybuilder survey.xlsx (This file contains raw data used for statistical analysis).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe Acknowledge Leena Salam, BS, from Pacific University School of Pharmacy, for her contribution to creating the educational flyer with the authoring team.\n\n\nReferences\n\nLoney T, Aw TC, Handysides DG, et al.: An analysis of the health status of the United Arab Emirates: the ‘Big 4’ public health issues. Glob. Health Action. 2013 Dec 1; 6(1): 20100. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNawar R, Ibrahim E, Abusnana S, et al.: Understanding the Gaps in Obesity Management in the UAE: Perceptions, Barriers, and Attitudes. Dubai Diabetes Endocrinol. J. 2021; 27(2): 37–49. Publisher Full Text\n\nDalibalta S, Majdalawieh A, Yousef S, et al.: Objectively quantified physical activity and sedentary behaviour in a young UAE population. BMJ Open Sport Exerc. 2021 Jan 1; 7(1): e000957. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYammine K: The prevalence of physical activity among the young population of UAE: a meta-analysis. Perspect. Public Health. 2017 Sep; 137(5): 275–280. PubMed Abstract \| Publisher Full Text\n\nCoquet R, Roussel P, Ohl F: Understanding the paths to appearance-and performance-enhancing drug use in bodybuilding. Front. Psychol. 2018; 9: 1431. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChristiansen AV, Vinther AS, Liokaftos D: Outline of a typology of men’s use of anabolic androgenic steroids in fitness and strength training environments. Drugs: Educ. Prev. Policy. 2017 May 4; 24(3): 295–305. Publisher Full Text\n\nSharif SI, Mohammed A, Mohammed I, et al.: Evaluation of knowledge, attitude and use of dietary supplements among people exercising in the gym in Sharjah-United Arab Emirates. Phys. Med. Rehabil. Res. 2018; 3(5): 1–5.\n\nAbdulla NM, Aziz F, Blair I, et al.: Prevalence of, and factors associated with health supplement use in Dubai, United Arab Emirates: a population-based cross-sectional study. BMC Complement. Altern. Med. 2019 Dec; 19(1): 1–1.\n\nMontuori P, Loperto I, Paolo C, et al.: Bodybuilding, dietary supplements and hormones use: behaviour and determinant analysis in young bodybuilders. BMC Sports Sci. Med. Rehabil. 2021 Dec; 13(1): 1–1. Publisher Full Text\n\nHeller S, Ulrich R, Simon P, et al.: Refined analysis of a cross-sectional doping survey among recreational triathletes: Support for the nutritional supplement gateway hypothesis. Front. Psychol. 2020 Sep 23; 11: 561013. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBackhouse SH, Whitaker L, Petróczi A: Gateway to doping? Supplement use in the context of preferred competitive situations, doping attitude, beliefs, and norms. Scand. J. Med. Sci. Sports. 2013 Mar; 23(2): 244–252. PubMed Abstract \| Publisher Full Text\n\nAbdullGaffar B: Illicit injections in bodybuilders: a clinicopathological study of 11 cases in 9 patients with a spectrum of histological reaction patterns. Int. J. Surg. Pathol. 2014 Dec; 22(8): 688–694. PubMed Abstract \| Publisher Full Text\n\nHearne E, Wazaify M, Van Hout MC, et al.: Anabolic-androgenic steroid use in the Eastern Mediterranean region: A scoping review of extant empirical literature. Int. J. Ment. Health Addict. 2021 Aug; 19(4): 1162–1189. Publisher Full Text\n\nAndreasson J, Johansson T: Bodybuilding and fitness doping in transition. Historical transformations and contemporary challenges. Soc. Sci. 2019 Mar 4; 8(3): 80. Publisher Full Text\n\nBates G, Begley E, Tod D, et al.: A systematic review investigating the behaviour change strategies in interventions to prevent misuse of anabolic steroids. J. Health Psychol. 2019 Sep; 24(11): 1595–1612. PubMed Abstract \| Publisher Full Text\n\nPetróczi A: Attitudes and doping: a structural equation analysis of the relationship between athletes' attitudes, sport orientation and doping behaviour. Subst. Abuse Treat. Prev. Policy. 2007 Dec; 2(1): 1–5. Publisher Full Text\n\nBates G, Van Hout MC, Teck JT, et al.: Treatments for people who use anabolic androgenic steroids: a scoping review. Harm Reduct. J. 2019 Dec; 16(1): 1–5.\n\nPetróczi A, Aidman E: Measuring explicit attitude toward doping: Review of the psychometric properties of the Performance Enhancement Attitude Scale. J. Sport Exerc. Psychol. 2009 May 1; 10(3): 390–396. Publisher Full Text\n\nFolkerts D, Loh R, Petróczi A, et al.: The Performance Enhancement Attitude Scale (PEAS) reached ‘adulthood’: Lessons and recommendations from a systematic review and meta-analysis. J. Sport Exerc. Psychol. 2021 Jun 8; 56: 101999. Publisher Full Text\n\nNicholls AR, Morley D, Thompson MA, et al.: The effects of the iPlayClean education programme on doping attitudes and susceptibility to use banned substances among high-level adolescent athletes from the UK: A cluster-randomised controlled trial. Int. J. Drug Policy. 2020 Aug 1; 82: 102820. PubMed Abstract \| Publisher Full Text\n\nNicholls AR, Fairs LR, Plata-Andrés M, et al.: Feasibility randomised controlled trial examining the effects of the Anti-Doping Values in Coach Education (ADVICE) mobile application on doping knowledge and attitudes towards doping among grassroots coaches. BMJ Open Sport Exerc. Med. 2020 Oct 1; 6(1): e000800. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSagoe D, Holden G, Rise EN, et al.: Doping prevention through anti-doping education and practical strength training: The Hercules program. Perform. Enhanc. Health. 2016 Sep 1; 5(1): 24–30. Publisher Full Text\n\nAl Nozha OM, Elshatarat RA: Influence of knowledge and beliefs on consumption of performance-enhancing agents in north-western Saudi Arabia. Ann. Saudi Med. 2017 Jul; 37(4): 317–325. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVargo EJ, James RA, Agyeman K, et al.: Perceptions of assisted cognitive and sport performance enhancement among university students in England. Perform. Enhanc. Health. 2014 Jun 1; 3(2): 66–77. Publisher Full Text\n\nYager Z, O’Dea JA: Relationships between body image, nutritional supplement use, and attitudes towards doping in sport among adolescent boys: implications for prevention programs. J. Int. Soc. Sports Nutr. 2014 Mar 27; 11(1): 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLucidi F, Mallia L, Alivernini F, et al.: The effectiveness of a new school-based media literacy intervention on adolescents’ doping attitudes and supplements use. Front. Psychol. 2017 May 9; 8: 749. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDeng Z, Guo J, Wang D, et al.: Effectiveness of the world anti-doping agency's e-learning programme for anti-doping education on knowledge of, explicit and implicit attitudes towards, and likelihood of doping among Chinese college athletes and non-athletes. Subst. Abuse Treat. Prev. Policy. 2022 Dec; 17(1): 1–3.\n\nWolff W, Schindler S, Brand R: The effect of implicitly incentivized faking on explicit and implicit measures of doping attitude: when athletes want to pretend an even more negative attitude to doping. PLoS One. 2015 Apr 22; 10(4): e0118507. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThomas D: Drug Use. [Dataset]. 2023. Publisher Full Text" }	[ { "id": "164451", "date": "14 Mar 2023", "name": "Narayana Goruntla", "expertise": [ "Reviewer Expertise Pharmacoepidemiology", "Pharmacoeconomics", "Pharmacovigilance", "Health Education", "Epidemiology", "Public health", "Clinical Pharmacy", "and Pharmacy Practice." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, the study was novel, interesting, and well-designed, and drew reliable findings by application of suitable statistical methods. The study shows the significance of pharmacist-led interventions in lowering the doping property PEAS in bodybuilders. This study will serve as new evidence of pharmacist contribution to Antidoping. With a few modifications given below, the work can be processed for publication.\nIn the background of the study, better to provide some evidence of generic names of drugs or chemicals that favors doping and causes health risks or complications.\n\nThough the PEAS short form is standard, validated, and internationally acceptable, the reliability of the tool in the study population can be given by providing Cronbach’s Alpha value. Because it was mentioned that the tool was modified according to the study need (applicable to bodybuilders and doping strategies).\n\nIn the sample size determination, though the recommended sample size is acceptable, the margin of error needs to be less than or equal to 5%.\n\nIn the results section, the total study population was divided into four groups, named non-sport employment bodybuilders, full-time bodybuilders, University students, and School students. It was mentioned that the median score was significantly different after intervention. There is a need to mention which group shows a high or low median score.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11406", "date": "21 Jun 2024", "name": "Dixon Thomas", "role": "Author Response", "response": "Many thanks for your valuable comments. Minor modifications are made to the paper based on the comments. Anabolic steroid use and its health risks are mentioned in the introduction. Cronbach’s Alpha could be used next time before start of the study, it is a nice suggestion. We felt the modifications did not affect the structure of statements in PEAS and thus found validation and reliability testing not essential to perform. We agree that the ideal margin of error is less. It was difficult to recruit more bodybuilders, and considering the study design of the pre-post intervention, we believe the relaxation of the sample size is justified. Median scores are added to the article for the four subgroups." } ] }, { "id": "236837", "date": "05 Mar 2024", "name": "Valentin Panayotov", "expertise": [ "Reviewer Expertise Sports science", "dietetics", "statistics", "strength training" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn my opinion several inaccuracies should be addressed: 1. A Bonferroni correction of the pre-post results should be performed. 2. Kruskal Wallis test results are not presented and interpreted. 3. \"When the average score is compared among the four groups by the median test, the median (average) of the overall prescore varied across the groups (p-value <0.001), but the average of the overall pre-score is almost the same between the groups (p-value 0.07). It implies that the post score changed significantly when compared with the average pre-score, but the average attitude level became stable and is matched among different types of participants\". This paragraph is absolutely incomprehensible. It does not become clear whether the terms \"among groups\" and \"across groups\" mean \"between groups\" or \"within groups\". The results of the statistical procedures used should be explained in more detail and visualized by tables or/and graphs. 4.In the results section the authors state that \" The distribution of attitude scores were reduced from before to after the intervention with statistical significance in addition to median of agreement decreased for 7 out of 8 items (Table 2).\" , but in the discussion and conclusion sections they assert that a decrease is measured in all eight items. This discrepancy should be addressed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11419", "date": "21 Jun 2024", "name": "Dixon Thomas", "role": "Author Response", "response": "Many thanks for the wonderful review comments. Statistical interpretation is clarified further with some additional sentences. Inconsistency of 7 out of 8 items was addressed. Eight items in Table 2 are also significant, with a p-value of 0.031, which is less than 0.05. The statements on discussion and conclusion that all 8 items show a statistically significant decrease in performance enhancement attitude are right statements." } ] }, { "id": "250949", "date": "25 Mar 2024", "name": "Nicholas Gibbs", "expertise": [ "Reviewer Expertise I am a qualitative social scientist with expertise in image and performance enhancing drug studies." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciated the background about physical culture and bodybuilding in the UAE and feel like the study was well-justified. The methodology of the work is sound, and the sample size is good enough for a small study like this, leading to credible results. However, I think that there is a blind spot in this paper about the willingness of IPED users to engage with medical services and pharmacists. Lots of literature has pointed to this and, although some improvements have been made with regard to building trust between the two communities, the question of who will actually see the flyer (those who actually engage with pharmacies) is pertinent. I’d like to see some understanding and caveat of that. How was the study advertised and how did recruitment actually take place? You say that you were ‘distributing a pre-intervention survey to registered study participants through email and WhatsApp’, but how did you get these participants’ details in the first instance? I’d like to see more on limitations of the study and a more tentative tone in your conclusion. Perhaps some acceptance that a qualitative aspect would bolster the data and a nod to the need for the flyer to be trailed for long-term effectiveness. By that I mean that, whilst your sample might have reported less inclination to use IPEDs immediately following the flyer, will this attitude be sustained, especially given the normalization of use in some communities?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11408", "date": "21 Jun 2024", "name": "Dixon Thomas", "role": "Author Response", "response": "Many thanks for the wonderful review comments. A pharmacist-athlete encounter study is an interesting future plan. More details on recruitment are added to the survey technique. A few modifications are made to the conclusion and limitations as per suggestion." } ] } ]	1	https://f1000research.com/articles/12-208
https://f1000research.com/articles/11-456/v1	25 Apr 22	{ "type": "Correspondence", "title": "‘Not finding causal effect’ is not ‘finding no causal effect’ of school closure on COVID-19", "authors": [ "Akira Endo" ], "abstract": "In a paper recently published in Nature Medicine, Fukumoto et al. tried to assess the government-led school closure policy during the early phase of the COVID-19 pandemic in Japan. They compared the reported incidence rates between municipalities that had and had not implemented school closure in selected periods from March–May 2020, where they matched for various potential confounders, and claimed that there was no causal effect on the incidence rates of COVID-19. However, the effective sample size (ESS) of their dataset had been substantially reduced in the process of matching due to imbalanced covariates between the treatment (i.e. with closure) and control (without closure) municipalities, which led to the wide uncertainty in the estimates. Despite the study title starting with \"No causal effect of school closures\", their results are insufficient to exclude the possibility of a strong mitigating effect of school closure on incidence of COVID-19. In this replication/reanalysis study, we showed that the confidence intervals of the effect estimates from Fukumoto et al. included a 100% relative reduction in COVID-19 incidence. Simulations of a hypothetical 50% or 80% mitigating effect hardly yielded statistical significance with the same study design and sample size. We also showed that matching of variables that had large influence on propensity scores (e.g. prefecture dummy variables) may have been incomplete.", "keywords": [ "COVID-19", "school closure", "Japan", "causal inference", "reanalysis" ], "content": "Introduction\n\nA paper recently published in Nature Medicine, Fukumoto et al. tried to assess the government-led school closure policy during the early phase of the COVID-19 pandemic in Japan. They compared the reported incidence rates between municipalities that had and had not implemented school closure in selected periods from March–May 2020, where they matched for various potential confounders, and claimed that they found no causal effect on the incidence rates of COVID-19. School closure as a means to control outbreaks has been studied mostly for influenza prior to the emergence of COVID-19, which generally suggested low-to-moderate effects, but the evidence on other respiratory infections including coronavirus diseases has been limited (Viner et al., 2020). Sometimes decisions need to be made in the lack of sufficient evidence in the earliest phase of the pandemic; nonetheless, such decisions should undergo retrospective policy assessment to provide insights and refinement for future pandemic responses.\n\nOne of the challenges in this type of analysis of the early COVID-19 epidemic in Japan is the limited statistical power due to low case counts. During the first wave of the epidemic from February to June 2020 that overlapped with the study period of Fukumoto et al., Japan never observed more than 1,000 COVID-19 cases per day. As a result, out of the total 79,989 municipality-level daily counts from the 847 municipalities included, 99.9% were less than 10 cases per day (Figure S2 of original study). Moreover, matching technique used to minimise confounding has a known side effect of limiting statistical power, especially when there is little overlap in the covariates between arms.\n\nUnfortunately, the analysis in Fukumoto et al. appear to suffer from these issues. The study title says “No causal effect”, which is a rather strong statement given the substantial uncertainty in their estimates. As the saying goes, “absence of evidence is not evidence of absence”—when the uncertainty range covers practically meaningful values, it should not be prematurely concluded that there is “no effect” just because the effect estimates is statistically insignificant. Here I highlight limitations of the analysis and discuss possible factors that may have rendered the study underpowered.\n\n\nRelative ATC and ATT estimates\n\nThe original study measures the effect of school closures as the absolute difference in incidence rates between the treatment and control municipalities. However, the theoretical ground is unclear for assuming a fixed additive effect of school closures to the incidence rate per capita. The effect estimates relative to the baseline incidence would be a more intuitive and interpretable measure for assessment of its practical use. It should also be noted that since incidence rates can only take non-negative values, the absolute mitigating effect of school closure can only be as high as the average incidence rate in the control group.\n\nI rescaled the reported average treatment effects (average treatment effect on the control: ATC and average treatment effect on the treatment: ATT) and their confidence intervals relative to the average outcome (incidence rate per capita) in the control group (Figure 1). The confidence intervals of the relative ATC and ATT cover most of the regions from 100% reduction to 100% elevation, suggesting the underpowered nature of the original study. An effect of 50% reduction (i.e. -50% relative effect), which most experts would agree is of practical significance, or even complete reduction (i.e. -100%) was within the confidence intervals over the substantial part of the period of interest. ESS of the matched arms of around 40–50 (Figure 1d) was likely insufficient to find a statistical significance because incidence of infectious diseases typically exhibits higher dispersion than independent- and identically-distributed settings due to its self-exciting nature (i.e. an increase in cases induces a further increase via transmission).\n\nThe turquoise vertical lines represent the date of treatment (school closure). The black lines and shaded areas represent the mean effect and 95% confidence intervals, respectively. (a) Relative ATC for the closure as of April 6, 2020. (b) Relative ATC for the closure as of April 10, 2020. (d) Relative ATT for the closure as of April 6, 2020. (d) Comparison of sample sizes. The number of all samples included for matching, the number of unique samples matched to at least one other sample and the effective sample size (ESS) of the matched samples are shown.\n\n\nStatistical power demonstration with assumed causal mitigating effect of 50%/80%\n\nTo further examine the statistical power of the study, I artificially modified the dataset such that school closure has a 50% or 80% mitigating effect on the incidence rate per capita. On the treatment reference date (April 6) and onward, the expected incidence rate of each municipality in the treatment group was assumed to be 50%/20% that of the matched control municipality plus Poisson noise (see Extended data: Supplementary document for details). The results suggested that, even with as much as 50%/80% mitigating effect, the approach in the original study might not have reached statistical significance (Figure 2). The absolute ATT for the 50% mitigating effect (Figure 2b) appears similar to what were referred to as “no effect” in the original study. ATT for the 80% mitigating effect was also statistically insignificant (Figure 2c and 2d), suggesting that the study was underpowered to find even moderate to high mitigating effects, if any. ATC estimates also yielded similarly insignificant/barely significant patterns (Figure 3).\n\n(a) The average outcome (incidence per capita) of the matched treatment (black) and control (red) groups for closure as of April 6, 2020. (b) Absolute ATT estimates (black line) and 95% confidence intervals (shaded area) for closure as of April 6. (c) Relative ATT estimates and 95% confidence intervals for closure as of April 6. (d)–(f) Those for closure as of April 10.\n\n(a) The average outcome (incidence per capita) of the unmatched treatment (dashed), matched treatment (black) and control (red) groups for closure as of April 6, 2020. (b) Absolute ATC estimates (black line) and 95% confidence intervals (shaded area) for closure as of April 6. (c) Relative ATC estimates and 95% confidence intervals for closure as of April 6. (d)–(f) Those for closure as of April 10.\n\n\nSeparation of propensity scores\n\nI also noticed that propensity scores computed for one of the subanalyses included, inverse-probability weighting, exhibited substantial/complete “separation” (Heinze & Schemper, 2002) and most samples were essentially lost due to the substantial imbalance in the assigned weights (Figure 4). Although separation of propensity scores can arise from overfitting, in this case it remained (while slightly ameliorated) even after addressing overfitting by Lasso regularisation (Figure 5). This indicates that the treatment assignments may have been nearly deterministic in the dataset, which can compromise the performance of quasi-experimental causal inference via “positivity violation” (Petersen et al., 2020).\n\n(a) Balance of propensity scores before and after matching for school closure as of April 6, 2021. (b) Balance of propensity scores before and after matching for school closure as of April 10, 2021. (c) All and effective sample sizes and the maximum weight among the samples. The effective sample size of NaN indicates that the all samples received zero weights.\n\n(a) The average outcome (incidence per capita) of the unmatched treatment (dashed), matched treatment (black) and control (red) groups for closure as of April 6, 2020. (b) Absolute ATC estimates (black line) and 95% confidence intervals (shaded area) for closure as of April 6. (c) Result of 10-fold cross validation. The x-axis represents the logarithm of the regularisation coefficient λ for each model; the number of included variables is also displayed above the panel. The left dotted vertical line denotes the selected model with best cross validation performance and the right dotted line the most parsimonious within the 1 standard error range of the performance from the best model (for reference purpose). (d) Balance of propensity scores before and after matching. (e)–(h) Those for closure as of April 10. (i) All and effective sample sizes and the maximum weight among the samples.\n\nThe authors did not use propensity scores in the Mahalanobis distance-based genetic matching for the main analysis as opposed to the general recommendation (Diamond & Sekhon, 2013) (the authors cite King & Nielsen, 2019 as a reason not to use propensity scores, the authors of which however clarifies that their criticism does not apply to genetic matching). This means that the covariates that strongly determined the treatment assignment may not have received large weights (and therefore were not prioritised) in the matching process, which could leave unadjusted bias arising from these potential confounders. For example, many regression coefficients for prefecture dummy variables had large values (~5 or larger) in the Lasso-regularised model, whereas 236 out of 483 matched pairs of municipalities in the original analysis for April 6 were from different prefectures. The robustness to the above concerns could be assessed by computing ESS from another genetic matching including propensity scores and a calliper (to ensure the matched pairs have sufficiently similar features), which I report in the next section.\n\n\nReanalysis with genetic matching with propensity scores and a calliper\n\nI reanalysed the original dataset with the genetic matching algorithm incorporating propensity scores and a calliper and estimated ATCs for school closures as of Aril 6 and 10, 2020. Propensity scores were estimated by a Lasso-regularised linear regression model and included in genetic matching with a calliper of 0.25 (Rosenbaum & Rubin, 1985). The results remained statistically insignificant and the confidence intervals for the relative effects covered most region from -100% to 100%, although the direction of the weak trend reversed for closure as of April 6 from the original study (Figure 6). ESS of the matched treatment group was only 7 and 3.8 for April 6 and 10, respectively, indicating that the results relied on only a small set of samples that were repeatedly used in matching. Genetic matching is generalisation of propensity score and Mahalanobis distance matching that searches for optimal covariate balance and thus should achieve no worse balance than matching using only Mahalanobis distance (Diamond & Sekhon, 2013). The substantial loss of ESS in the updated genetic matching with propensity scores suggests that improved matching required more samples to be discarded and that both the original and current results are likely unreliable.\n\n(a) The average outcome (incidence per capita) of the unmatched treatment (dashed black), matched treatment (solid black) and control (red) groups for closure as of April 6, 2020. (b) Absolute ATC estimates (black line) and 95% confidence intervals (shaded area) for closure as of April 6. (c) Relative ATC estimates and 95% confidence intervals for closure as of April 6. (d)–(f) Those for closure as of April 10.\n\n\nConclusion\n\nThe reanalysis of Fukumoto et al. suggested that the study was inherently underpowered to identify the presence of causal effects of school closure on COVID-19. While I recognise the importance of their attempt to assessing the school closure policy given its collateral effect imposed onto students and their family, I argue that their conclusion of “no causal effect” was not well supported by data due to the limited statistical power. Finding no mitigating effect itself would not be surprising as children were not the centre of the outbreak especially in the earliest phase (Davies et al. 2020); nonetheless, evidence claiming “no effect” would need to show that effects were at least below the level of practical significance.\n\nAltogether, these limitations represent difficulties in post-hoc causal analysis of mass interventions implemented without a built-in evaluation design such as randomisation. The fact that even the reasonably designed approach of Fukumoto et al. suffers insufficient power emphasises the importance of the \"evidence-generating\" philosophy in policy planning as has been promoted for medicine (Embi & Payne, 2013).\n\n\nData availability\n\nThis study did not generate original data. The underlying dataset is available from the repository associated with the original study:\n\nHarvard Dataverse. Replication Data for: No causal effect of school closures in Japan on the spread of COVID-19 in spring 2020. DOI: https://doi.org/10.7910/DVN/N803UQ (Fukumoto et al. 2021a).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver.\n\nReplication code along with the full analysis report (Extended data: Supplementary document) is available from a GitHub repository: https://github.com/akira-endo/reanalysis_Fukumoto2021.\n\nArchived version of the above repository at time of publication is available from: Zenodo. akira-endo/reanalysis_Fukumoto2021: ‘Not finding causal effect’ is not ‘finding no causal effect’ of school closure on COVID-19. DOI: https://doi.org/10.5281/zenodo.6457916 (Endo, 2022)\n\nThis project contains the following data:\n\n- main.html/main.ipynb (Extended data: Supplementary document).\n\n- replication codes and data from the original study (Fukumoto et al. 2021a) which are partially modified and reused.\n\n- replication codes for the analysis conducted in this study.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgement\n\nI thank Takahiro Kinoshita for insightful discussion.\n\n\nReferences\n\nDavies NG, Klepac P, Liu Y, et al.: Age-dependent effects in the transmission and control of COVID-19 epidemics. Nat. Med. 2020; 26(26): 1205–1211. PubMed Abstract \| Publisher Full Text\n\nDiamond A, Sekhon JS: Genetic Matching for Estimating Causal Effects: A General Multivariate Matching Method for Achieving Balance in Observational Studies. Rev. Econ. Stat. 2013; 95(3): 932–945. Publisher Full Text\n\nEmbi PJ, Payne PRO: Evidence Generating Medicine. Med. Care. 2013; 51(8 Suppl 3): S87–S91. Publisher Full Text\n\nEndo A: akira-endo/reanalysis_Fukumoto2021: ’Not finding causal effect’ is not ’finding no causal effect’ of school closure on COVID-19 (v.1.0.0). Zenodo. 2022. Publisher Full Text\n\nFukumoto K, McClean CT, Nakagawa K: No causal effect of school closures in Japan on the spread of COVID-19 in spring 2020. Nat. Med. 2021a; 27: 2111–2119. PubMed Abstract \| Publisher Full Text\n\nFukumoto K, McClean CT, Nakagawa K: Replication data for: no causal effect of school closures in Japan on the spread of COVID-19 in spring 2020. Harvard Dataverse. 2021b; 27: 2111–2119. (Accessed: 8 November 2021). Publisher Full Text\n\nHeinze G, Schemper M: A solution to the problem of separation in logistic regression. Stat. Med. 2002; 21: 2409–2419. PubMed Abstract \| Publisher Full Text\n\nKing G, Nielsen R: Why propensity scores should not be used for matching. Polit. Anal. 2019; 27(4): 435–454. Publisher Full Text\n\nPetersen ML, Porter KE, Gruber S, et al.: Diagnosing and responding to violations in the positivity assumption. Stat. Methods Med. Res. 2020; 21(1): 31–54. PubMed Abstract \| Publisher Full Text\n\nRosenbaum PR, Rubin DB: Constructing a Control Group Using Multivariate Matched Sampling Methods That Incorporate the Propensity Score. Am. Stat. 1985; 39(1): 33–38. Publisher Full Text\n\nViner RM, Russell SJ, Croker H, et al.: School closure and management practices during coronavirus outbreaks including COVID-19: a rapid systematic review. Lancet Child Adolesc. Health. 2020; 4(5): 397–404. PubMed Abstract \| Publisher Full Text" }	[ { "id": "136223", "date": "29 Apr 2022", "name": "Koichiro Shiba", "expertise": [ "Reviewer Expertise Public health", "epidemiology", "causal inference" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article provides a critical re-assessment of the recent paper that concluded that school closures had no causal effect on the spread of COVID-19 in Spring 2020 (Fukumoto et al., 2021). The author of this article argued that the original analysis (and the refined version presented in the current article) was likely underpowered and unreliable. The author raised a great point about the potential violation of positivity, about which the original paper provided little discussion. I appreciate the author for bringing our attention to these important issues and allowing me to engage in carefully reading the original article. I agree with the author that it is vital to be mindful that the absence of “evidence” defined by the lack of statistical significance is not evidence of absence. Hence, I find this type of article assessing alternative explanations for the null findings in the original paper particularly valuable.\n\nI provide some major and minor suggestions to strengthen the current manuscript further.\nMajor points:\nThe manuscript is currently written as if the lack of statistical power is the primary (and perhaps only) issue that might explain the original paper’s null findings. The author does discuss the possibility of unadjusted confounding later in the paper, but the way the Introduction and the Conclusion were written made it seem a secondary problem. I suggest the author provide a more in-depth discussion on other potential issues. There are at least two other issues I think are worth discussing: the choice of causal estimand and residual confounding.\n\nTo me, the most significant limitation of the original article is its focus on identifying and estimating ATC. The controls in the study were the municipalities that did not (need to) enforce school closures in the Spring of 2020; that is, they were most likely the areas that do not benefit from school closures because they were not experiencing the spread of COVID-19 to begin with, which is supported by the extremely low (nearly zero) confirmed cases in the control group shown in Figure 1. ATC, in this context, is of little policy relevance because such municipalities would have few cases regardless of the implementation of the school closures (the counterfactual “what would happen had they closed the schools” would not differ much from the reality). The null finding for ATC is somewhat expected. What we want to know instead is if the spread in the treated (i.e., municipalities that were experiencing the rise in confirmed cases and had to decide to close schools) would have been worse without the school closures (i.e., ATT). I know that the original article did investigate ATT as a sensitivity analysis, but it was based on the data stemming from the school closure on only one date (April 6) with a much smaller matched sample size (as the treated was smaller in number). They did not provide key supplementary information for the ATT analysis (e.g., covariate balance after matching) either. I understand that, with the available data, ATC (versus ATT) was easier to estimate as there were more controls; but that does not justify their oversimplified conclusion that there is no effect of school closures in Japan because the effect of a hypothetical intervention can vary substantially depending on the target populations.\n\nThe original article and the current article took a careful approach to mitigating bias due to confounding; yet, I see some evidence of residual confounding. The two articles indicate that ATC immediately after the school closures was positive point-estimate-wise, at least for some dates. The original article's authors wrote: “The ATC values suggest that municipalities that closed their schools mostly increased the number of cases”. If matching was successful and there was no unadjusted confounding, this statement would be true. Yet, they provide no compelling explanation for why school closures may causally “increase” confirmed cases. I cannot think of any. If not causal, the increase in cases among the treated municipalities in the matched sample is likely due to residual confounding—they had a reason to be concerned about the spread and decided to close the school, which was not captured by the observed covariates, including the prior outcome values and school closure status. The author of the current article raised an excellent point regarding residual bias, but some additional discussion on this issue would be appreciated.\nMinor points:\nPage 3: “Moreover, matching technique used to minimise confounding has a known side effect of...” needs citation.\n\nPage 3: “The effect estimates relative to the baseline incidence would be a more intuitive and interpretable measure for assessment of its practical use.” This needs more justification. The additive effect measure has its own advantage because it can speak directly to the population impacts of the intervention.\n\nPage 3: The sentence starting, “However, the theoretical ground is unclear...” seems incomplete.\n\nPage 3: “ATC and average treatment effect on the treatment: ATT) and their confidence intervals relative to the average outcome (incidence rate per capita) in the control group (Figure 1).” This sentence seems incomplete. Perhaps delete the part after “relative to...“.\n\nPage 3: Spell out ESS and provide a bit more context of what it is.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Partly\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Yes\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Partly", "responses": [ { "c_id": "11394", "date": "27 Jun 2024", "name": "Akira Endo", "role": "Author Response", "response": "> I thank the reviewers for their constructive feedback. While I regret the extended time it took to revise the manuscript in response to their comments, I believe the revised version and the following responses will address the reviewers' concerns. Specifically, I added two key discussion points that both reviewers agreed should be included: (i) choice of the estimand (ATC vs ATT) and (ii) potential residual confounding. This article provides a critical re-assessment of the recent paper that concluded that school closures had no causal effect on the spread of COVID-19 in Spring 2020 (Fukumoto et al., 2021). The author of this article argued that the original analysis (and the refined version presented in the current article) was likely underpowered and unreliable. The author raised a great point about the potential violation of positivity, about which the original paper provided little discussion. I appreciate the author for bringing our attention to these important issues and allowing me to engage in carefully reading the original article. I agree with the author that it is vital to be mindful that the absence of “evidence” defined by the lack of statistical significance is not evidence of absence. Hence, I find this type of article assessing alternative explanations for the null findings in the original paper particularly valuable. I provide some major and minor suggestions to strengthen the current manuscript further. > I thank the reviewer for appreciating my criticism and providing useful suggestions. Major points: The manuscript is currently written as if the lack of statistical power is the primary (and perhaps only) issue that might explain the original paper’s null findings. The author does discuss the possibility of unadjusted confounding later in the paper, but the way the Introduction and the Conclusion were written made it seem a secondary problem. I suggest the author provide a more in-depth discussion on other potential issues. There are at least two other issues I think are worth discussing: the choice of causal estimand and residual confounding. To me, the most significant limitation of the original article is its focus on identifying and estimating ATC. The controls in the study were the municipalities that did not (need to) enforce school closures in the Spring of 2020; that is, they were most likely the areas that do not benefit from school closures because they were not experiencing the spread of COVID-19 to begin with, which is supported by the extremely low (nearly zero) confirmed cases in the control group shown in Figure 1. ATC, in this context, is of little policy relevance because such municipalities would have few cases regardless of the implementation of the school closures (the counterfactual “what would happen had they closed the schools” would not differ much from the reality). The null finding for ATC is somewhat expected. What we want to know instead is if the spread in the treated (i.e., municipalities that were experiencing the rise in confirmed cases and had to decide to close schools) would have been worse without the school closures (i.e., ATT). I know that the original article did investigate ATT as a sensitivity analysis, but it was based on the data stemming from the school closure on only one date (April 6) with a much smaller matched sample size (as the treated was smaller in number). They did not provide key supplementary information for the ATT analysis (e.g., covariate balance after matching) either. I understand that, with the available data, ATC (versus ATT) was easier to estimate as there were more controls; but that does not justify their oversimplified conclusion that there is no effect of school closures in Japan because the effect of a hypothetical intervention can vary substantially depending on the target populations. The original article and the current article took a careful approach to mitigating bias due to confounding; yet, I see some evidence of residual confounding. The two articles indicate that ATC immediately after the school closures was positive point-estimate-wise, at least for some dates. The original article's authors wrote: “The ATC values suggest that municipalities that closed their schools mostly increased the number of cases”. If matching was successful and there was no unadjusted confounding, this statement would be true. Yet, they provide no compelling explanation for why school closures may causally “increase” confirmed cases. I cannot think of any. If not causal, the increase in cases among the treated municipalities in the matched sample is likely due to residual confounding—they had a reason to be concerned about the spread and decided to close the school, which was not captured by the observed covariates, including the prior outcome values and school closure status. The author of the current article raised an excellent point regarding residual bias, but some additional discussion on this issue would be appreciated. > I thank the reviewer for pointing out the existence of potential issues that I did not emphasise in the paper. I believe these additional issues are indeed worth mentioning in the manuscript. Meanwhile, I would prefer to retain the lack of statistical power as the primary issue because the present manuscript leverages the results of re-analysis focusing on the statistical power. Moreover, the two additional points suggested would also eventually come down to the problem of limited sample size and reporting results without considering the statistical power / effective size. For example, as the reviewer suggests, the choice of ATC was probably not ideal in the original study’s context because of low incidence levels in the control group in the first place. However, the same study design focusing on ATC could still have found an effect (if there is a true effect and) if the sample size (in this case both the number of included municipalities and the number of cases reported in these municipalities) was sufficient. Instead, I would like to propose changing the previous Conclusion section to the “Discussion and Conclusion” section and citing reviewers’ reports to discuss the suggested two points there. This allows me to separate the criticisms derived from my own analysis from those that were not, and also to appropriately acknowledge that the ideas came from the reviewers’ suggestions. I am aware that it may be a rather unusual practice in academic publications; however, given the nature of the publishing model of F1000 with citable open reviews and the fact that the reviewers provided new discussion points that were absent from the original version, I would like to opt for offering credit to the reviewers who contributed their time for the scholarly discussion. (Added to Discussion and Conclusion section): In addition to this issue of insufficient statistical power, which I demonstrated in the present reanalysis, two additional issues have been raised during the peer review process of this article. For one: the authors’ choice of ATC as the main estimand may have been suboptimal as Shiba has pointed out in his comment (Shiba, 2022). The control group in the original study may have consisted of municipalities that did not need school closures because of low incidence. ATC in this context would represent the effect in settings where the policy was not needed, which is of limited political implication. To counterargue against school closures as a control policy, the authors should have aimed to robustly show insufficient effect of such a policy even in municipalities in which school closures had been a selectable option (possibly because of higher incidence rate, where an effective policy could be more impactful). For the other: residual confounding may have remained among the matched samples. Both (Shiba, 2022) and (Hayashi, 2022) expressed concern on the immediate positive effect on incidence rate (e.g. increased incidence) immediately after the implementation of school closures in the treated group, which Fukumoto et al. left unexplained. Unless a plausible causal mechanism in which school closures could increase COVID-19 incidence is provided, this gap between the treated and control group may indicate residual bias, which is unsurprising given my reanalysis results suggesting matching failure. Hayashi additionally suggested that the trend in incidence (e.g. increasing/decreasing) may be one of the potential confounding variables that had not been adjusted for in the original study (Hayashi, 2022). Minor points: Page 3: “Moreover, matching technique used to minimise confounding has a known side effect of...” needs citation. > We have newly cited King et al. (2017). Page 3: “The effect estimates relative to the baseline incidence would be a more intuitive and interpretable measure for assessment of its practical use.” This needs more justification. The additive effect measure has its own advantage because it can speak directly to the population impacts of the intervention. > We have added an explanation that the relative risk reduction is particularly relevant because of the dynamic nature of the infectious disease transmission: Infectious disease risks are inherently dynamic; more current infections in a population would result in a greater risk of infection among susceptible individuals through increased encounters with infectious others. This means that the effect of school closures, which intended to reduce contacts at schools, should also depend on the baseline incidence in the population because the risk of infection averted would be the reduction in contacts multiplied by the probability that the contacts were otherwise with infectious individuals. Page 3: The sentence starting, “However, the theoretical ground is unclear...” seems incomplete. > I have replaced “to” with “on” but believe the sentence itself is complete (“theoretical ground is unclear”). Page 3: “ATC and average treatment effect on the treatment: ATT) and their confidence intervals relative to the average outcome (incidence rate per capita) in the control group (Figure 1).” This sentence seems incomplete. Perhaps delete the part after “relative to...“. > I have added a semicolon and a comma to clarify the structure of the sentence. This sentence is meant to indicate that both the ATC (or ATT) and their confidence intervals were rescaled to a relative value, where the incidence rate per capita in the control group is the reference. Page 3: Spell out ESS and provide a bit more context of what it is. > I have spelled it out with a brief explanation and citation: “The effective sample size (ESS; a proxy measure for the amount of information contained in weighted samples (Shook-Sa and Hudgens))…”" } ] }, { "id": "136221", "date": "04 Jul 2022", "name": "Takehiko I. Hayashi", "expertise": [ "Reviewer Expertise Risk analysis", "statistical causal inference", "and environmental data analyis" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article reanalyzed Fukumoto et al. (2021), which concluded that school closures had no causal effect on the spread of COVID-19 in Spring 2020 in Japan. The author first examined the robustness of the conclusion of Fukumoto et al. (2021) to the way the indicator is set up. The author then conducted simulations of cases with hypothetical 50% or 80% mitigating effects using the same study design and sample size as Fukumoto et al. (2021). As I state below (see Major points), I agree that these results (Figs. 1 and 2) support the author's main argument that Fukumoto et al. (2021) did not provide sufficient statistical power to conclude there was “no causal effect.” The author also pointed out the risk of positivity violation and the resulting small effective sample size in propensity score analysis (Figs. 4 and 5). I believe this issue should be further examined because there was a possibly nonnegligible level of residual confounding (see Minor points), but the additional examination may be beyond the scope of this article. Overall, I agree that the authors' arguments are adequately supported by the results presented. In general, the issue of statistical power tends to receive less focus than the issue of identification in the practice of causal inference. However, statistical power is always important when discussing the effects of policies in real-world contexts. This paper is a good practice example to remind us of the fundamentals of statistical inference.\nMajor points: The primary purpose of this study is to examine the statistical power of the analysis of Fukumoto et al. (2021). Although Fukumoto et al. (2021) is an elaborate study that examined most possible considerations, it lacks an examination of statistical power, and statistical power is a logically essential issue if one is to conclude “no causal effect” based on the lack of statistical significance.\nThe author first addressed the issue of outcome measures. I agree with the author that effect estimates relative to the baseline incidence may be superior to per-capita incidence rates as an outcome measure. As the author stated, taking only non-negative values for the incidence rate can be a large problem when the incidence rate of the control population is very low, as it was in this case. I think that the spikes in the red line of the control population in Figures 1c and 1i of Fukumoto et al. (2021) (which diverge from the black line of the matched treatment population, indicating a failure to construct an adequate counterfactual) also suggest a disadvantage of using per capita rates, given the explanation that these spikes were caused by the small sizes of the focal municipalities (see the Supplementary Information of Fukumoto et al. 2021, P. 11, Lines 3–11). Although I do not immediately conclude that the advantage of using effect estimates relative to the baseline incidence as the indicator is absolute, using this indicator is one of the possible reasonable choices. The results using this indicator (Fig. 1) showed an inherent lack of power in the analysis, illustrating that the conclusions of Fukumoto et al. (2021) (implicitly assuming a degree of statistical power of the analyses) are not robust to the way the indicator is set up.\nThe author's next approach is more direct. The author conducted simulations of cases with hypothetical 50% or 80% mitigating effects using the same study design and sample size as Fukumoto et al. (2021). The simulation showed that statistical significance was hardly detected even for substantial effects (Fig. 2). I believe these results convincingly demonstrate that the design and data of Fukumoto et al. (2021) did not provide sufficient statistical power to conclude “no causal effect.”\nThe above results (Figs. 1 and 2) logically support the author's main argument that Fukumoto et al. (2021) did not provide sufficient statistical power to conclude \"no causal effect.\"\nMinor points: Although the following comments may address issues that are beyond the scope of this study, the issues themselves are essential. These comments are intended as suggestions and not mandatory revisions of this article.\nFirst, as the other reviewer (Dr. Shiba) stated, the validity of the estimand is essential. I agree that ATT should have been the main estimand if Fukumoto et al. (2021) mention the efficacy of the policy in the real-world context. I recommend that the author discuss this point further.\nSecond, I think more consideration needs to be given to the possibility of insufficient adjustment (i.e., residual confounding). The author's mention of the risk of positivity violation and the resulting small effective sample size in propensity score analysis is a good point (Figs. 4 and 5). The separation of the propensity score distribution implies the inherent difficulties in matching important factors, especially those having a large effect on both treatment and outcome, which can introduce confounding. This is a real concern because many major covariates were not sufficiently adjusted. A well-known recommendation for an acceptable degree of ASMD after matching is ≤0.1 (Nguyen et al. 2017). However, the ASMDs of many covariates were actually ≥0.2 in this case (Table S3 in the Supplementary Information of Fukumoto et al. 2021). In general, I think it is difficult to state that “differences between the matched groups cannot be attributed to previous levels of infection or any other covariates” when the absolute value of ASMD was ≥0.2 in many covariates. I recommend the author check the loveplot of the matching of April 6, 10, and some cases for ATTs with the reference dashed line at 0.1 ASMD. I also recommend presenting the importance of covariates (e.g., specifying covariates having high standardized coefficient values in the propensity score estimation with red symbols) in the loveplots (see the Note below concerning the need for a loveplot).\nThird, discussing the possibility of missing important covariates may also be worthwhile. Some unexpected behavior of the Fukumoto et al. (2021) data suggests the possibility of residual confounding (due to the lack of incorporation of important covariates). For example, in Figure 1g of Fukumoto et al. (2021), large (see the absolute values) spikes appear only in the matching treated municipalities (and no spikes appear in all treated municipalities). In general, matching is expected to reduce the difference between treated and untreated baselines. Thus, it seems difficult to naturally explain the occurrence of large spikes only in the matched municipalities (unless the treatment actually increased outcomes or the effective sample size is very small). It is possible that important covariates were missed. For example, the trends (not sum) of the incidence rate before treatment was not included as covariates, but they might cause such spikes as follows. In the matching process, matched municipalities tend to have a similar value of the sum of the 7-day incidence rate. Here, the same value of this sum (e.g., 100 incidents per unit) can arise from municipalities that have different time trends (i.e., both increasing and decreasing trends are possible). In this situation, if the treatment (school closure) decision-making was affected by the increasing/decreasing trend, the treated group may tend to include municipalities (with 100 incidents per unit before 7 days) when there is an increasing trend. Similarly, the untreated group may tend to include municipalities (with 100 incidents per unit before 7 days) when there is a decreasing trend. In this case, the spikes (i.e., the difference in post-treatment outcomes) only in matched treated municipalities (as in Fig. 1g of Fukumoto et al., 2021) could occur as an artifact of the inertia of the temporal trend (not sum) from the preceding 7 days.\nNote on the need for a loveplot: The following description in Fukumoto et al. (2021, P. 2114) is not sufficiently correct in two points: “Moreover, the differences in other covariates between the treated and control groups were also much smaller after matching than before (Supplementary Fig. 1 and Supplementary Table 3). Therefore, differences between the matched groups cannot be attributed to previous levels of infection or any other covariates.” First, whether confounding was removed or not does not depend on the relative ratio before/after ASMD; rather, it depends on the absolute magnitude of ASMD. Even if ASMD becomes relatively much smaller after matching, if the absolute magnitude of ASMD was over 0.2 in many covariates, it is difficult to state that “differences between the matched groups cannot be attributed to previous levels of infection or any other covariates” in a general sense. Second, a smaller average ASMD of many covariates does not assure the removal of confounding. The removal of confounding needs to balance important covariates satisfying a backdoor criterion (not an average of all covariates). Practically, we can speculate about the importance of covariates from the effects of these covariates on treatments and outcomes (c.f., VanderWeele 2019). Figure S1 in the Supplementary Information of Fukumoto et al. (2021) did not provide good information with which to judge these two essential points in terms of the reduction of confounding. To make such a judgment, a loveplot with a reference line at 0.1 is suitable and is also a standard practice.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Yes\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Yes\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "11395", "date": "27 Jun 2024", "name": "Akira Endo", "role": "Author Response", "response": "> I thank the reviewers for their constructive feedback. While I regret the extended time it took to revise the manuscript in response to their comments, I believe the revised version and the following responses will address the reviewers' concerns. Specifically, I added two key discussion points that both reviewers agreed should be included: (i) choice of the estimand (ATC vs ATT) and (ii) potential residual confounding. This article reanalyzed Fukumoto et al. (2021), which concluded that school closures had no causal effect on the spread of COVID-19 in Spring 2020 in Japan. The author first examined the robustness of the conclusion of Fukumoto et al. (2021) to the way the indicator is set up. The author then conducted simulations of cases with hypothetical 50% or 80% mitigating effects using the same study design and sample size as Fukumoto et al. (2021). As I state below (see Major points), I agree that these results (Figs. 1 and 2) support the author's main argument that Fukumoto et al. (2021) did not provide sufficient statistical power to conclude there was “no causal effect.” The author also pointed out the risk of positivity violation and the resulting small effective sample size in propensity score analysis (Figs. 4 and 5). I believe this issue should be further examined because there was a possibly nonnegligible level of residual confounding (see Minor points), but the additional examination may be beyond the scope of this article. Overall, I agree that the authors' arguments are adequately supported by the results presented. In general, the issue of statistical power tends to receive less focus than the issue of identification in the practice of causal inference. However, statistical power is always important when discussing the effects of policies in real-world contexts. This paper is a good practice example to remind us of the fundamentals of statistical inference. > I thank the reviewer for supporting the points discussed in the manuscript and for offering additional comments on its content. Major points: The primary purpose of this study is to examine the statistical power of the analysis of Fukumoto et al. (2021). Although Fukumoto et al. (2021) is an elaborate study that examined most possible considerations, it lacks an examination of statistical power, and statistical power is a logically essential issue if one is to conclude “no causal effect” based on the lack of statistical significance. The author first addressed the issue of outcome measures. I agree with the author that effect estimates relative to the baseline incidence may be superior to per-capita incidence rates as an outcome measure. As the author stated, taking only non-negative values for the incidence rate can be a large problem when the incidence rate of the control population is very low, as it was in this case. I think that the spikes in the red line of the control population in Figures 1c and 1i of Fukumoto et al. (2021) (which diverge from the black line of the matched treatment population, indicating a failure to construct an adequate counterfactual) also suggest a disadvantage of using per capita rates, given the explanation that these spikes were caused by the small sizes of the focal municipalities (see the Supplementary Information of Fukumoto et al. 2021, P. 11, Lines 3–11). Although I do not immediately conclude that the advantage of using effect estimates relative to the baseline incidence as the indicator is absolute, using this indicator is one of the possible reasonable choices. The results using this indicator (Fig. 1) showed an inherent lack of power in the analysis, illustrating that the conclusions of Fukumoto et al. (2021) (implicitly assuming a degree of statistical power of the analyses) are not robust to the way the indicator is set up. The author's next approach is more direct. The author conducted simulations of cases with hypothetical 50% or 80% mitigating effects using the same study design and sample size as Fukumoto et al. (2021). The simulation showed that statistical significance was hardly detected even for substantial effects (Fig. 2). I believe these results convincingly demonstrate that the design and data of Fukumoto et al. (2021) did not provide sufficient statistical power to conclude “no causal effect.” The above results (Figs. 1 and 2) logically support the author's main argument that Fukumoto et al. (2021) did not provide sufficient statistical power to conclude \"no causal effect.\" > I thank the reviewer for appreciating and further discussing in detail the main points of my criticism. Regarding the choice of indicator, in response to Reviewer 1 (Dr Shiba)’s comment, I have included additional reasoning why relative effect is more relevant to this infectious disease context. Minor points: Although the following comments may address issues that are beyond the scope of this study, the issues themselves are essential. These comments are intended as suggestions and not mandatory revisions of this article. First, as the other reviewer (Dr. Shiba) stated, the validity of the estimand is essential. I agree that ATT should have been the main estimand if Fukumoto et al. (2021) mention the efficacy of the policy in the real-world context. I recommend that the author discuss this point further. > Discussion on the choice of estimand (along with that on residual confounding) has been included in the Discussion and Conclusion section. Please also see the response to Reviewer 1. Second, I think more consideration needs to be given to the possibility of insufficient adjustment (i.e., residual confounding). The author's mention of the risk of positivity violation and the resulting small effective sample size in propensity score analysis is a good point (Figs. 4 and 5). The separation of the propensity score distribution implies the inherent difficulties in matching important factors, especially those having a large effect on both treatment and outcome, which can introduce confounding. This is a real concern because many major covariates were not sufficiently adjusted. A well-known recommendation for an acceptable degree of ASMD after matching is ≤0.1 (Nguyen et al. 2017). However, the ASMDs of many covariates were actually ≥0.2 in this case (Table S3 in the Supplementary Information of Fukumoto et al. 2021). In general, I think it is difficult to state that “differences between the matched groups cannot be attributed to previous levels of infection or any other covariates” when the absolute value of ASMD was ≥0.2 in many covariates. I recommend the author check the loveplot of the matching of April 6, 10, and some cases for ATTs with the reference dashed line at 0.1 ASMD. I also recommend presenting the importance of covariates (e.g., specifying covariates having high standardized coefficient values in the propensity score estimation with red symbols) in the loveplots (see the Note below concerning the need for a loveplot). > I thank the reviewer for constructive suggestion to further investigate the appropriateness of matching in the original study. While I agree that a loveplot would provide more in-depth understanding of what might have gone wrong with the original analysis, the aim of my article is to highlight the existence of the issue (not necessarily revealing every detail of the individual issues), which I believe has already been demonstrated. Once the potential issue is identified as such, in principle the original authors should be responsible for conducting robust analysis to defend their findings. Third, discussing the possibility of missing important covariates may also be worthwhile. Some unexpected behavior of the Fukumoto et al. (2021) data suggests the possibility of residual confounding (due to the lack of incorporation of important covariates). For example, in Figure 1g of Fukumoto et al. (2021), large (see the absolute values) spikes appear only in the matching treated municipalities (and no spikes appear in all treated municipalities). In general, matching is expected to reduce the difference between treated and untreated baselines. Thus, it seems difficult to naturally explain the occurrence of large spikes only in the matched municipalities (unless the treatment actually increased outcomes or the effective sample size is very small). It is possible that important covariates were missed. For example, the trends (not sum) of the incidence rate before treatment was not included as covariates, but they might cause such spikes as follows. In the matching process, matched municipalities tend to have a similar value of the sum of the 7-day incidence rate. Here, the same value of this sum (e.g., 100 incidents per unit) can arise from municipalities that have different time trends (i.e., both increasing and decreasing trends are possible). In this situation, if the treatment (school closure) decision-making was affected by the increasing/decreasing trend, the treated group may tend to include municipalities (with 100 incidents per unit before 7 days) when there is an increasing trend. Similarly, the untreated group may tend to include municipalities (with 100 incidents per unit before 7 days) when there is a decreasing trend. In this case, the spikes (i.e., the difference in post-treatment outcomes) only in matched treated municipalities (as in Fig. 1g of Fukumoto et al., 2021) could occur as an artifact of the inertia of the temporal trend (not sum) from the preceding 7 days. > Discussion on possible residual confounder has been included in the Discussion and Conclusion section. Please also see the response to Reviewer 1. Note on the need for a loveplot: The following description in Fukumoto et al. (2021, P. 2114) is not sufficiently correct in two points: “Moreover, the differences in other covariates between the treated and control groups were also much smaller after matching than before (Supplementary Fig. 1 and Supplementary Table 3). Therefore, differences between the matched groups cannot be attributed to previous levels of infection or any other covariates.” First, whether confounding was removed or not does not depend on the relative ratio before/after ASMD; rather, it depends on the absolute magnitude of ASMD. Even if ASMD becomes relatively much smaller after matching, if the absolute magnitude of ASMD was over 0.2 in many covariates, it is difficult to state that “differences between the matched groups cannot be attributed to previous levels of infection or any other covariates” in a general sense. Second, a smaller average ASMD of many covariates does not assure the removal of confounding. The removal of confounding needs to balance important covariates satisfying a backdoor criterion (not an average of all covariates). Practically, we can speculate about the importance of covariates from the effects of these covariates on treatments and outcomes (c.f., VanderWeele 2019). Figure S1 in the Supplementary Information of Fukumoto et al. (2021) did not provide good information with which to judge these two essential points in terms of the reduction of confounding. To make such a judgment, a loveplot with a reference line at 0.1 is suitable and is also a standard practice." } ] } ]	1	https://f1000research.com/articles/11-456
https://f1000research.com/articles/12-1091/v1	01 Sep 23	{ "type": "Software Tool Article", "title": "Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2", "authors": [ "Marie Lataretu", "Oliver Drechsel", "René Kmiecinski", "Kathrin Trappe", "Martin Hölzer", "Stephan Fuchs", "Oliver Drechsel", "René Kmiecinski", "Kathrin Trappe", "Martin Hölzer" ], "abstract": "Background: Accurate genome sequences form the basis for genomic surveillance programs, the added value of which was impressively demonstrated during the COVID-19 pandemic by tracing transmission chains, discovering new viral lineages and mutations, and assessing them for infectiousness and resistance to available treatments. Amplicon strategies employing Illumina sequencing have become widely established for variant detection and reference-based reconstruction of SARS-CoV-2 genomes, and are routine bioinformatics tasks. Yet, specific challenges arise when analyzing amplicon data, for example, when crucial and even lineage-determining mutations occur near primer sites.\n\nMethods: We present CoVpipe2, a bioinformatics workflow developed at the Public Health Institute of Germany to reconstruct SARS-CoV-2 genomes based on short-read sequencing data accurately. The decisive factor here is the reliable, accurate, and rapid reconstruction of genomes, considering the specifics of the used sequencing protocol. Besides fundamental tasks like quality control, mapping, variant calling, and consensus generation, we also implemented additional features to ease the detection of mixed samples and recombinants.\nResults: Here, we highlight common pitfalls in primer clipping, detecting heterozygote variants, and dealing with low-coverage regions and deletions. We introduce CoVpipe2 to address the above challenges and have compared and successfully validated the pipeline against selected publicly available benchmark datasets. CoVpipe2 features high usability, reproducibility, and a modular design that specifically addresses the characteristics of short-read amplicon protocols but can also be used for whole-genome short-read sequencing data.\nConclusions: CoVpipe2 has seen multiple improvement cycles and is continuously maintained alongside frequently updated primer schemes and new developments in the scientific community. Our pipeline is easy to set up and use and can serve as a blueprint for other pathogens in the future due to its flexibility and modularity, providing a long-term perspective for continuous support. CoVpipe2 is written in Nextflow and is freely accessible from https://github.com/rki-mf1/CoVpipe2 under the GPL3 license.", "keywords": [ "SARS-CoV-2", "genome reconstruction", "whole-genome sequencing", "short reads", "Illumina", "amplicons", "WGS", "Nextflow pipeline", "virus bioinformatics" ], "content": "Introduction\n\nSince the publication of the first genome sequence of the novel SARS-CoV-2 virus in January 2020 – just 12 days after the initial report of the virus – the international GISAID database1–3 now includes more than 15.5 million SARS-CoV-2 whole-genome sequences (accessed May 23, 2023). The genomic data and metadata collected in GISAID and other resources such as EBI’s COVID-19 Data Portal4 are pivotal for the largest worldwide genomic surveillance effort ever undertaken to track the evolution and spread of the virus causing the COVID-19 disease. Important viral genome regions have been monitored for mutations, for example, in the spike gene and other immunologically relevant loci. The reconstruction of accurate SARS-CoV-2 genomic sequences is paramount to detect and track substitutions, insertions, and deletions correctly; interpret them in terms of vaccine development, test the efficiency of target regions and antibody binding sites, detect outbreaks and transmission chains, and finally inform public health authorities to consider adjustment of containment measures.5\n\nAccording to Ewan Birney, director of EMBL-EBI in Cambridge, U.K., “Genome sequencing is routine in the same way the U.S. Navy routinely lands planes on aircraft carriers. Yes, a good, organized crew does this routinely, but it is complex and surprisingly easy to screw up.”.6\n\nThis quote is no less accurate for genome reconstruction, a crucial step in SARS-CoV-2 genomic surveillance. While sequencing efforts were scaling up rapidly around the globe, several pipelines for the reference-based assembly of SARS-CoV-2 genomes were developed in parallel and in an attempt to rapidly generate the necessary genome sequences (Table 1). During the first lockdown in Germany in mid-March 2020, the Bioinformatics unit at the Robert Koch Institute (RKI), Germany’s Public Health institute, also started developing a genome reconstruction pipeline, specifically targeting Illumina amplicon sequencing data and amplicon schemes. During the development, the pipeline was extensively tested and has gone through continuous improvement due to adjusted wet lab protocols and primer schemes, to accurately call variants in low-coverage regions and near primer sites, to deal with deletions and low-coverage regions correctly, and to robustly reconstruct high-quality SARS-CoV-2 consensus sequences for downstream analyses and genomic surveillance. Due to these features and tests, CoVpipe1 was successfully used in the past at RKI’s sequencing facility and several labs nationwide.7–10 If not addressed appropriately, genotyping errors can lead to wrong consensus sequences and thus impact downstream analyses such as phylogenetic reconstructions and transmission chain tracking in outbreaks.11\n\nHere, we mainly focus on open-source pipelines with available source code, specifically targeting the reconstruction of SARS-CoV-2 genomes, also including general pipelines adapted to work with SARS-CoV-2 sequencing data (e.g., V-pipe). Publ. – Publication focusing on the pipeline in a preprint or a peer-reviewed journal, Seq. tech. – focused sequencing technology, Implementation – main software backbone to run the tool (please note that not all pipelines use a workflow management system such as Nextflow25 or Snakemake26), Dependencies – a list of options to handle necessary software dependencies, Latest release – latest available release version as accessed May 23, 2023. mNGS – sequencing approach not based on amplicons but rather sequencing all available RNA/cDNA (metatranscriptomics/genomics).\n\nWhile sequencing intensity and turnaround times on variant detection increased in different countries, there are also major disparities between high-, low- and middle-income countries in the SARS-CoV-2 global genomic surveillance efforts.12 A recent study also found significant differences between bioinformatics approaches that use the same input data but detect different variants in SARS-CoV-2 samples.13 In addition, each technology and sequencing approach has its own advantages and limitations, challenging a harmonized genomic surveillance of the virus.14\n\nIn Germany, sequencing efforts increased tremendously in January 2021 following the entry into force of a federal directive (Coronavirus Surveillance Verordnung—CorSurV). Subsequently, a large-scale, decentralized genomic sequencing and data collection system (“Deutscher Elektronischer Sequenzdaten-Hub”, DESH)15 has been established, accompanied by a medium-scale integrated molecular surveillance infrastructure (IMS-SC2) at the RKI.8 By May 22, 2023, 1,227,036 whole-genome SARS-CoV-2 sequences that met the quality criteria were transmitted to the RKI via DESH. Due to their low cost, sensitivity, flexibility, specificity, and efficiency, amplicon-based sequencing designs are broadly used for SARS-CoV-2 sequencing and reference-based genome reconstruction.16–20 From the ∼1,2 million DESH genomes (publicly available at github.com/robert-koch-institut/SARS-CoV-2-Sequenzdaten_aus_Deutschland), ∼1,1 million (90.91%) were sequenced with Illumina devices, highlighting the importance of the technology for genomic surveillance (Table 2). Illumina technology has a lower share at the international level (78.57%), while Oxford Nanopore Technologies (ONT) increased to 12.73% (Table 2). However, Illumina remains the most widely used approach among the various sequencing technologies, followed by ONT sequencing by a wide margin. A recent benchmark study also showed the advantages of using Illumina MiSeq compared to ONT GridION for SARS-CoV-2 sequencing, resulting in a higher number of consensus genomes classified by Nextclade21 as good and mediocre.22 However, these results are, of course, also dependent on the bioinformatics tool chains and could change as ONT becomes more accurate.23 In addition, although both technologies require the same computational steps for reference-based genome reconstruction (preprocessing, mapping, variant calling, consensus), they need different tools optimized for either short- or long-read data and the associated error profiles to produce high-quality consensus sequences. Therefore, we developed one pipeline, especially for ONT data,24 and CoVpipe2, specifically targeting high-accuracy SARS-CoV-2 amplicon data derived from short-read Illumina sequencing. CoVpipe2 is a Nextflow re-implementation of CoVpipe1 (written in Snakemake, gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe) and comes with additional features, simplified installation, full container support, and continuous maintenance.\n\nData based on 1,2 million and 15,5 million whole-genome sequences submitted to the German DESH portal (“Deutscher Elektronischer Sequenzdaten-Hub”) and to the GISAID database, respectively (accessed: May 22, 2023). To the best of our knowledge, we corrected typos such as Nanonopore, Nasnopore, and Illunima in the GISAID metadata and summarized the available terms into the broader categories shown in this table (e.g., NextSeq500 ⇒ Illumina). Entries we could not assign to one of the listed sequencing technologies were added to the Other/Unknown category. Please note that most German DESH sequences are also part of the GISAID data set. # – Number of sequences, % – Percentage of sequences on total data set.\n\nHere we present CoVpipe2, our pipeline engineered over nearly three years of pandemic genome sequencing that accurately reconstructs SARS-CoV-2 consensus sequences from Illumina short-read sequencing data, focusing on challenges associated with amplicon sequencing on a large scale. Besides implementation details, we also highlight pitfalls we discovered and solved during the pipeline development.\n\n\nMethods\n\nCoVpipe2 is implemented using the workflow management system Nextflow25 to achieve high reproducibility and performance on various platforms. The user can choose to use CoVpipe2 with Conda or Mamba support,36 or containers (Docker,37 Singularity38) to handle all software dependencies. The Conda/Mamba environments and the container images are preconfigured and have fixed versions of the incorporated tools. The precompiled Docker containers are stored on hub.docker.com/u/rkimf1. Containers and environments are downloaded and cached automatically when executing CoVpipe2. If needed, the Docker images can also be converted into Singularity images by the pipeline. CovPipe2 includes Nextclade39 and pangolin40 for lineage assignment. Both tools rely on their latest code and database versions. To address this, we implemented the --update option inspired by poreCov,24 which triggers an update to the latest available version from anaconda.org or hub.docker.com/u/rkimf1, respectively. --update is disabled by default; the tool versions can also be pinned manually.\n\nWhen CoVpipe2 is running on a high-performance computing (HPC) cluster (e.g., SLURM, LSF) or in the cloud (e.g., AWS, GCP, Azure), all resources (CPUs, RAM) are pre-configured for all processes but can be customized via a user-specific configuration file. We use complete version control for CoVpipe2, from the workflow itself (releases) to each tool to guarantee reproducible results. To this end, all Conda/Mamba environments and containers use fixed versions. In addition, each CoVpipe2 release can be invoked and executed individually, and the tool versions used during genome reconstruction and analysis are listed in Nextflow report files.\n\nCoVpipe2 is publicly available under a GPL-3.0 license at github.com/rki-mf1/covpipe2, where details about the implementation and different executions of CoVpipe2 can be found. We use GitHub’s CI for various pipeline tests, particularly a dry-run to check for integrity and an end-to-end test with special attention to the called variants to ensure continuous code quality and robust results.\n\nAs a minimal setup, Nextflow (minimal version 22.10.1, nextflow.io) and either Conda, Mamba, Docker, or Singularity need to be installed for CoVpipe2. Nextflow can be used on any POSIX-compatible system, e.g., Linux, OS X, and on Windows via the Windows Subsystem for Linux (WSL). Nextflow requires Bash 3.2 (or later) and Java 11 (or later, up to 18) to be installed. Initial installation and further updates to the workflow and included tools can be performed with simple commands:\n\n# install (or update) the pipeline\n\nnextflow pull rki-mf1/CoVpipe2\n\n# check available pipeline versions\n\nnextflow info rki-mf1/CoVpipe2\n\n# run a certain release version\n\nnextflow run rki-mf1/CoVpipe2 -r v0.4.1 --help\n\n# test the installation with local execution and Conda\n\nnextflow run rki-mf1/CoVpipe2 -r v0.4.1 -profile local,conda,test --cores 2 --max_cores 4\n\nThe pipeline can be executed on various platforms controlled via the Nextflow -profile parameter, which makes it easily scalable, e.g., for execution on an HPC. Each run profile is created via combining different Executors (local, slurm) and Engines (conda, mamba, docker, singularity); the default execution-engine combination (profile) is -profile local,conda.\n\nAn overview of the workflow is given in Figure 1. FASTQ files and a reference genome sequence (FASTA) are the minimum required pipeline inputs. If no reference genome sequence is provided, the SARS-CoV-2 index case reference genome with accession number MN908947.3 (identical to NC_045512.2) is used by default (as well as the corresponding annotation GFF), and then only FASTQ files are required. All files can be provided via file paths or defined via a comma-separated sample sheet (CSV); thus, CoVpipe2 can run in batch mode and analyze multiple samples in one run. Optionally, raw reads are checked for mixed samples with the tool LCS.41 Next, raw reads are quality-filtered and trimmed using fastp42 and optionally filtered taxonomically by Kraken2.43 We provide an automated download of a precalculated Kraken2 database composed of SARS-CoV-2 and human genomes from Zenodo. However, the user is free to use a custom database. The reads are aligned to the reference genome using BWA,44 and the genome coverage is calculated by BEDTools genomecov.45 Primers can be optionally clipped after mapping with BAMclipper,46 which is essential to avoid contaminating primer sequences in amplicon data. To locate the primer sequences, a browser extensible data paired-end (BEDPE) file containing all primer coordinates is required as input. If only a BED file is provided, CoVpipe2 can automatically convert it to a BEDPE file. The user can also choose from provided popular VarSkip (github.com/nebiolabs/VarSkip) and ARTIC primer schemes.47 Next, FreeBayes48 calls variants (default thresholds: minimum alternate count of 10, minimum alternate fraction of 0.1, and minimum coverage of 20), which are normalized with BCFtools norm.49 Resulting variants are analyzed and annotated with SnpEff,50 filtered by QUAL (default 10), INFO/SAP (default disabled), and INFO/MQM (default 40) values, and optionally adjusted for the genotype (default enabled with minimum variant frequency 0.9). Thus, in the case of mixed variants, the predominant variant can be defined as a homozygous genotype if its frequency reaches a certain threshold. With these settings, alternate variants with a frequency of more than 90% are set as alternative nucleotides. Furthermore, CoVpipe2 filters out indels below a certain allele frequency, which is, by default, enabled with a minimum allele frequency of 0.6. We create a low coverage mask, without deletions, from the mapping file and the adjusted and filtered VCF file (default coverage cutoff 20), which is then used in the consensus calling with BCFtools consensus. We output an ambiguous consensus sequence with IUPAC characters51 (RYMKSWHBVDN) and a masked one only containing ACTG and Ns. Then, PRESIDENT (GitHub) assesses the quality of each reconstructed genome via pairwise alignment to the SARS-CoV-2 index case (NC_045512.2) using pblat52 with an identity threshold of 0.9 and N threshold of 0.05 per default. pangolin assigns a lineage and Nextclade annotates the mutations; the Nextclade alignment serves as input for sc2rf (original repository from github.com/lenaschimmel/sc2rf, with updates from github.com/ktmeaton/ncov-recombinant) for detection of recombinants. If an annotation file is provided, the reference annotation is mapped to the reconstructed genome with Liftoff.53\n\nThe illustration shows all input () and output () files as well as optional processing steps and optional input (). For each computational step, the used parameters and default values (in brackets [...]) are provided, as well as additional comments ((...)). The arrows connect all steps and are colored to distinguish different data processing steps: green – read (FASTQ) quality control and taxonomy filtering, yellow – reference genome (FASTA) and reference annotation (GFF) for lift-over, blue – mapping files (BAM) and low coverage filter (BED), purple – variant calls (VCF), orange – consensus sequence (FASTA). The icons and diagram components that make up the schematic figure were originally designed by James A. Fellow Yates and nf-core under a CCO license (public domain).\n\nAll results are summarized via an R Markdown template. The resulting HTML-based report summarizes different quality measures and mapping statistics for each input sample, thus allowing the user to spot low-performing samples even in extensive sequencing runs with many samples. A conditional notification warns the user if samples identified as negative controls (by matching the string ’NK’) show high reference genome coverage (threshold over 0.2).\n\nCommon challenges in amplicon-based genome reconstruction and solutions in CoVpipe2\n\nHere, we highlight some implementation decisions that prevent common pitfalls and thus improve the quality of reconstructed SARS-CoV-2 genomes. Although amplicon-based approaches are widely used, these technologies are associated with flaws and limitations that must be considered to ensure that the genotypes obtained, and thus the resulting genome sequences, are reliable.13,54 While some of these implementations might seem obvious and easy to fix, we frequently observed specific errors in the vast amount of consensus genome sequences sent to us via the DESH system.\n\nAccurate primer clipping to avoid dilution and edge effects Primer clipping is an essential step for amplicon sequencing data because primers are inherent to the reference sequence and can disguise true variants in the sample.13 However, removing primers before the mapping step can result in unwanted edge effects.55 For example, deletions located close to the end of amplicons may be soft-clipped by the mapping software and hence can not be called as variants subsequently (Figure 2). Therefore, primer clipping should be performed after mapping to prevent any soft clipping of variants close to the amplicon ends.\n\n(A) Primer sequences need clipping to call true variants (red) and not mask them via reference bases (blue). (B) Early primer clipping may result in missed deletions due to algorithmic soft clipping (primer sequence in light gray). (C) Genotyping parameters must be carefully set to reliably call different variant cases and represent them in the final consensus. CoVpipe2 puts primer clipping after the mapping step to prevent B) and implements carefully chosen default parameters for robust genotyping also of mixed variants, C).\n\nAs an example and worst-case scenario, clipping primer sequences before mapping bears the risk of missing a critical deletion used to define the previous VOC B.1.1.7, namely deletion HV69/70 in the spike gene (S:H69-, S:V70-). We observed such a misclassification using Paragon CleanPlex amplicon-based sequencing. The kit uses primers similar to the ARTIC protocol V3, where the deletion S:HV69/70 is close to the end of an amplicon. If primer clipping is performed before mapping, the mapping tool might soft clip the amplicon end rather than opening a gap, which is more expensive than masking a few nucleotides (Figure 2). We checked 151,565 B.1.1.7 sequences obtained via DESH for the characteristic S:H69, S:V70 deletions and found that 139,891 (92.3%) included the deletion. The remaining sequences contained the deletion only partially or lacked it completely. It is unlikely that these B.1.1.7 sequences lost this characteristic deletion. Thus we assume that some of the reconstructed Alpha sequences sent to the RKI from different laboratories in Germany do not account for the described effect and thus miss the detection of this deletion. Unfortunately, we don’t know which bioinformatics pipelines the submitting laboratories were using and can only assume an error because of missing or incorrect primer clipping. To avoid this problem, we shift primer clipping after the read mapping step in CoVpipe2; otherwise, a vital feature of an emerging virus lineage might be missed if mutations accumulate close to amplicon ends.\n\nGenotype adjustment to exclude sporadic variant calls As an additional feature, we provide the option to adjust the genotype for sites where the vast majority of reads support a variant call, but the variant was called heterozygous. By default, the genotype of these locations is set to homozygous if a particular variant call is supported by 90% of the aligned reads.\n\nDeletion-aware masking of low-coverage regions We ensure that only low-coverage positions that are not deletions are masked. Several pipelines implement a feature to mask low-coverage regions. However, deletions are basically genomic regions with no coverage, and if not appropriately implemented, a pipeline might accidentally mask deletions as low-coverage regions. To prevent this, CoVpipe2 creates a low coverage mask (default minimum coverage 20) from the BAM file with BEDtools genomecov. In the second step, BEDtools subtract removes all deleted sites from the low-coverage mask. Finally, the mask is used in the consensus generation with BCFtools consensus.\n\nIUPAC consensus generation with indel filter CoVpipe2 generates different consensus sequences based on the IUPAC code. First, an explicit consensus is generated where all ambiguous sites and low-covered regions are hard-masked. Second, a consensus where only low-covered regions are hard-masked. The pipeline includes as much information as possible in the unambiguous consensus sequence by adding low-frequency variants with the respective IUPAC symbol. However, no symbol represents “indel or nucleotide”, so indels are always incorporated into the consensus sequence. As a result, low-frequency or heterozygote indels, often false positives, can introduce frameshifts into the consensus sequence. We overcome this with an indel filter based on allele frequency before consensus generation. Thus, indels below a defined threshold (per default 0.6) are not incorporated in the consensus sequences but can still be looked up in the VCF file.\n\nAdditional features beyond genome reconstruction\n\nOver time, we added features beyond genome reconstruction to CoVpipe2 to answer newly emerging questions during the pandemic. The modular design of our implementation makes this seamless.\n\nMixed infections and recombinants We included LCS for raw reads. LCS was originally developed for the SARS-CoV-2 lineage decomposition of mixed samples, such as wastewater or environmental samples.41 In the context of amplicon-based SARS-CoV-2 sequencing, we use LCS results for indications for potential new recombinants, and possible mixed infections (co-infections with different SARS-CoV-2 lineages).\n\nFurther, we added sc2rf to detect potential new recombinants via screening the consensus genome sequences. Like other tools and scripts, sc2rf depends on up-to-date lineage and mutation information, specifically, on a manually curated JSON file. We switched to another repository (JSON GitHub project) than the original one that includes the sc2rf scripts because of more frequent updates on the JSON file.\n\nKeeping up to date with lineage and clade assignments We implemented an update feature for pangolin and Nextclade. Both tools, especially pangolin, rely on the latest datasets for the lineage assignment of newly designated Pango lineages.56 Depending on the selected engine, Conda/Mamba or container execution, CoVpipe2 checks for the latest available version from Anaconda or our DockerHub, respectively. The tool versions can also be pinned manually.\n\nPrediction of mutation effects The called variants are annotated and classified based on predicted effects on annotated genes with SnpEff. SnpEff reports different effects, including synonymous or non-synonymous SNPs, start codon gains or losses, stop codon gains or losses; and classifies them based on their genomic locations. Lastly, CoVpipe2 uses Liftoff to generate an annotation for each sample if a reference annotation is provided.\n\n\nResults\n\nWe compared the results of CoVpipe2 (v0.4.0) with publicly available benchmark datasets for SARS-CoV-2 surveillance57 (GitHub CDC data). For our study, we selected from the available benchmark datasets all samples that were sequenced with the ARTIC V3 primer set (according to CDC data, release v0.7.2), ending up with in total 54 samples from three datasets:\n\n• i) 16 samples from VOI/VOC lineages (dataset 4)\n\n• ii) 33 samples from non-VOI/VOC lineages (dataset 5)\n\n• iii) 5 samples from failed QC (dataset 6)\n\nWe stick to the naming scheme (dataset 4, 5, and 6) as declared in the original study.57 For all 54 samples, we downloaded the raw reads from ENA with nf-core/fetchngs (v1.9).58 For 49 samples, we downloaded the available consensus sequences from GISAID1–3 (samples from dataset 4 and 5). We run CoVpipe2 with Singularity, species filtering (--kraken) and the latest pangolin and Nextclade versions at that point (containers: rkimf1/pangolin:4.2-1.19--dec5681, rkimf1/nextclade2:2.13.1--ddb9e60). We further examined the consensus sequences from dataset 4 and 5, comparing CoVpipe2 and GISAID sequences: We compared lineages information of the reconstructed genomes assigned by pangolin with the indicated lineages from CDC data. Note that the pangolin versions and datasets differ. Also, we run Nextclade (same container version as noted above) to compare the mutation profile, and MAFFT,59 v7.515 (2023/Jan/15), for comparison on sequence level of the unambiguous IUPAC consensus of CoVpipe2.\n\nThe HTML report consists of several sections and summarizes different results. The first table aggregates critical features for each sample: the number of reads, genome QC, the assigned lineage, and recombination potential, see Figure 3. Furthermore, read properties such as the number of bases and the length of reads (before/after trimming) are summarized. An optional table lists the species filtering results emitted by Kraken2.43 The report summarizes reads mapped to the reference genome (number and fraction of input) and the median/standard deviation of fragment sizes, shown as a histogram plot. Genome-wide coverage plots allow users to observe low-coverage regions and potential amplicon drop-outs to optimize primers. We summarize the output for all samples in different tables: i) genome quality from PRESIDENT output, ii) lineage assignments from pangolin output, and iii) variants in amino acid coordinates and detected frameshifts from Nextclade output.\n\nThe standalone HTML report summarizes different quality measures and tool results. The overview table can include a conditional notification for negative controls with high reference genome coverage (not shown in this example). All tables are searchable and sortable.\n\n\nDiscussion\n\nHere, we compare the results of CoVpipe2 against a selection of available benchmark datasets57 and their respective consensus genome sequences available from GISAID.1–3 We discuss the observed differences. No software is perfect, and CoVpipe2 may have problems with certain combinations of amplicon schemes and sequencing designs, leading to specific borderline cases in variant detection, which we also highlight and discuss. In addition, in conflicting cases, the real sequence often stays unknown until further sequencing efforts are performed. This makes continuous development and testing of bioinformatics pipelines all the more critical.\n\nDataset 4, VOI/VOC lineages\n\nLineages Despite the different pangolin tool versions and lineage definitions that changed over time, all pangolin lineages from CoVpipe2 match the corresponding lineages reported at github.com/CDCgov/datasets-sars-cov-2, see Extended data, Table S1.\n\nPairwise alignment The sequence identity ranges from 98.44 % to 99.79 % (including Ns) between the corresponding GISAID and CoVpipe2 genome pairs (Extended data, Table S2). Nine out of 16 sequences are identical when mismatches resulting from gaps are not considered. For one sample, the corresponding GISAID and CoVpipe2 sequences contain three ACGT-nucleotide mismatches. Seven out of 16 GISAID consensus sequences do not contain any Ns, possibly indicating that low coverage regions have been not masked. The respective reconstructed genomes from CoVpipe2 contain Ns located in the first or last 150 nucleotides of the genome sequences, thus masking low coverage regions (Extended data, Table S3). Due to tiled PCR amplicons, 5′ and 3′ ends of the genome usually have too little coverage or are not sequenced. The genome ends containing Ns seem to be trimmed in 14 GISAID genomes. Overall, the number of Ns in the GISAID and CoVpipe2 genomes is comparable, with CoVpipe2 genomes tending to have more Ns due to the low coverage filter resulting in Ns at genome ends. In addition, CoVpipe2 does not trim Ns from the genome ends and might be more conservative with its default settings, as positions below 20 X coverage (--cns_min_cov) will be masked with ambiguous N bases in the consensus sequence.\n\nMutations Although all genomes reconstructed from CoVpipe2 were assigned to the same lineage as previously reported (CDC data), there are minor differences in Nextclade’s mutation profile, Extended data, Table S4. Three of 16 reconstructed genomes have one or two nucleotide substitutions more than the respective GISAID genome.\n\nDataset 5, non-VOI/VOC lineages\n\nLineages Pangolin lineages from CoVpipe2 exactly match the reported lineages at CDC data in 27 of 33 samples, see Extended data, Table S5. For five samples, the pangolin lineage based on the genome sequence reconstructed by Covpipe2 is the parent lineage of the expected sub-lineage. For example, the genome sequence of sample SAMN15919634 was assigned to the B.1.1 lineage after CoVpipe2 reconstruction, whereas the corresponding GISAID sequence is assigned to B.1.1.431 (CDC data). Since the lineage assignments of Nextclade exactly match for each CoVpip2-GISAD pair, the different pangolin and pangolin data versions used in CoVpipe2 and Xiaoli and Hagey et al.57 are most likely the reason for this discrepancy. Different parameter thresholds can also lead to different lineage assignments. For example, the genome sequence of SAMN17571193 was assigned to B.1.1.450 by CoVpipe2 compared to B.1.1.391 in Xiaoli and Hagey et al.57 The mutation profile differs by two additional SNPs (genome coordinates: C3037T and C3787T) constituting one mutation on amino acid level (ORF1a:D1962E) in the GISAID consensus sequence. Both positions (3037 and 3787) have a read coverage below 20, so they are not eligible for variant calling with default settings in CoVpipe2 and are masked with N. Therefore, this difference in lineage assignment is due to CoVpipe2’s more restrictive approach to integrating the called variants into the consensus.\n\nPairwise alignment The pairwise sequence identity ranges from 95.96 % to 99.80 % (including Ns) between the GISAID and CoVpipe2’s reconstructed genome sequences (Extended data, Table S6). Ignoring gap mismatches, 13 out of 33 sequences are identical. No sample contains ACGT mismatches. 18 out of 33 GISAID consensus sequences do not contain any Ns. Sixteen of the respective reconstructed genomes have Ns, all located in the first or last 150 nucleotides (Extended data, Table S7). Because of tiled PCR amplicons, the 5′ and 3′ ends typically have too little coverage or are not sequenced. The 5′ and 3′ genome ends containing Ns seem trimmed in 30 GISAID genomes. Overall, the number of Ns in the GISAID and CoVpipe2 genomes is comparable, with CoVpipe2 genomes tending to have more Ns. CoVpipe2 does not trim Ns from the genome ends and might be more conservative with its default settings, as positions below 20 (--cns_min_cov) will be masked with N in the consensus sequence.\n\nMutations There are minor differences in Nextclade’s mutation profile (Extended data, Table S8). Five of the 33 reconstructed genomes have one or two more nucleotide substitutions compared to the GISAID genome.\n\nDataset 6, samples failing quality control\n\nFor the five samples from the failed QC dataset by Xiaoli and Hagey et al.,57 CoVpipe2 correctly labeled four samples with failed genome QC. Three samples contain at least one frameshift, whereas two samples, SAMN17486862 and SAMN17822806, were reconstructed by CoVpipe2 without frameshifts (Extended data, Table S9). The consensus sequence of sample SAMN17486862 passed QC according to CoVpipe2’s genome QC criteria.\n\nAll the selected samples from this dataset have originally failed QC because of a VADR60 alert number greater than one.57 VADR is part of the TheiaCoV (formerly ‘Titan’) 1.4.4 pipeline,61 which was used to analyze the samples in Xiaoli and Hagey et al.57 Among other things, VADR considers frameshifts, which do not occur in two genomes reconstructed with CoVpipe2. However, one of these two consensus genomes (SAMN17822806) contains too many Ns to pass CoVpipe2’s genome QC.\n\nThe nature of a computational pipeline is that it is a chain of existing individual tools. Especially given the rapid evolution of SARS-CoV-2 during the pandemic, many reference-based tools rely on up-to-date databases and resources to reflect the current situation. For example, LCS depends on a variant marker table and user-defined variant groups. Similarly, sc2rf relies on a list of common variants for each lineage. In addition, Nextclade and pangolin periodically publish up-to-date datasets. Therefore, it is critical for a pipeline, especially in the context of a surveillance tool for rapidly evolving pathogens such as SARS-CoV-2, to allow for regular updates to the underlying data structures. While we have implemented some functionality to update tools such as Nextclade and pangolin automatically, this is not possible for all resources and can only be achieved through the continuous development and maintenance of a pipeline. Furthermore, our default settings may not fit all input data and must be selected carefully.\n\nFinally, there must be enough good-quality input reads to reconstruct a genome successfully. In particular, with amplicon sequencing data, some regions might have a lower coverage due to amplicon dropouts. Thus, the genome as a whole can be reconstructed with acceptable quality. However, some essential mutations can be missing due to low coverage or variant-calling quality.\n\n\nConclusions\n\nAccurate and high-throughput genotyping and genome reconstruction methods are central for monitoring SARS-CoV-2 transmission and evolution. CoVpipe2 provides a fully automated, flexible, modular, and reproducible workflow for reference-based variant calling and genome reconstruction from short-read sequencing data, emphasizing amplicon-based sequencing schemes. Due to the implementation in the Nextflow framework, the setup and automatic installation of the required tools and dependencies is simple and allows the execution on different computing platforms. The comparison with a benchmark dataset showed comparable results where differences could be pinned down to different parameters, filtering thresholds, and tool versions used for lineage assignments. The pipeline is optimized for SARS-CoV-2 amplicon data but can also be used for other viruses and whole-genome sequencing protocols. Amplicon-optimized default parameters and the ability to customize critical parameters, combined with comprehensive reporting, ensure the quality of reported genomes and prevent the inclusion of low-quality sequences in downstream analyses and public repositories. Furthermore, CoVpipe2 will form the basis for additional genomic surveillance programs at the Public Health Institute of Germany that will extend to other viruses.", "appendix": "Data availability\n\nAll SRA accession IDs of raw reads and GISAID IDs of consensus sequences are listed at 57 and github.com/CDCgov/datasets-sars-cov-2; and in our Open Science Framework repository osf.io/26hyx (Extended data: https://doi.org/10.17605/OSF.IO/MJ6EQ). 62 We used ARTIC V3 samples from dataset 4 (VOI/VOC lineages, 16 samples), dataset 5 (non-VOI/VOC lineages, 33 samples), and dataset 6 (failedQC, 5 samples) from the original study of Xiaoli and Hagey et al. 57\n\nOpen Science Framework. Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2, https://doi.org/10.17605/OSF.IO/MJ6EQ. 62\n\nThis project contains the following extended data:\n\n• Data folder Accession ID. (SRA and GISAID accession ID lists)\n\n• Data folder Comparison. (Scripts and results of the benchmark comparison)\n\n• Data folder CoVpipe2 results. (Results of CoVpipe2 for each benchmark dataset)\n\n• Data folder Extended data. (Supplementary tables S1-S9)\n\n\nAcknowledgements\n\nWe gratefully acknowledge all data contributors, i.e., the Authors and their originating laboratories responsible for obtaining the specimens, and their submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID Initiative, on which this research is based. We also thank all German Electronic Sequence Data Hub contributors, the IMS-SC2 laboratory network, and all data providers, i.e., the originating laboratories responsible for obtaining samples and the submitting laboratories where genetic sequence data were generated and shared. We are incredibly grateful to Petra Kurzendörfer, Tanja Pilz, Aleksandar Radonić, and Aaron Houterman for outstanding sequencing support. We thank Marianne Wedde for manually checking and validating consensus sequences and called variants and Thorsten Wolff and Max von Kleist for fruitful discussions. We thank Ben Wulf, Fabian Rost, and Alexander Seitz – early users of the first version of CoVpipe for valuable feedback and reporting issues.\n\n\nReferences\n\nShu Y, McCauley J: GISAID: Global initiative on sharing all influenza data – from vision to reality. Eurosurveillance. 2017; 22(13): 30494.\n\nElbe S, Buckland-Merrett G: Data, disease and diplomacy: Gisaid’s innovative contribution to global health. Global Chall. 2017; 1(1): 33–46. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhare S, Gurry C, Freitas L, et al.: GISAID Core Curation Team, and Sebastian Maurer-Stroh. Gisaid’s role in pandemic response.2021. 2096-7071. Reference Source\n\nHarrison PW, Lopez R, Rahman N, et al.: The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. Nucleic Acids Res. 2021; 49(W1): W619–W623. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobishaw JD, Alter SM, Solano JJ, et al.: Genomic surveillance to combat COVID-19: challenges and opportunities. Lancet Microbe. 2021; 2(9): e481–e484. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJulianna LeMieux Genetic Engineering & Biotechnology News: All Aboard the Genome Express: Is a new generation of DNA sequencing technology about to hit the fast track? last accessed December 01, 2022. Reference Source\n\nHufsky F, Lamkiewicz K, Almeida A, et al.: Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief. Bioinform. 2021; 22(2): 642–663. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDjin Ye O, Hölzer M, Paraskevopoulou S, et al.: Advancing precision vaccinology by molecular and genomic surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021. Clin. Infect. Dis. 2022; 75(Supplement_1): S110–S120. Publisher Full Text\n\nBaumgarte S, Hartkopf F, Hölzer M, et al.: Investigation of a limited but explosive COVID-19 outbreak in a German secondary school. Viruses. 2022; 14(1): 87. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLoss J, Wurm J, Varnaccia G, et al.: Transmission of sars-cov-2 among children and staff in german daycare centres. Epidemiol. Infect. 2022; 150: e141. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDe Maio N, Walker C, Borges R, et al.: Issues with SARS-CoV-2 sequencing data. last accessed November 25, 2022. Reference Source\n\nBrito AF, Semenova E, Dudas G, et al.: Global disparities in SARS-CoV-2 genomic surveillance. Nat. Commun. 2022; 13(1): 1–13.\n\nConnor R, Yarmosh DA, Maier W, et al.: Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance. bioRxiv. 2022.\n\nChiara M, D’Erchia AM, Gissi C, et al.: Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Brief. Bioinform. 2021; 22(2): 616–630. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobert Koch Institute: Deutscher Elektronischer Sequenzdaten-Hub (DESH). last accessed November 25, 2022. Reference Source\n\nGrubaugh ND, Gangavarapu K, Quick J, et al.: An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol. 2019; 20(1): 1–19. Publisher Full Text\n\nResende PC, Motta FC, Roy S, et al.: SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms. BioRxiv. 2020.\n\nBrinkmann A, Ulm S-L, Uddin S, et al.: Amplicov: Rapid whole-genome sequencing using multiplex PCR amplification and real-time Oxford Nanopore MinION sequencing enables rapid variant identification of SARS-CoV-2. Front. Microbiol. 2021; 12: 1703. Publisher Full Text\n\nHilaire BGS, Durand NC, Mitra N, et al.: A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing. BioRxiv. 2020.\n\nGohl DM, Garbe J, Grady P, et al.: A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2. BMC Genomics. 2020; 21(1): 1–10. Publisher Full Text\n\nHadfield J, Megill C, Bell SM, et al.: Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018; 34(23): 4121–4123. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTshiabuila D, Giandhari J, Pillay S, et al.: Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq. BMC Genomics. 2022; 23(1): 1–17. Publisher Full Text\n\nLuo J, Meng Z, Xingyu X, et al.: Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing. Front. Microbiol. 2022; 4059.\n\nBrandt C, Krautwurst S, Spott R, et al.: poreCov – an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing. Front. Genet. 2021; 1397.\n\nDi Tommaso P, Chatzou M, Floden EW, et al.: Nextflow enables reproducible computational workflows. Nat. Biotechnol. 2017; 35(4): 316–319. PubMed Abstract \| Publisher Full Text\n\nKöster J, Rahmann S: Snakemake – a scalable bioinformatics workflow engine. Bioinformatics. 2012; 28(19): 2520–2522. PubMed Abstract \| Publisher Full Text\n\nPatel H, Monzón S, Varona S, et al.: nf-core/viralrecon: nf-core/viralrecon v2.6.0 - Rhodium Raccoon.March 2023. Publisher Full Text\n\nNasir JA, Kozak RA, Aftanas P, et al.: A comparison of whole genome sequencing of SARS-CoV-2 using amplicon-based sequencing, random hexamers, and bait capture. Viruses. 2020; 12(8): 895. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPosada-Céspedes S, Seifert D, Topolsky I, et al.: V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. Bioinformatics. 2021; 37(12): 1673–1680. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim K, Park K, Lee S, et al.: Virpipe: an easy and robust pipeline for detecting customized viral genomes obtained by nanopore sequencing. Bioinformatics. 2023; 39: btad293. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDezordi FZ, da Silva Neto AM , de Lima Campos T , et al.: Viralflow: a versatile automated workflow for sars-cov-2 genome assembly, lineage assignment, mutations and intrahost variant detection. Viruses. 2022; 14(2): 217. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLo C-C, Shakya M, Connor R, et al.: EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts. Bioinformatics. 2022; 38(10): 2700–2704. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaier W, Bray S, van den Beek M , et al.: Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nat. Biotechnol. 2021; 39(10): 1178–1179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNguyen PTT, Plyusnin I, Sironen T, et al.: HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. BMC Bioinformat. 2021; 22(1): 1–8. Publisher Full Text\n\nOliveira RRM, Negri TC, Nunes G, et al.: PipeCov: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification. PeerJ. 2022; 10: e13300. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrüning B, Dale R, Sjödin A, et al.: Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat. Methods. 2018; 15(7): 475–476. Publisher Full Text\n\nBoettiger C: An introduction to Docker for reproducible research. Oper. Syst. Rev. 2015; 49(1): 71–79. Publisher Full Text\n\nKurtzer GM, Sochat V, Bauer MW: Singularity: Scientific containers for mobility of compute. PLoS One. 2017; 12(5): e0177459. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAksamentov I, Roemer C, Hodcroft EB, et al.: Nextclade: clade assignment, mutation calling and quality control for viral genomes. J. Open Source Softw. 2021; 6(67): 3773. Publisher Full Text\n\nO’Toole Á, Scher E, Underwood A, et al.: Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 2021; 7(2): veab064. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nValieris R, Drummond RD, Defelicibus A, et al.: A mixture model for determining SARS-Cov-2 variant composition in pooled samples. Bioinformatics. 2022; 38(7): 1809–1815. PubMed Abstract \| Publisher Full Text\n\nChen S, Zhou Y, Chen Y, et al.: fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34(17): i884–i890. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWood DE, Jennifer L, Langmead B: Improved metagenomic analysis with Kraken 2. Genome Biol. 2019; 20: 1–13. Publisher Full Text\n\nLi H: Aligning sequence reads, clone sequences and assembly contigs with bwa-mem.2013.\n\nQuinlan AR: BEDTools: the Swiss-army tool for genome feature analysis. Curr. Protoc. Bioinformat. 2014; 47(1): 11–12.\n\nChun Hang A, Ho DN, Kwong A, et al.: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing. Sci. Rep. 2017; 7(1): 1–7.\n\nTyson JR, James P, Stoddart D, et al.: Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. BioRxiv. 2020.\n\nGarrison E, Marth G: Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907. 2012.\n\nDanecek P, Bonfield JK, Liddle J, et al.: Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2): giab008. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCingolani P, Platts A, Coon M, et al.: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012; 6(2): 80–92. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCornish-Bowden A: Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 1985; 13(9): 3021–3030. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang M, Kong L: pblat: a multithread blat algorithm speeding up aligning sequences to genomes. BMC Bioinformat. 2019; 20(1): 1–4.\n\nShumate A, Salzberg SL: Liftoff: accurate mapping of gene annotations. Bioinformatics. 2021; 37(12): 1639–1643. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKubik S, Marques AC, Xing X, et al.: Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples. Clin. Microbiol. Infect. 2021; 27(7): 1036.e1–1036.e8. Publisher Full Text\n\nSatya RV, DiCarlo J: Edge effects in calling variants from targeted amplicon sequencing. BMC Genomics. 2014; 15(1): 1073–1077. Publisher Full Text\n\nRambaut A, Holmes EC, O’Toole Á, et al.: A dynamic nomenclature proposal for sars-cov-2 lineages to assist genomic epidemiology. Nat. Microbiol. 2020; 5(11): 1403–1407. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXiaoli L, Hagey JV, Park DJ, et al.: Benchmark datasets for sars-cov-2 surveillance bioinformatics. PeerJ. 2022; 10: e13821. Publisher Full Text\n\nEwels PA, Peltzer A, Fillinger S, et al.: The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 2020; 38(3): 276–278. PubMed Abstract \| Publisher Full Text\n\nKatoh K, Standley DM: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 2013; 30(4): 772–780. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchäffer AA, Hatcher EL, Yankie L, et al.: Vadr: validation and annotation of virus sequence submissions to genbank. BMC Bioinformat. 2020; 21: 1–23.\n\nLibuit K, RA P III, Ambrosio F, et al.: Public health viral genomics: bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens, especially the sars-cov-2 virus.2022.\n\nLataretu M, Hölzer M: Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2. [Dataset]. 2023, June 27. Publisher Full Text\n\nMarieLataretu: rki-mf1/CoVpipe2: Version v0.4.3 (v0.4.3). Zenodo.2023. Publisher Full Text" }	[ { "id": "203328", "date": "20 Sep 2023", "name": "Wolfgang Maier", "expertise": [ "Reviewer Expertise Bioinformatics", "pathogen genomics", "genetics" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Lataretu et al. describes CoVpipe2, a bioinformatics pipeline for constructing viral consensus sequences from SARS-CoV-2 short sequenced reads obtained using the Illumina platform. It discusses the current state of the pipeline, various design decisions that have led to that state, and typical analysis pitfalls that the authors hope to overcome with their pipeline design.\nThe pipeline itself is implemented as a Nextflow pipeline and comes under a free and open-source license, which means that its exact steps and parameters can be explored down to any desired level of detail. Still the authors provide a very helpful overview in the manuscript text and in Figure 1 through both of which the reader can gain a good understanding of the pipeline layout and its components.\nThe authors point out the existence of multiple alternative analysis pipelines with similar scope as CoVpipe2 and list many of them in Table 1. I would expect most of these alternative pipelines to produce consensus genomes of similar quality as CoVpipe2, and most of the steps that CoVpipe2 is composed of are relatively standard in the field. From this perspective, the manuscript could be said to lack novelty. Beyond the core steps shared in similar form with many other pipelines, there are, however, some smart extra steps built into CoVpipe2 that are innovative ideas, like screening steps for mixed-infection and recombinant samples and consensus genome annotation with Liftoff.\nMore importantly, however, the authors are not just advertising yet another pipeline for SARS-CoV-2 genome analysis, but their manuscript is the kind of documentation that you wish every such pipeline came with: it explains not only individual analysis steps, but also their purpose, special analysis tweaks found to be necessary, and provides links to all relevant resources.\nIn summary, the manuscript describes a robust and mature resource for reproducible data analysis and does an excellent job at that. I enjoyed reading it and even though I've spent a considerable amount of time on developing similar pipelines I still picked up a few new ideas from it.\nI have no concerns regarding publication of this valuable manuscript, just one comment that the authors may wish to address in the manuscript directly or in a separate reply: For some steps in CoVpipe2 it seems there would have been several tools to choose from, and I'm wondering whether the authors of the pipeline have evaluated alternatives. In particular, I'd be interested in learning why freebayes was chosen as the variant caller and why primer trimming is done with BAMclipper, as I don't think these two tools are used by many other comparable pipelines. If the authors had specific reasons to prefer these tools over alternatives, it might add to the value of the manuscript if these were added to the text.\nBeyond that, I have found a small number of inconsistencies and typos that I think should be fixed before publication:\n1. the authors have done a very careful citation job, in general, but I think the following resources/specifications also deserve links/citations:\nZenodo\n\nThe \"precalculated Kraken2 database\" deposited at Zenodo\n\nThe BEDPE format (https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format)\n\nInstead of providing a general anaconda.org link (as done twice in the Methods section), it would be more helpful to provide direct links to the latest versions of pangolin and nextclade (https://anaconda.org/bioconda/pangolin and https://anaconda.org/bioconda/nextclade), which also includes channel information.\n\n2. In the introduction \"While sequencing intensity and turnaround times on variant detection increased in different countries\" is probably intended to mean increasing sequencing intensity, but decreasing turnaround times?\n3. In the introduction, when DESH genomes statistics are given, the numbers should be 1.2 million and 1.1 million (period instead of comma), and in the discussion of Dataset 5 -> Lineages \"for each CoVpip2-GISAD pair\" has a typo in the pipeline name.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "11400", "date": "15 May 2024", "name": "Martin Hölzer", "role": "Author Response", "response": "[1] Reviewer Question: For some steps in CoVpipe2 it seems there would have been several tools to choose from, and I'm wondering whether the authors of the pipeline have evaluated alternatives. In particular, I'd be interested in learning why freebayes was chosen as the variant caller and why primer trimming is done with BAMclipper, as I don't think these two tools are used by many other comparable pipelines. If the authors had specific reasons to prefer these tools over alternatives, it might add to the value of the manuscript if these were added to the text. Author Response: Thanks for the question. You are absolutely right; as with almost any bioinformatics pipeline, there are different options when choosing tools for steps such as quality control, mapping, and variant calling. Our final selection of tools is based on our experience in analyzing sequencing data throughout the SARS-CoV-2 pandemic. Especially in the early days, we performed various internal benchmarks on SARS-CoV-2 Illumina data and manually investigated mapping results and variant calls together with colleagues from our expert unit for respiratory viruses. Thus, our main objective in CoVpipe2 was to reliably detect variants with high allelic depth and good read support. Low-frequency variants were not the primary focus of the pipeline, as the tool is intended to reconstruct robust consensus genomes from patient samples that can be used for genomic surveillance. However, if a user wants to use CoVpipe2 for different research questions, the implementation allows full customization of the necessary parameters (allele frequency, genotype adjustment, …) By screening the literature and examining other pipelines and community standards, we carefully selected the tools that performed best in our internal benchmarks for SARS-CoV-2 short-read data. Regarding variant calling, we first tested LoFreq (Wilm et al. 2012). Although very sensitive, LoFreq lacks a strong genotyping module that was crucial for our downstream processing of the called variants. Furthermore, the output files were hard to process (non-standard VCF formats). We implemented GATK as a second choice, which is a standard tool for eukaryotic genomic variant calling (McKenna et al. (2010), Van der Auwera & O'Connor (2020)) but was also shown to perform well on non-human targets (Lefouili et al. 2022). Performance and output standards were excellent, but it turned out that GATK misses a low amount of viral genomic variants in some samples, although multisample calling was employed. Single false negative variants, which we identified via a comprehensive investigation of the BAM files, were deemed to be too important to stick with the tool. Finally, we chose freebayes (Garrison et al. 2012), which excelled with high performance, high precision, and output files that were straightforward to process in downstream steps of the pipeline. In addition to the variant callers, there is indeed a large selection of quality processing tools. We opted for fastp rather than Trimmomatic because the processing speed is much faster, and the output quality is at least as good. It was shown, that “data filtered by Trimmomatic, SOAPNuke, Cutadapt and fastp were detected with 7174, 7040, 6942 and 6708 false positive variants respectively” (Chen et al. 2018), highlighting that fastp preprocessing can even improve the specificity of downstream analysis. In addition, fastp is equipped with a broader portfolio of parameter options. Another crucial step in read processing is primer clipping, which may promote mapping artifacts and dilution of variant calls if done before read alignment. If InDels occur close to the end of amplicons, a gap open penalty is more expensive than a few mismatches in mapping. For example, this caused trouble with the Spike DEL69/70 in several amplicon kits and made it necessary to use the artificial primer as a mapping anchor. Hence we replaced cutadapt, which clips adapters before mapping, with BAMclipper, which removes adapters after mapping. In our opinion, primer clipping should generally be performed after mapping in reference-based analysis. We, therefore, also discuss late primer clipping more prominently in connection with CoVpipe2. Furthermore, we fully agree that continuous benchmarking is a necessary process to adapt pipelines to changing wet lab procedures, adapted priming schemes, and pathogen evolution. If we find problems, we will also adapt CoVpipe2 accordingly and release new stable versions for reproducible research. We added the following text to the manuscript: “We carefully selected the bioinformatics tools integrated into CoVpipe2 based on internal benchmarks and in-depth manual reviews of sequencing data, mapping results, and called variants. Based on our hands-on experience with SARS-CoV-2 sequencing datasets during the pandemic, this approach ensured that tools that can robustly detect high allele depth and well-covered variants are used for detection. Despite the primary goal of CoVpipe2 to identify high-confidence variants to reconstruct robust consensus genomes for genomic surveillance, the pipeline also provides flexibility for adaptation to different research environments.” -------------------------------------------------------------------------------------------------------------------------- [2] Reviewer Question: the authors have done a very careful citation job, in general, but I think the following resources/specifications also deserve links/citations]: Author Response: Thanks for the comment. We fully agree and added more precise references for various sources such as Zenodo, the custom Kraken 2 database, BEDPE format, and Nextcalde/pangolin on anaconda.org. -------------------------------------------------------------------------------------------------------------------------- [3] Reviewer Question: In the introduction \"While sequencing intensity and turnaround times on variant detection increased in different countries\" is probably intended to mean increasing sequencing intensity, but decreasing turnaround times? Author Response: Yes, you are right; thanks for catching this. We changed the text accordingly: “While sequencing intensity increased and turnaround times on variant detection decreased in different countries, there are also major disparities between high-, low- and middle-income countries in the SARS-CoV-2 global genomic surveillance efforts.” -------------------------------------------------------------------------------------------------------------------------- [4] Reviewer Question: In the introduction, when DESH genomes statistics are given, the numbers should be 1.2 million and 1.1 million (period instead of comma), and in the discussion of Dataset 5 -> Lineages \"for each CoVpip2-GISAD pair\" has a typo in the pipeline name. Author Response: Thanks, we corrected that." } ] }, { "id": "233668", "date": "17 Jan 2024", "name": "Sondes Haddad-Boubaker", "expertise": [ "Reviewer Expertise Virology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper presents a comprehensive bioinformatics workflow designed for the reconstruction of SARS-CoV-2 genomes using short-read sequencing data. The workflow description offers a detailed overview of the processes involved; however, there are opportunities for improvement to enhance the overall quality of the paper.\n1-Organization: While the overall structure is clear, introducing numbering at both the heading and sub-heading levels would enhance clarity and facilitate better distinction between various steps in the workflow.\n2-Technical Terminology: Given the diverse audience, including virologists and other biologists, it is crucial to ensure accessibility by providing clear definitions for all technical terms and acronyms. This will make the paper more easy to readers who may not be familiar with specific bioinformatics or genomics terminology.\n3- References and Sources: Include proper references and sources for the tools and databases mentioned by providing specific URLs for easy access to external resources.\n4-Methods and Results: - Introduce a dedicated \"Pipeline Evaluation\" subsection in both the \"Methods\" and \"Results\" sections and change the abstract section accordingly. -Include details on the investigated sequences, with a thorough description of sample types, cycle threshold (ct) values, and sample categories. -Consider expanding the evaluation by incorporating additional samples/sequences, especially failed sequences from samples with varying ct values (especially high ct values). The Investigation of the contribution of the pipeline in obtaining reliable sequences from samples with high ct values may be helpfull for virologist who are dealing with such challenges especially in samples obtained from long-term excretors. - Please Illustrate \"common challenges\" with a graph or figure for better presentation and understanding. 5- Discussion: - Emphasize and discuss the added value of the pipeline in obtaining reliable sequences from samples with high ct values. Compare the results obtained using this pipeline with those from other existing pipelines to highlight its superiority. - Provide detailed insights into how this pipeline can be applied to study other viruses,\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [ { "c_id": "11401", "date": "15 May 2024", "name": "Martin Hölzer", "role": "Author Response", "response": "(I) - Organization: [1] Reviewer Concern: While the overall structure is clear, introducing numbering at both the heading and sub-heading levels would enhance clarity and facilitate better distinction between various steps in the workflow. Author Response: Thanks for the suggestion. Numbering (sub)sections helps to structure the text better and distinguish which parts belong together semantically. However, there is little we can do about it, as this is the journal's style. Nevertheless, we will ask the editor/typesetting team if that’s possible. -------------------------------------------------------------------------------------------------------------------- (II) - Technical Terminology: [2] Reviewer Concern: Given the diverse audience, including virologists and other biologists, it is crucial to ensure accessibility by providing clear definitions for all technical terms and acronyms. This will make the paper more easy to readers who may not be familiar with specific bioinformatics or genomics terminology. Author Response: Thanks for the comment. We agreed and added a list of Abbreviations to the manuscript to make it easier for readers to follow the story. COVID-19 - Coronavirus disease 2019 SARS-CoV-2 - Severe acute respiratory syndrome coronavirus 2 GPL3 license - GNU General Public License GISAID - Global Initiative on Sharing All Influenza Data EBI - European Bioinformatics Institute EMBL - European Molecular Biology Laboratory RKI - Robert Koch Institute CorSurV - Coronavirus Surveillance Verordnung (eng., Coronavirus Surveillance Regulation) DESH - Deutscher Elektronischer Sequenzdaten-Hub (eng., German Electronic Sequence Data Hub) IMS-SC2 - Integrated Molecular Surveillance for SARS-CoV-2 ONT - Oxford Nanopore Technologies NGS - Next-Generation Sequencing HPC - High-Performance Computing WSL - Windows Subsystem for Linux CSV file - Comma-Separated Values file GFF file - General Feature Format file BEDPE file - Browser Extensible Data Paired-End file VCF file - Variant Call Format file HTML - Hypertext Markup Language BAM file - Binary Alignment and Map file BED file - Browser Extensible Data file CCO license - Creative Commons Zero license VOC - Variants of Concern VOI - Variants of Interest IUPAC - International Union of Pure and Applied Chemistry indel - Insertion/Deletion Variant JSON file - JavaScript Object Notation file CDC - Centers for Disease Control and Prevention ENA - European Nucleotide Archive QC - Quality Control PCR - Polymerase Chain Reaction ID - Identifier SRA - Sequence Read Archive -------------------------------------------------------------------------------------------------------------------- (III) - References and Sources [3] Reviewer Concern: Include proper references and sources for the tools and databases mentioned by providing specific URLs for easy access to external resources. Author Response: We agree that it’s crucial to acknowledge all tools and resources properly. When there is an original publication for a tool or database, we cite the publication. If not, we cite the code repository or the URL to the resource (such as GitHub or Zenodo). We carefully checked the text again and added citations/URLs if they were missing and necessary. For example, Rev #1 also commented that the specific URL to the custom Kraken 2 database on Zenodo was missing. We added that. -------------------------------------------------------------------------------------------------------------------- (IV) - Methods and Results [4] Reviewer Concern: Introduce a dedicated \"Pipeline Evaluation\" subsection in both the \"Methods\" and \"Results\" sections and change the abstract section accordingly. Author Response: We fully agree that presenting the implementation of a pipeline together with its evaluation with additional analysis can be confusing. So what are the \"Methods\" and the \"Results\" parts, then? This is often a problem when simultaneously presenting and evaluating a new software implementation. But we also need to adhere to the style guidelines for journals. We wrote a “Software Tool Articles” and have to follow this structure: https://f1000research.com/for-authors/article-guidelines/software-tool-articles. As you can see in these guidelines, “Software Tool Articles typically contain the following sections: Introduction, Methods, Results (Optional), Use Cases (Optional), Conclusions/Discussion.” In the first version, we skipped the “Use Cases” section to discuss our example data sets for pipeline evaluation directly in the “Results” section. However, thanks to your comment, we believe that also skipping the “Results” section entirely makes our manuscript clearer. We deleted the “Results” section and added the subsections “Selection of benchmark datasets and pipeline evaluation” and “Reporting” at the end of the “Methods”. We changed the subsection “Selection of benchmark datasets” to “Selection of benchmark datasets and pipeline evaluation” to include your suggestion. We think that the structure is now clearer because we first describe in the “Methods” the implementation of the pipeline and how to operate it, according to the journal guidelines for “Software Tool Articles”: The Methods should “Include a subsection on Implementation describing how the tool works and any relevant technical details required for implementation; and a subsection on Operation, which should include the minimal system requirements needed to run the software and an overview of the workflow.” Then, we describe some specific implementation decisions followed by the example data sets for pipeline evaluation and, finally, the report structure we implemented. According to the journal guideline for “Software Tool Articles”: “Abstracts are structured into Background, Methods, Results, and Conclusions”, thus, we can not change sections in the abstract. Although we generally agree that different subheadings would help follow the story, we must also stick to the journal guidelines. -------------------------------------------------------------------------------------------------------------------- [5] Reviewer Concern: Include details on the investigated sequences, with a thorough description of sample types, cycle threshold (ct) values, and sample categories. Author Response: We only use publicly available data sets and reference the original sources (publication, GitHub, and ENA repositories). We suggest that readers should refer to the original sources for further details. However, the description of the benchmark datasets is now also part of the “Methods”. Here, we describe: “We compared the results of CoVpipe2 (v0.4.0) with publicly available benchmark datasets for SARS-CoV-2 surveillance 57 ( GitHub CDC data).” [57] Xiaoli L, Hagey JV, Park DJ, et al.: Benchmark datasets for sars-cov-2 surveillance bioinformatics. PeerJ. 2022;10:e13821. 10.7717/peerj.13821 We do not want to mirror the details of the benchmark data sets that are described in the original sources. In addition, we can not provide additional information, such as Ct values, because, to the best of our knowledge, this information is not available in the original publication or in the data source (GitHub, ENA). -------------------------------------------------------------------------------------------------------------------- [6] Reviewer Concern: Consider expanding the evaluation by incorporating additional samples/sequences, especially failed sequences from samples with varying ct values (especially high ct values). The Investigation of the contribution of the pipeline in obtaining reliable sequences from samples with high ct values may be helpful for virologist who are dealing with such challenges especially in samples obtained from long-term excretors. Author Response: Thanks for the comment. We agree that investigating challenging samples is especially interesting for users of CoVpipe2. As described above (Q [5]), we selected a publicly available benchmark dataset for SARS-CoV-2 surveillance (Xiaoli et al. 2022) to compare our results directly with previous calculations. In addition, this data set also includes difficult samples that should not withstand automatic quality control (QC) and could mimic high Ct values. CoVpipe2 was developed as a robust and standardized workflow to support genome reconstruction in genomic surveillance programs. Thus, our main goal in developing CoVpipe2 was to provide a robust bioinformatics pipeline for short-read sequencing data that recognizes important mutations with decent allele frequency and automatically identifies and masks ambiguous positions. We implemented parameters (20X coverage to consider a position for variant calling, 90% ACGT nucleotide identity to the reference) to discover low-quality samples that might originate from high Ct values. Running the pipeline on amplicon sequencing data from samples with high Ct can result in \"read stacks\" with high sequence depth for certain well-amplified amplicons, but it could also lead to low horizontal genome coverage due to low input RNA quantity. CoVpipe2 will report such samples as “failed” in the QC report. Thus, only samples with a decent vertical (sequencing depth) and horizontal genome coverage should be used for downstream genomic surveillance and trustworthy lineage assignment. Nevertheless, CoVpipe2 also reports the full intermediate results, such as BAM files and unfiltered VCF files. Experienced users can investigate all variant calls and their respective allele frequencies - also for QC-failed samples. Thus, it is also possible to investigate mixed variant calls (co-infection, recombinants) and low-frequency variants with the help of CoVpipe2. However, for routine genomic surveillance applications, such challenging samples will be automatically flagged as QC-failed in the pipeline, supporting non-expert users in decision-making and selecting suitable samples for surveillance. Obtaining reliable consensus genomes from high Ct samples is generally difficult. In our experience, it is better to flag such samples with a warning and inform the user that those are of lower quality and probably not suited for further downstream analysis. Thus, CoVpipe2 helps virologists identify such challenging samples so that they can be selected for re-sequencing or exclusion from downstream analysis. -------------------------------------------------------------------------------------------------------------------- [7] Reviewer Concern: Please Illustrate \"common challenges\" with a graph or figure for better presentation and understanding. Author Response: Here, we present a bioinformatics pipeline with the specific objective of reconstructing robust SARS-CoV-2 consensus genomes from patient samples and short-read data, which is also reflected in the title of our paper. We present CoVpipe2 as a solution to overcome such challenges in reconstructing robust SARS-CoV-2 genomes from short-read (amplicon) data. In Figure 2, we explicitly illustrate common challenges regarding variant calling, which is one of the main obstacles in many reference-based virus bioinformatics pipelines, and where we specifically integrated solutions in CoVpipe2 to overcome such challenges. Besides the dedicated figure for variant calling challenges, we examine other relevant challenges in the context of the CoVpipe2 implementation, such as amplicon drop-outs, in the text. For a general overview, we think that common challenges in the context of amplicon sequencing and virus bioinformatics need to be more broadly addressed in dedicated benchmark studies such as those already available from Beerenwinkel et al. 2012; Murray et al. 2015; Fitzpatrick et al. 2022; Liu et al. 2021. -------------------------------------------------------------------------------------------------------------------- (V) - Discussion: [8] Reviewer Concern: Emphasize and discuss the added value of the pipeline in obtaining reliable sequences from samples with high ct values. Compare the results obtained using this pipeline with those from other existing pipelines to highlight its superiority. Author Response: As described in [6], we developed CoVpipe2 as a robust and modular surveillance pipeline focusing on amplification protocols and short-read data. Thus, for samples with high Ct values and where amplification can not yield enough output, CoVpipe2 will mark them as “failed” in the reporting. High Ct samples will usually result in regions (amplicons) with low coverage. Such regions are then automatically masked by “N” bases in the final consensus. We don't think a bioinformatics pipeline should construct any “reliable” consensus genome sequence when the data is insufficient. Thus, it is more important to identify such low-quality samples and flag them with a user warning. Our filtering and reporting aims to fit the needs of large-scale surveillance programs with detailed QC information and provide a quick overview of sample results, to identify such challenging samples easily. Thus, CoVpipe2 helps virologists to identify such problematic samples so that they can be selected for re-sequencing or excluded from downstream analysis. Regarding the comparison to other pipelines, we implicitly did that by selecting the test data sets. Those come from another independent benchmark study (Xiaoli et al. 2022), and we compare our CoVpipe2 results against those from the original benchmark paper. The original authors wrote in their publication: > The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. All available pipelines (Tab. 1 in manuscript) excel in various properties. While some strive to have high detection rates for minor variants for research settings, CoVpipe2 was developed to be easily extendable and adjustable to new requirements in surveillance or other viruses [see 9]. Thus, we would like to stick to our decision of utilizing a publicly available and carefully constructed, independent benchmark data set instead of including more samples and pipelines. Our study focuses on presenting the CoVpipe2 implementation and highlighting various implementation decisions in the context of reconstructing robust genome sequences for surveillance tasks. Nevertheless, we agree that another large-scale and up-to-date benchmark study comparing all available pipelines (Tab. 1), including CoVpipe2, would be interesting but is beyond the scope of our Software article. -------------------------------------------------------------------------------------------------------------------- [9] Reviewer Concern: Provide detailed insights into how this pipeline can be applied to study other viruses Author Response: The predecessor of CoVpipe2, the snakemake pipeline CoVpipe1, was used to create adapted pipelines for RSV and Influenza. In this context, we discovered that other viruses might need other tools and parameters to reflect their characteristics (genome size, segmentation, reference selection). Also, the needs for final reporting may differ depending on the virus under investigation, and changes in the pipeline may be necessary. Besides, we successfully used CoVpipe2 on Polio and Measles viruses for genome reconstruction and variant calling from short-read sequencing data. In short, for Polio viruses, we sequenced the same 24 samples with Sanger, Illumina, and Nanopore, and CoVpipe2 was able to identify the same variants compared to the other sequencing technologies and associated bioinformatic steps (unpublished preliminary data). In general, the basic software framework - the generic sub-processes of raw data quality control, read alignment, variant calling, and consensus building - and the bioinformatic challenges for data derived from amplicon sequencing are equally applicable to other viruses. CoVpipe2 can serve as a blueprint for other pathogens, especially other unsegmented viruses, and provide first insights into the variants and consensus sequences. Tools, parameters, and thresholds might need careful adjustments depending on the pathogen. Similarly, the downstream analysis might be pathogen-specific, e.g., require pathogen-specific datasets (such as reference sequences for Influenza from Nextclade). We are currently working on a harmonized multi-pathogen pipeline with different profiles (tools, parameter settings) tailored towards specific viruses. Besides, interested users can already run CoVpipe2 on other (non-segmented) viruses by simply switching to another reference genome as we did before successfully for analyzing Polio virus amplicon data (parameter --ref_genome). We extend the “Conclusion” accordingly: “We used CoVpipe1 and CoVpipe2, which were initially developed for SARS-CoV-2, to reconstruct the genomes of other viruses. By selecting different reference genomes for polio, measles, RSV, and influenza viruses and modifying the analysis processes for the latter two viruses, we were able to demonstrate the workflow's potential as a universal blueprint for viral genome analysis. This adaptability has been demonstrated by the ability to identify consistent variants and the successful application to different viral characteristics, such as varying genome size and segmentation. However, it should also be noted that for segmented viruses, more customization is required than simply replacing the (non-segmented) reference genome. However, our experience suggests that customization of tools, parameters, and reporting requirements is needed for each virus, pointing to developing a harmonized pipeline for multiple pathogens. CoVpipe2 thus proves to be a robust tool for SARS-CoV-2 and paves the way for broad application in virology research by highlighting its ability to serve as a fundamental framework for building customized pipelines for a wide range of pathogens.”" } ] } ]	1	https://f1000research.com/articles/12-1091
https://f1000research.com/articles/13-279/v1	16 Apr 24	{ "type": "Systematic Review", "title": "Digital Tools for Boosting the Impact of Fiscal Decentralization in Africa's Local Economies", "authors": [ "Nara Monkam", "Maonei Gladys Mangwanya", "Maonei Gladys Mangwanya" ], "abstract": "Background Fiscal decentralization offers potential for stimulating local economic development in Africa, empowering subnational governments to control revenue and spending. However, challenges such as urbanization, poverty, inequality, insufficient infrastructure, and governance issues hinder the successful implementation of the core tenets of fiscal decentralization. This paper explores the role of digital technologies in promoting greater fiscal decentralization and revenue enhancement, as a strategic response to these local economic development challenges in Africa.\n\nMethod Through a systematic literature review, this study explores the role of fiscal decentralization in driving local economic development, with a focus on leveraging digital technologies to boost revenue generation and strengthen governance and institutional capacity at the subnational level.\n\nResults The research underscores the importance of investing in digital infrastructure, skill development, and regulatory frameworks, while addressing data privacy and security concerns.\n\nConclusion By emphasizing the transformative impact of digital technologies fiscal decentralization and property taxation, this paper contributes to the existing literature and highlights avenues for promoting local economic development across Africa.", "keywords": [ "Fiscal decentralization", "Property tax", "Subnational government finance", "Local economic development", "Digital technologies" ], "content": "1. Introduction\n\nIn recent years, there has been a notable increase in focus on fiscal decentralization (FD), as researchers and policymakers acknowledge its capacity to stimulate local economic development (LED) in Africa (Kamara, 2017; Khumalo, 2014); Mosikari and Stungwa (2023). To realize LED, one important approach is for subnational governments (SNGs) in Africa to implement the fundamental principles of FD. These principles include the necessity of transferring authority and autonomy to SNGs to foster decision-making pertaining to the allocation and expenditure of funds within their respective jurisdictions (Martinez, Qian, Wang, & Zou, 2006). This henceforth stimulates SNGs to generate revenue through varied avenues, including property taxes, user charges, licensing fees, and registration fees. Through the strategic implementation of revenue diversification, SNGs can effectively minimize their reliance on central government transfers, thereby establishing a more resilient and sustainable fiscal framework (Bello & Mackson, 2023; Martinez-Vazquez, 2008). FD also aids in facilitating the transfer of financial resources from the top tier of government to the regional and local levels. The transfer of funds plays a crucial role in maintaining a balance between the financial demands of various tiers of subnational government (Bahl, 2000; Martinez-Vazquez & Searle, 2007; Rutto, Minja, & Kosimbei, 2022). It is also important for SNGs to prudently manage their annual expenditures revenues, and transfers to avoid fiscal deficits, thereby posing a significant risk to the financial stability of the country. Faced with fiscal risk, SNGs may receive a bailout from the central government as a means to fulfill their financial obligations whilst continuing their regular operations (Dabla-Norris, 2006; Oppong, 2020). Under ideal conditions where the core tenets of fiscal decentralization are faithfully executed, even though not a panacea for the developmental challenges confronting numerous African countries at the local level, it still holds the potential to stimulate local economic development (Haas, Knebelmann, & Nyirakamana, 2021). This potential is particularly significant when harnessed in conjunction with the advantages offered by digital technologies. For example, through the use of digital platforms, governments have been able to streamline administrative processes, improve financial management, and enhance service delivery at the local level. This has resulted in a more efficient allocation of resources, reduced corruption, and increased citizen participation in decision-making processes. Moreover, as technology continues to advance, African countries have the opportunity to further leverage digital innovations to expedite LED and drive economic prosperity at the local level.\n\nThe aim of this paper is to explore the prospective role those digital technologies may assume in promoting greater fiscal decentralization and revenue enhancement, particularly via property taxation, to strategically address the challenges of local economic development in Africa. To fulfill this aim, the paper employs a methodical review of the literature to examine the potential of fiscal decentralization and its core pillars to act as driving forces for local economic development within the African context. Through an analysis of best practices and successful case studies from a variety of countries, this paper compiles instances of successful implementation of digital technologies that bolster revenue streams for SNGs while enhancing their governance and institutional capacity.\n\nThis paper contributes to the existing body of literature by emphasizing the transformative capabilities of digital technologies in reinforcing fiscal decentralization and property taxation, which in turn catalyzes local economic development in Africa. It further underscores that facilitating economic expansion at the local level can promote Sustainable Development Goals (SDGs) through various avenues. These include generating own sources of revenue via local taxes (e.g., property taxes), service charges, and licensing fees; enhanced delivery of public services; increased local accountability; and the creation of policies designed to attract investments, support local enterprises, or advance specific industries or sectors. Such strategies can give rise to employment opportunities, stimulate entrepreneurship, and boost productivity. These elements contribute to alleviating poverty, promoting social inclusion, and improving living standards, thereby addressing several critical components of the SDGs.\n\nThis paper is organized as follows: Section 2 presents a comprehensive overview of the systematic review methodology, as guided by the PRISMA 2020 framework. Section 3 provides an overview of how the core tenets of fiscal decentralization can act as catalysts for local economic development. Section 4 delves into the challenges faced by SNGs that impede local economic development. Section 5 details how digital technology can be strategically employed to promote greater fiscal decentralization and revenue enhancement in response to the local economic development challenges outlined in Section 4. Lastly, Section 6 offers concluding remarks and discusses potential policy implications.\n\n\n2. Methods\n\nThis study employed a systematic review methodology, designed to investigate the field of fiscal decentralization in Africa. This investigative process entailed a comprehensive search aimed at delineating the scope of existing scholarship within this field.\n\nFor the literature review search the following keywords were used by Monkam and Mangwanya (2024): “fiscal decentralization”, “revenue generation”, “local economic development” and “service delivery” within the African context. Additionally, the search extended to include “digital technologies” and their implications for “subnational government’” in a global framework.\n\nThis study involved a thorough analysis of both successful practices and challenges in the field of fiscal decentralization. The identification of these challenges underscores the critical need for SNGs across Africa to embrace digital technologies. Through the utilization of digital tools, SNGs can improve their revenue collection mechanisms, especially focusing on property taxation.\n\nThe literature review comprehensively integrates a wide array of sources, ranging from peer-reviewed academic journals and conference proceedings to dissertations, policy briefs, and digitally accessible materials. These materials include newspaper articles, blogs, and reports, all hyperlinked within the text for direct reference. This inclusive approach ensures a multidimensional examination of the topic, facilitating a rich and nuanced understanding rooted in scholarly discourse and broader societal reflections. By embracing diverse sources, the review aims to construct a holistic perspective, bridging academic rigor with real-world applications and interpretations.\n\nThe primary repository for this search was Google Scholar, covering the period from May 2023 to August 2023. To capture the evolving discourse on fiscal decentralization and provide a comprehensive overview of scholarly perspectives, the temporal filter for publications was set from 2006 to the present.\n\nIn conducting this research, an initial search yielded 246 sources, with an additional 14 websites considered. After careful examination of abstracts, findings, and conclusions for relevance, 108 sources were identified as pertinent to the study’s focus. This selection process aimed to gather insights into best practices and challenges of fiscal decentralization in Africa, as well as identify successful examples of digital technology adoption. Among these 108 sources, 30 case studies were specifically chosen to highlight these practices, providing concrete examples for analysis. The remaining 138 sources were excluded as they did align with the research objectives. As depicted in Figure 1, the Prisma framework was systematically applied to guide the execution of the literature review. This approach facilitated a structured and transparent methodology for the identification, screening, and inclusion of relevant studies, thereby ensuring the rigor and reproducibility of the review process (PRISMA, 2020). EndNote software was instrumental in efficiently organizing and referencing these selected sources, facilitating their systematic arrangement and citation.\n\nThe inclusion criteria were explicitly defined to ensure the relevance and rigor of the literature review. Included were empirical studies and systematic reviews that:\n\n• Examined the best practices and challenges associated with fiscal decentralization in the African context.\n\n• Investigated the global adoption of digital technologies to enhance property tax systems, providing potential solutions to challenges faced by SNGs in Africa\n\nConversely, the exclusion criteria were applied to\n\n• Studies that did not specifically address fiscal decentralization and subnational government finance in the African context.\n\nThis comprehensive review of the literature establishes the study’s basis in current academic work and identifies unexplored areas that this research intends to address. It contributes to the ongoing discourse surrounding fiscal decentralization and the potential of digital technologies to improve property tax revenue collection.\n\nThe researchers acknowledge the limitations of the current review, notably the emphasis on digital technologies as a solution to fiscal decentralization challenges. This emphasis may inadvertently overlook non-technological factors such as political will, cultural acceptance, and social dynamics, which could equally influence success in implementing fiscal decentralization measures. However, the paper lays the groundwork for future empirical research aimed at assessing the potential impact of digital technologies in promoting greater fiscal decentralization and revenue mobilization. Such research will serve as a strategic response to local challenges in Africa, providing valuable insights into the holistic factors shaping effective fiscal governance.\n\n\n3. Background: understanding the potential of fiscal decentralization to drive local economic development in Africa\n\nIn this section, the objective is to demonstrate how the effective application of fiscal decentralization’s key principles can play a pivotal role in fostering a sustainable environment for local economic development in Africa, thereby bolstering robust economies. We will build upon the premise that effective fiscal decentralization, in addition to its four pillars, necessitates political empowerment (political decentralization) and regulatory empowerment (administrative decentralization) as a foundational basis. The four pillars we will discuss include the distribution of expenditure responsibilities, the assignment of revenue sources, the allocation of intergovernmental fiscal transfers or grants, and the regulations surrounding subnational borrowing, budget deficits, and the accrual of subnational debt.\n\nThe establishment of subnational elections as an approach to political decentralization offers the potential of augmenting the effectiveness of governance by empowering voters with increased autonomy (Bahl, 2000). Voters have more control and decision-making power in shaping the policies and direction of their communities. When SNG officials are appointed, a system of upward accountability is inadvertently put in place, whereby local officials tend to be liable to the individuals responsible for their appointment. On the other hand, the establishment of SNGs through elections fosters a sense of downward accountability, as they become accountable to the local electorate (Shrestha, Martinez-Vazquez, & Hankla, 2023). A study carried out by Wagana, Iravo, Nzulwa, and Kihoro (2017) found that there is a positive correlation between political decentralization and the effective delivery of public services such as water and sanitation, health, roads and sewer services at the local level in Kenya. Political decentralization in Kenya has paved the way for greater citizen involvement in shaping policies that directly impact their local water and sanitation services. This participatory approach empowered individuals to enhance their quality of life by advocating for more efficient and effective service delivery.\n\nIn addition, civil service organizations (CSOs) play a crucial role as independent “watchdogs” continuously monitoring elected local officials’ performance. They function as an intermediary to mitigate potential conflicts of interest that may arise among local authorities due to political affiliations. CSOs have an integral part in advocating for the communities they represent, as they actively promote citizen participation. This enables local authorities to receive valuable feedback on matters relating to service provision. As a result, they help ensure transparency, accountability, and effective governance within the SNGs (Daughters & Harper, 2007; Devas, 2005).\n\nAdministrative decentralization seeks to redistribute power, responsibility, and financial resources for the delivery of public services among various tiers of governance (Engdaw, 2022; Mollah, 2007). With administrative or regulatory decentralization, SNGs have control over local civil service matters, which include aspects such as salaries, hiring, and termination of employment. Additionally, they govern the local regulatory framework, implying that decisions concerning the nature and method of service delivery should be determined at the local level. As a result, the likelihood of corruption and mismanagement decreases, and public resources are more likely to be used efficiently and effectively (Bellé & Ongaro, 2014). As for financial management, SNGs enjoy discretion over spending, albeit with monitoring and oversight facilitated by the central government.\n\nThe subsidiarity principle suggests that public services should be handled by the lowest level of government capable of addressing that matter effectively. However, there are exceptions where public services might be better managed by a higher level of government for reasons of efficiency or economies of scale, interregional spillovers, and redistribution of income. For instance, services like national defense are usually handled by the central government (Marshall, 2008). Expenditure assignments therefore require the optimal allocation of responsibilities among different tiers of government pertaining to the provision and delivery of public services1, the policy formulation and regulation, financial management, and administrative functions2 of said services. The optimization of expenditure assignments is commonly accomplished through the allocation of exclusive responsibilities across different tiers of government, as opposed to overlapping responsibilities.\n\nExpenditure assignments in local governments in Africa can have significant direct and indirect impacts on local economic development. These assignments allow local governments to effectively deliver public services and make investments in critical areas like infrastructure, business support, and vocational training, tailored to local needs. By leveraging their understanding of the local context, they can deliver services more efficiently, leading to cost savings and better outcomes. For example, to ensure that citizens have access to basic services in Cote d`Ivoire, the central government devolved revenue raising responsibilities. Linked to this fiscal authority is the responsibility to provide basic services such water and sanitation, health, education and roads (Sanogo, 2019). In addition, Malawi adopted its National Decentralization Policy (NDP) in 1998 which plays a pivotal role in providing a unique classification of functions and responsibilities between the central and local governments. The NDP delegated the responsibilities of service delivery and governance to local governments in Malawi resulting in enhanced improved autonomy and capacity. This also led to greater local decision-making, more efficient allocation of resources, accountability, governance effectiveness, and local empowerment. The implementation of the NDP was in line with the objective of establishing a well-defined and streamlined allocation of duties, thereby fostering improved provision of public services and facilitating LED in Malawi.\n\nThe correspondence principle implies that if a local government is responsible for providing a particular service, then it should also have the ability to generate or be assigned the revenue necessary to provide that service (Bahl & Martinez-Vazquez, 2006). For example, if a local government is responsible for maintaining a local park, then it should have the ability to collect taxes or receive funds (the revenue) from the people who use the park or benefit from it. This ensures that the costs of providing the service are covered by the beneficiaries, and that the local government has enough resources to provide the service effectively.\n\nLocal municipalities have the ability to generate revenue through various means including property taxes, user fees such as refuse collection, license and registration fees, as well as public utility charges and admissions to recreational facilities (Bahl, 2008; Bello & Mackson, 2023). These revenue sources enable SNGs to effectively meet their clearly defined expenditure responsibilities. For example, in recent times, Kenya, Nigeria, and South Africa implemented constitutional changes, including modifications to the legal framework governing local governance and finance, that have had an impact on the manner in which cities in these countries generate own source of revenue, giving them more autonomy and control (Kithatu-Kiwekete, 2018). Greater autonomy and capacity to generate their own revenue sources will enhance SNGs’ autonomy to align spending decisions with local needs, leading to more effective public services and investments that stimulate local economic activity. Revenue assignment also provides a more stable funding base, crucial for long-term planning and investment. SNGs may collect certain taxes, like property taxes or local business taxes more efficiently due to their close proximity to taxpayers (Rodríguez-Pose & Krøijer, 2009). Furthermore, this fosters increased accountability to how funds are spent, leading to better governance and resource use. Finally, the incentive to promote LED is heightened for SNGs reliant on their own revenues, as this expands their tax base and boosts their income. Additionally, SNGs can potentially implement more equitable tax policies that consider local conditions and ability to pay.\n\nDespite the given authority to generate revenue, SNGs may fail to achieve anticipated outcomes if there is a lack of sufficient enforcement mechanisms to ensure compliance with tax payment obligations (Sebele-Mpofu, 2020). The effectiveness of revenue collection methods relies heavily on the cooperation of citizens in fulfilling their tax obligations and responsibilities. Without proper enforcement such as penalties on non-compliance, taxpayers may opt to evade their tax obligation, leading to a negative impact on revenue generation for the SNGs (Bhushan, Samy, & Medu, 2013). In Sierra Leone, for example, research found a noteworthy correlation between increase in enforcement efforts on tax collections by city councils in the region and a marked increase in compliance. The efficiency of these enforcement initiatives was particularly notable when they were directed towards taxpayers with the highest income (Prichard, Nyirakamana, & Stewart-Wilson, 2022).\n\nWhile property tax is commonly recognized as a crucial revenue source for local governments, many countries in Africa still do not rely on this form of taxation for generating revenue. In some countries, property taxes may constitute a small portion of local government revenue due to factors like inadequate administrative capacity, lack of up-to-date property valuations, or difficulties in tax collection. For example, property tax is not the primary revenue source for local governments in Cape Verde, instead the local economy thrives on community-based tourism, which fosters employment opportunities and enables them to generate their own revenues through user fees for water and sewage treatment, as well as from tourism-related activities in resort areas (Bozzato & Pollice, 2022; López-Guzmán, Borges, & Castillo-Canalejo, 2011).\n\nThe effectiveness of LED hinges on several critical factors, including the capacity of SNGs to generate revenue and their access to intergovernmental transfer systems. SNGs with the capacity to generate revenue can utilize these transfer systems to collect additional revenue (Smoke, 2015). This financial advantage allows them to invest in infrastructure projects that create employment opportunities, thus stimulating the local economies through increased tax revenue from the employed citizens. Furthermore, SNGs can explore the option of public-private partnerships to develop and manage assets (public buildings and facilities, water supply systems, transportation infrastructure etc.), which generates revenue through shared profits (Lee, 2013). Intergovernmental fiscal transfers3 contribute to equalizing fiscal capacities (thus reducing regional inequalities), providing funds for specific programs or projects to be carried out by local governments, encouraging policies or reforms, promoting fiscal autonomy, and enhancing public service delivery at the regional or local level. These mechanisms help reduce fiscal disparities and ensure equitable access to public services across different levels of government.\n\nIn South Africa, the Intergovernmental Fiscal Relations Act (1997) assumes a crucial role in the distribution of revenues among the national, provincial, and local governments (de Visser & de Visser, 2022). This legislation guarantees every municipality’s constitutional entitlement to receive a fair and proportionate allocation of revenue. Municipalities are better able to provide essential services to the community such as healthcare, education, infrastructure development, and social welfare programmes when they receive an equitable share of the revenue. Bvuma and Joseph (2019) noted that the effective provision of essential services by municipalities plays an integral part in fostering the holistic welfare and advancement of the local economy. Similarly, in 2019, Zimbabwe introduced intergovernmental transfers, with Mashonaland Central Province, for instance, receiving 5% of the national revenue (Munyede, Chikwawawa, & Mazambani, 2021). The province used the funds from the intergovernmental transfers to improve service delivery in education, water, sanitation and health. As part of this initiative, the province undertook key projects such as drilling of boreholes, building classroom blocks, and setting up a new clinic.\n\nIf SNGs do not carefully balance their annual expenditures with revenues and transfers, this may result in subnational deficits and the incurrence of subnational debt. SNGs may take on debt through issuing bonds or taking loans, as a way of financing their activities. This can have both direct and indirect impacts on LED in Africa (Dabla-Norris, 2006). In Ghana, borrowing practices within the Metropolitan, Municipal, and District Assemblies (MMDAs) are bound by some constraints. MMDAs have the ability to secure loans and overdrafts, subject to a prescribed maximum threshold of 2,000 Cedi, without requiring authorization. Any level of borrowing surpassing this specified threshold is subject to stringent limitations and regulatory supervision. In Guinea Bissau, municipalities can engage in borrowing activities through loans and securities (municipal bonds and notes) at all maturities. In Ivory Coast, municipalities are allowed to borrow, although under strict conditions unspecified by the government. In Senegal, the local government has the authority to issue domestic and international bonds and borrow funds contingent on the approval of the central government and a comprehensive evaluation of their financial capabilities.\n\nBorrowing, when used prudently, enables local governments to invest in large-scale infrastructure projects crucial to economic development that may not be feasible with current revenues. The influx of borrowed funds can stimulate the local economy, supporting businesses and creating jobs. Spreading the cost of substantial investments over time via borrowing ensures local governments maintain fiscal sustainability to continue providing services and fostering development (Smoke, 2019). Furthermore, demonstrating responsible borrowing and debt management can enhance a local government’s creditworthiness, leading to lower borrowing costs and increased access to future financing. Borrowing publicly, such as through issuing bonds, can heighten government accountability as bondholders have a vested interest in the local government’s financial health. Lastly, the obligation to service debt can instill financial discipline, encouraging local governments to manage their finances responsibly and efficiently (Jose, 2022).\n\nIn conclusion, under ideal conditions where the core tenets of fiscal decentralization have been effectively implemented, it holds the potential to stimulate local economic development. However, SNGs in Africa have not yet fully capitalized on this opportunity. They continue to grapple with a myriad of obstacles tied to fiscal decentralization that hinder the effective realization of local economic development. It is nonetheless important to underscore that the impacts of fiscal decentralization can depend on many factors, including the extent and quality of the decentralization process, the capacity of local governments, and the broader political and economic context. It is also possible for decentralization to have negative impacts, for example, if it leads to a duplication of efforts, increased corruption, or greater regional inequalities. The next section explores the challenges SNGs face in achieving local economic development in Africa.\n\n\n4. Fiscal decentralization challenges impeding local economic development in Africa\n\nIn the African context, numerous challenges can impede the successful application of fiscal decentralization principles and their ensuing positive impacts on local economic development. This section highlights the key obstacles tied to fiscal decentralization that local governments across Africa grapple with, obstructing the effective implementation of local economic development initiatives.\n\nMany local governments in Africa face challenges due to weak institutional capacity, which often results in inefficiencies, poor service delivery, and missed local economic development opportunities due to lack of administrative and technical capacity. Additionally, corruption and governance issues present significant problems in some areas, siphoning resources away from developmental efforts and eroding public trust in institutions.\n\nFor example, according to Thusi and Selepe (2023), the failure of effective governance in South Africa can be attributed to shortcomings in knowledge and skills, corruption, the practice of cadre deployment4, and the erratic nature of coalitions5 at the local government level.\n\nAccording to South Africa’s Auditor General “the local government has been characterized by dysfunctional municipalities, financial mismanagement, administrative instability, and crumbling municipal infrastructure. This leads to deteriorating standards of living and service delivery failures, resulting in protests”. The effectiveness and productivity of public services have been hindered by various challenges, including the late registration of projects, irregularities in procurement practices [which undermine the fairness and transparency of the process], and council decisions. This has posed significant challenges to the overall functioning of public services. In addition, municipalities are experiencing financial losses as a result of inefficient revenue billing and collection processes, inequitable procurement practices, and expenditures made for goods and services that were either unused or not received.\n\nThis South African experience highlights other local governance issues that significantly impact municipal finance, service delivery, and overall development in Africa. First, many local governments grapple with transparency and accountability issues, often due to inaccessible information about government operations and budgets. Coupled with inadequate citizen participation in decision-making processes, this can foster corruption and impede accountability (Managa, 2012). Second, many local governments lack the institutional capacity for effective governance (including well-trained staff, robust administrative systems, and sound financial management practices), leading to inefficiencies and poor service delivery. Third, the legal and regulatory frameworks that govern local governments can sometimes be inadequate or inconsistently applied, causing uncertainty and disputes (Masuku & Jili, 2019). Finally, unclear roles and responsibilities in inter-governmental relations can also hinder the autonomy local governments need to respond effectively to local needs (Atkinson, 2021).\n\nResearch institutions could play a crucial role in strengthening effective governance by offering cutting-edge analysis and recommendations to increase decision-making processes and operational effectiveness (Nkrumah, 2022). According to Vilakazi and Adetiba (2020), there is not enough collaboration between research institutions and the government in South Africa, resulting in some policies becoming incompatible with local government’s objectives. To address this issue, researchers can conduct comprehensive studies that assist policy makers in developing evidence-based strategies, enabling the successful implementation and execution of policies that genuinely meet the needs of the communities they serve.\n\nMany local governments in Africa experience limited revenue generation due to factors like a small tax base, widespread informality, poor tax compliance, and weak tax administration, resulting in heavy dependence on often unreliable central government transfers (Awasthi, Nagarajan, & Deininger, 2021). Moreover, these fiscal transfers often fall short of what is needed to fulfill devolved responsibilities, leading to a financial strain on local governments. Despite legislated fiscal decentralization processes, local governments frequently lack tax autonomy as central governments tend to retain control over local tax policy and administration, such as setting tax rates (Masaki, 2018). With financial autonomy, SNGs are entrusted with the authority to exercise independent judgment pertaining to their revenue, expenditures, investments, and financial targets. Consequently, this diminishes their dependence on external entities for financial support. For example, the majority of teachers in Tanzania, according to a study conducted by Mtasigazya (2019), contended that the council lacked autonomy in financial management and authority over funds allocated for primary education service delivery. Furthermore, a study by Lameck and Kinemo (2021) argued that local governments in Tanzania struggled to generate sufficient revenue, making them reliant on intergovernmental transfers. Yet, even with this supplemental funding, to the resources fell short of meeting the growing demands for urban services and infrastructure.\n\nSNGs often attempt to foster tax compliance by strategically prioritizing immovable property taxation, recognizing its potential as a lucrative revenue generator (Collin, Di Maro, Evans, & Manang, 2022). However, people are often reluctant to pay property taxes because they do not see any tangible benefits, particularly in areas characterized by poor infrastructure with sporadic or non-existent service delivery (Monkam & Moore, 2015). Madagascar’s efforts to mobilize property tax revenue are severely constrained by limitations on the operational capacities of local governments in various facets of property taxation, including property identification, valuation, collection, enforcement mechanisms, and dispute resolution. Some studies in Tanzania and Kenya, for example, Collin et al. (2022) and Mwangi (2019), found that property tax policies were often neglected due to taxpayers’ skepticism about the government’s use of the revenue. With a focus on larger properties, local authorities in both countries had a limited tax base, resulting in reduced revenue and compromised service delivery efficiency.\n\nWhile revenue collection can be influenced by political, economic, and technical factors, it is crucial to recognize the significant impact of the COVID-19 pandemic on both local and global economic activities. The financial strain from the pandemic reduced individuals’ ability to meet tax obligations, further impeding tax compliance. For instance, in South Africa, the extended lockdown is estimated to have decreased tax revenue by ZAR285 billion (Madhi et al., 2020). This significantly impacted local governments by reducing intergovernmental transfers, leading to a shortfall in the effective delivery of services. Furthermore, poor compliance with tax obligations, coupled with limited enforcement and the administrative challenges of local governments, has hindered regional economic growth. When local governments are unable to harness adequate revenue, it poses a major obstacle their agility in responding to emerging needs, their capacity to allocate resources toward critical sectors and nurture domestic enterprises. This is not merely a fiscal challenge; it is a bottleneck to holistic regional development, stymieing innovation, and impeding the realization of broader economic potential (Martínez-Córdoba, Benito, & García-Sánchez, 2021).\n\nOther local economic development challenges include rapid urbanization, which strains local governments’ capacity to deliver essential services, manage urban planning, and promote sustainable development. Additionally, high levels of poverty and inequality can significantly impede local economic development, as they can restrict the local tax base, increase the demand for public services, and lead to socio-economic exclusion. Moreover, environmental challenges, including climate change, pollution, and natural resource depletion, pose significant hurdles for local economic development, with local governments often lacking the resources and capacity to tackle these issues effectively.\n\nIn the context of Africa, several challenges can hinder the successful implementation of these forms of decentralization and their positive effects on local economic development. Numerous local governments in Africa face capacity constraints, lacking the human, financial, and technical resources necessary to fully assume the responsibilities that come with decentralization. This can lead to inefficiencies, poor service delivery, and challenges in implementing local development projects. Furthermore, political interference from higher government levels can undermine decentralization, limiting local governments’ autonomy and distorting local development priorities (Abdulai, Tundyiridam, & Alhassan, 2016; Otu & Anam, 2019; Phillip & Ajibade, 2016). In the Katima Mulilo Town Council (KMTC) of Namibia, local officials were appointed based on political affiliations. This politicization compromised the efficiency and effectiveness of service delivery, stemming for example, from a lack of foresight in knowledge management (Kalonda & Govender, 2021). It is frequently observed that leaders tend to give higher priority to political interests as opposed to the implementation of efficient management principles, resulting in negative impact on the provision of public services (Ndevu & Muller, 2018). advanced that political instability has an adverse effect on civic tax compliance, thereby eroding the credibility of government institutions, particularly those mandated with tax administration. The author substantiated this argument by providing instances of civil conflicts in Burundi and Rwanda, which led to a reduction in tax-generated revenue.\n\nThe Mogalakwena municipality situated in the Limpopo Province of South Africa also demonstrated that political conflicts, initially perceived as confined to the national level, permeate subnational governments. Consequently, officials operating within these SNGs find themselves immersed in an environment characterized by intense politicization, polarization, and poor working conditions. This inevitably creates an impact on the capacity of SNGs to provide public goods and services (Chilenga-Butao, 2020). In Zimbabwe, the selection of councilors responsible for the administration of local authorities primarily hinges on their political party affiliations, often resulting in a lack of the requisite technical proficiency essential for sound policy formulation and effective execution. Although there are no specific qualifications required, these councilors are responsible for supervising the activities of local authorities. As a result, the management of local authorities in Zimbabwe lacks professionalism and instead is often subject to political biases, driven by politicians’ concerns over potential political protests.\n\nWhen elected, local authorities must ensure the effectiveness and productivity of service delivery to be accountable to their constituents. However, in certain instances, the challenge arises when attempting to terminate or impose disciplinary measures on the individuals. In their study in Namibia, Kalonda and Govender (2021) also highlighted that a significant proportion of the participants in their study noted that KMTC faced administrative challenges and municipal authorities were aware of these issues, though failed to take appropriate action due to a lack of control and insufficient collaboration with the community.\n\nAs underscored in prior sections, weak institutional capacity is a prevalent challenge among numerous subnational governments in Africa. This is particularly apparent in their insufficient human capacity to fully embrace the duties associated with fiscal decentralization and to manage their finances and affairs effectively (Kwabena Obeng, 2021).\n\nThe lack of skilled human capital in South African municipalities, for example, has caused problems with the provision of services, thus limiting the availability of vital amenities across various communities (Masuku & Jili, 2019). There is an apparent shortage of skilled personnel including civil engineers, technologists,6 and technicians, which affects the maintenance and improvement of infrastructure within local municipalities. The shortage of capacity is notably apparent in key sectors such as water and sewage treatment facilities, distribution networks, and transportation infrastructure. For example, limited resources and a shortage of expertise have led to a cholera outbreak in the Hammanskraal region, situated in the Northern Gauteng Province of South Africa. This was a result of the fact that not enough planning, maintenance, and updates were done on the existing facilities. To address these challenges, information technology (IT) can offer solutions. For example, SALGA is using a digital factory, supported by cloud-based technology, to develop and implement innovative solutions that address specific challenges. This initiative, which has been gaining traction, is part of SALGA’s strategy to enhance service delivery to South Africa’s citizens. In addition, IT can play a vital role in identifying high-risk cholera prone areas through data analytics and predictive analytics (Boukenze, Mousannif, & Haqiq, 2016). Health professionals can leverage mobile applications and popular online platforms such as Twitter (now referred to as “X”), Facebook, and TikTok to disseminate essential information on cholera prevention and management. By tapping into technology and the reach of social media, we can enhance our efforts to contain cholera and safeguard public health. Despite the potential solutions offered by IT, progress remains hindered by the shortage of skilled professionals capable of utilizing these solutions within local governance. The slow adoption of efficient digital solutions for enhancing service delivery continues to stall progress.\n\nRegarding property taxation, the City of Harare in Zimbabwe, for example, has experienced challenges in retaining skilled personnel, particularly engineers and valuators. As a result, the city has become dependent on external valuators to assess property values (Nengeze, 2018). In addition, local government authorities’ struggles with revenue collection are not just a matter of capability but also of commitment. As highlighted by Nkuna (2021), the root of this challenge lies in the inadequate incentives and low salaries. When revenue collection falters due to lack of motivation, this does not only limit infrastructure development and the provision of essential services but also erodes public trust.\n\nA study conducted by Thusi and Selepe (2023) revealed various disconcerting aspects related to appointment practices, skill development programmes, and institutional management across South African municipalities. The study highlighted a prevalence of irregular and/or unsuitable appointments, coupled with below-average competencies and insufficient initiatives to foster skill development. Moreover, the research revealed that while 7% of municipalities opted for the utilization of consultants to address staffing shortages during the 2020-21 period, 62% of municipalities enlisted the services of consultants to mitigate the deficiency in expertise within their finance departments. The utilization of consultants in the remaining 31% of municipalities was attributed to a scarcity of skills and a vacancy gap.\n\nFurthermore, staff changes, including retirements, transfers, and resignations, have eroded the institutional memory of local governments. As seasoned professionals depart, they take with them a wealth of expertise, leaving a knowledge void that could have been pivotal in addressing the multifaceted challenges faced by SNGs (Cong & Pandya, 2003; Obwaka, Kwanya, & Mwai, 2019). Take South Africa’s local government as a case in point; it is not just grappling with the immediate loss of knowledge from retirements but also with the longer-term implications of not having systems in place to capture and leverage this invaluable intellectual capital (Mothamaha & Govender, 2014). Moreover, in both South Africa and Zimbabwe, local governments seem hesitant to share knowledge among employees. This reluctance is rooted in a pervasive mistrust among employees and stakeholders within these authorities, raising critical questions about the foundational trust and transparency within these governmental structures (Mothamaha & Govender, 2014; Mutandwa & Hendriks, 2022).\n\nHaving outlined the major obstacles that can obstruct the successful execution of fiscal decentralization and its beneficial impacts on local economic development, the subsequent section presents potential strategies to counteract these challenges.\n\n\n5. Leveraging digital technology for fiscal decentralization and property taxation in Africa\n\nIn this section, we delve into the prospective role those digital technologies may assume in promoting greater fiscal decentralization and revenue enhancement, specially through property taxation, as a strategic response to the local economic development challenges in Africa.\n\nWhile certain African nations grapple with technological advancements, they possess the potential to adopt cost-effective technologies that align with their limited resources. Through strategic and judicious adoption of these technologies, these countries have the potential to narrow the digital divide and harness technology to tackle their unique challenges tied to fiscal decentralization and property taxation. The introduction of technology has been linked to enhanced administration of land and as in low- and middle-income countries, demonstrating that they can readily adapt to technological changes (Bahl, McCluskey, & Franzsen, 2022). Despite the slower pace of technological progress in some African nations others have embraced digital technologies to strengthen fiscal decentralization and implement property tax reforms that promote local economic development (Joubert, Murawski, & Bick, 2023). These countries have made substantial investments towards creating robust digital infrastructure, successfully employing digital platforms for property tax administration. Furthermore, they have harnessed mobile technology to streamline and accelerate property tax administration processes.\n\nDeveloping countries possess untapped revenue potential through property taxation, yet the realization of this potential often meets significant challenges, such as prolonged and cumbersome administrative procedures and unfavorable political incentives such as political interference and lack of political will, which can delay substantial property tax revenue accumulation (Kangave, Occhiali, & Kamara, 2023). However, the introduction of technological innovations in property registration, valuation, and tax compliance has simplified these procedures, reducing associated paperwork and administrative burdens.\n\nSo, while digital platforms can streamline property registration, advanced algorithms and data analytics have the capacity to improve the accuracy of property identification and valuations, considering factors such as geographical location and current market trends. Automated systems facilitate monitoring of property tax obligations and identifying non-compliance by tracking transactions and changes in ownership. These technological advancements hold the potential to boost operational efficiency, enhance transparency, and encourage compliance with tax regulations, thereby streamlining and optimizing property tax collection procedures (Saragih, Reyhani, Setyowati, & Hendrawan, 2022). Governments worldwide are increasingly integrating Artificial Intelligence (AI) and machine learning into their operations, thereby facilitating significant enhancements in public services, including property taxation. For instance, tax authorities are employing AI-powered systems to autonomously analyze extensive volumes of financial data and identify potential tax evasion or fraudulent activities. Sophisticated algorithms facilitate rapid detection of patterns and anomalies, enabling governments to promptly undertake necessary measures and uphold adherence to tax regulations (Henman, 2020).\n\nFurthermore, AI-driven chatbots and virtual assistants are being leveraged to assist taxpayers in navigating complex tax codes, providing tailored guidance, and addressing inquiries. This improvement in user experience not only enhances overall satisfaction but also reduces the workload on government call centers. The integration of AI and machine learning (ML) into property taxation systems empowers governments to bolster their revenue generation, enhance compliance levels, and provide citizens with more streamlined and impactful services (Engstrom, Ho, Sharkey, & Cuéllar, 2020; Henman, 2020).\n\nDigital technologies, artificial intelligence (AI), and machine learning (ML) hold transformative potential for strengthening the institutional capacity of SNGs in Africa. Institutional capacity is key to the effective functioning of local governments, encompassing areas such as administrative efficiency, financial management, human resource development, and data management.\n\nBy automating routine tasks and improving the accuracy of administrative functions, digital technologies can significantly enhance the efficiency and productivity of local government employees. AI-powered software, for instance, can automate functions like data entry, document processing, and financial reporting, thereby increasing the efficiency of local government operations and allowing staff to focus on strategic tasks. In a study by Yigitcanlar, Agdas, and Degirmenci (2023), city managers in Australia and United States of America expressed optimism regarding the potential of AI to deliver improved efficiency within local governance. For example, in the local government context, AI is being utilized in various ways, such as managing city assets through structural health monitoring, detecting and diagnosing energy infrastructure faults, enhancing customer service accessibility with chatbots, and automating transportation with autonomous shuttle buses (Yigitcanlar, Wilson, & Kamruzzaman, 2019). The overall process can be bolstered through e-government, i.e., the deliberate use of ICT within the sphere of public administration and political decision-making processes (Von Haldenwang, 2004).\n\nIn addition, digital platforms can be instrumental in building the human capacity of local governments by providing online training and skills development. Such platforms can enable staff to acquire essential skills in areas like strategic planning, financial management, project management, and data analysis, thereby augmenting their capacity to serve their communities effectively (Sivarajah, Irani, & Weerakkody, 2015). By analyzing large volumes of data, digital technologies, through predictive analytics, can forecast revenue, expenditure, and demand for public services, thereby generating insights that inform policy decisions, and assist with budgeting and planning. Additionally, digital technologies can streamline financial management processes. For example, blockchain technology can increase transparency and reduce fraud in financial transactions, which is critical for the prudent management of public resources. It can also offer meticulous tracking, documentation, and security for each stage of the procurement process on an immutable platform. By implementing blockchain, an unalterable “digital ledger” can be created. This ledger serves as a powerful tool for public sector auditors, providing an unimpeachable record of transactions and contributing to increased transparency and accountability (Kahn, Baron, & Vieyra, 2018). Furthermore, digital technologies can increase transparency and accountability by making government data open and accessible. Open data portals, for instance, can provide citizens with information on local government budgets, expenditures, and performance metrics.\n\nAI and ML can also optimize the delivery of public services. For instance, geospatial data can help identify areas in greatest need of services such as healthcare, education, and infrastructure, allowing for more efficient and effective allocation of resources (Anshari & Hamdan, 2022). Lastly, digital platforms can enhance citizen engagement by providing channels for feedback and participation in local decision-making. For example, mobile apps can enable citizens to report service delivery issues, pay taxes, and access information about local government services. In Uruguay, a mobile and web-based platform application called “Por Mi Barrio” was launched in 2015 to allow residents of Montevideo to report issues, such as public infrastructure malfunctions or acts of vandalism. These reported issues, along with the government’s corresponding responses, are visually represented on a publicly accessible website in the form of a map. This allows for public visibility and accountability and enables more direct and effective community involvement in local governance (Peixoto & Fox, 2016). In addition, e-Government tools can be leveraged to emphasize transparency and participation as central principles guiding municipal-citizen interactions. Portugal’s high e-Government development index, for example, reflects the public sector’s outstanding performance in efficiency, effectiveness, and service delivery, a success significantly tied to the adoption of e-Government strategies (Tejedo-Romero et al., 2022).\n\nSouth Africa has taken proactive steps to bridge the skills gap within its public sector through the establishment of the National School of Government. This institution provides robust training and development programs designed for public servants at all tiers - national, provincial, and local (Msomi, Munapo, & Choga, 2016). To enhance the reach and flexibility of these educational programs, the school has integrated synchronous e-learning methodologies.7 Notably, such e-learning platforms are already having a positive impact in countries like the USA, Canada, and Korea, where civil servants have harnessed these digital platforms to boost their competencies and enhance the efficiency of service delivery (Lai, 2017).\n\nBig data, according to Androutsopoulou and Charalabidis (2018) presents a significant opportunity to address the skills gap particularly in the development of policies that effectively cater to constituent needs. The authors propose a methodological framework for leveraging big data in policymaking, consisting of seven distinct stages: problem identification, data understanding, data mining, policy development and modeling, policy simulation, results visualization, and knowledge consolidation. This approach underscores the potential of evidence-based policies to deliver the intended outcomes. Collaborations between governments and data scientists or analysts could be pivotal. Experts in data science can examine large datasets to inform effective policy decisions, using statistical analysis and machine learning techniques. A case in point is Brazil’s Observatory of Public Spending, under the Office of the Comptroller General. This body successfully integrated data mining tools, enabling government officials to audit a vast amount of public expenditure, approximately US$5 trillion. In 2015, this process unearthed over 7,500 cases of unclean audits which amounted to US$104 million (Kahn et al., 2018). The example highlights the transformative potential of big data in enhancing governance and improving public spending efficiency (Tejedo-Romero, Araujo, Tejada, & Ramírez, 2022).\n\nThe advent of digital technologies has ushered in transformative opportunities for local governments in Africa to enhance their revenue base, improve enhance their tax systems’ efficiency and fairness, and drive local economic development. The application of these technologies, when done strategically, can help to rectify inefficiencies and loopholes within the existing fiscal systems.\n\nFirst, the ability to expand the local tax base is a significant advantage provided by digital technology. By harnessing and analyzing data from various sources, potential taxpayers who are currently not in the system can be identified. Here, machine learning algorithms can play a crucial role by automating the scrutiny of large datasets to pinpoint discrepancies, thereby uncovering businesses and individuals who may be under-reporting or evading taxes (Politou, Alepis, & Patsakis, 2019). Second, improvements in tax administration can be achieved through the automation and streamlining of processes, reducing bureaucratic inefficiencies and human error (Tetteh, 2012; Xusan o‘g‘li, 2023). Software solutions can manage taxpayer databases, calculate tax liabilities, generate tax bills, and track payments. The integration of AI can further enhance these processes by predicting future revenue trends and identifying potential issues before they escalate.\n\nIn the context of property identification and assessment, digital technologies can be transformative. One of the main challenges in property taxation is accurately identifying properties and estimating their value. In many African cities, property records are incomplete or out of date, and valuation methods are often rudimentary. Geographical Information Systems (GIS) and remote sensing technologies can be used to create detailed maps of properties, ensuring the accuracy and fairness of property tax assessments (Lambin et al., 2014). For example, spatial data (information about the physical location and shape of geographic features) and remote sensing data (information collected from satellites or airborne sensors) from datasets such as Copernicus and World Settlement Footprint on land use and settlement patterns, can be used to identify and assess properties and their characteristics for tax purposes (Csorba, Bánóczki, & Túri, 2022; Marconcini, Metz-Marconcini, Esch, & Gorelick, 2021). Night-Time Light Data can be used to assess the level of development and economic activity in a given area, which can inform property valuations (Keola, Andersson, & Hall, 2015). Google Open Building and AID data offer detailed building and infrastructure data that can also be used in property assessments. Geo-boundaries and GADM data could provide detailed geographic boundaries, which can help local governments analyze revenue data at different geographic levels, such as neighborhoods or districts. This can support more granular and targeted policymaking. By combining this data with AI and ML techniques, local governments can automate and identify properties currently outside the tax system, thus expanding the property tax base. They determine appropriate tax values, considering factors such as property size, location, and market trends. This will lead to more equitable and efficient property taxation and increased revenues.\n\nDigital enhancements in tax collection can be manifested in the form of e-payment systems, making it easier for taxpayers to fulfill their obligations and increasing compliance rates (McCluskey, Franzsen, Kabinga, & Kasese, 2018). AI can also be used to identify late-paying taxpayers, allowing for targeted and timely enforcement actions. These enforcement mechanisms can also benefit from AI and ML by identifying patterns of non-compliance and predicting potential defaults (Kamil, 2022).\n\nFinally, digital platforms can significantly improve services for taxpayers, providing easy access to information, facilitating tax filings and payments, and enabling communication with tax authorities. AI-driven chatbots can offer round-the-clock customer support, answering common queries and guiding taxpayers through complex processes. For example, Digital Financial Services (DFS) have seen significant adoption in Africa, bringing a host of economic benefits. One major advantage, as highlighted by Santoro, Amine, and Magongo (2022), is the ability to monitor transactions through digital pathways, such as mobile money. With the integration of third-party data, DFS can improve the efficiency of verifying property tax declarations and payments. This can pave the way for data-driven audits and promote transparent property tax administration. Moreover, the mandatory implementation of e-filing for tax compliance in some countries, combined with DFS, can enhance financial administration by improving operational effectiveness, transparency, compliance, and inclusivity. As a result, resource allocation becomes more efficient, decision-making improves, and sustainable economic growth is encouraged (Munoz, Mascagni, Prichard, & Santoro, 2022). The following are examples of countries that have effectively leveraged digital technologies to enhance local revenue generation.\n\nIn Rwanda, drones have been utilized for collecting land data, leading to significant improvements in property surveying and registration. These unmanned aerial vehicles (UAVs) enable the acquisition of highly accurate images, facilitating the identification and demarcation of property boundaries. Such advancements have positively impacted sectors like construction and agriculture, as well as land information systems (Mihgo & Magina, 2022). Similarly, Zanzibar implemented a comprehensive fiscal cadastre using drone imagery between 2011 and 2016, fostering transparency and mitigating the risk of property data manipulation and mismanagement.\n\nIn Warsaw, Poland, local government officials have utilized GIS and remote sensing technology to collect critical data regarding building characteristics such as the number of storeys and the technical state of facades, which has significantly improved the accuracy of property tax assessments (Dąbrowski & Latos, 2015). Similarly, Sierra Leone, Malawi, and Lagos State in Nigeria have incorporated IT systems into their administrative processes. These systems monitor data input, identifying any discrepancies in valuation or payment data, and flag potential misconduct. As a result, these countries have been able to enhance their property tax administration processes, including enforcement strategies, and boost revenue collection.\n\nIn countries like Kenya and Zambia, local government authorities (LGAs) have autonomy to develop indigenous ICT solutions or adopt Commercial Off-The-Shelf (COTS) solutions (McCluskey et al., 2018). This autonomy empowers them to devise innovative and cost-effective approaches to use technology to improve governance and service delivery. For instance, Kenya has successfully developed CountyPro, a software solution designed to optimize county revenue management efficiently. This web-based e-governance solution facilitates smooth information exchange among various county departments, marking a shift towards effective governance. It provides a user-friendly online interface for citizens and a specialized administrative interface for county personnel (McCluskey et al., 2018).\n\nDigital technologies, along with AI and machine learning, also offer transformative potential for enhancing public service delivery in local governments across Africa. Leveraging these technologies with spatial data, such as the geocoded Afrobarometer data, may equip local governments with insights into their service landscapes, helps identify gaps, and provides strategic direction for more effective and efficient service planning and delivery (Konte & Vincent, 2021).\n\nThe first significant utility of spatial data is in identifying service gaps. Data from sources such as Copernicus, World Settlement Footprint, or Google Open Building can provide exhaustive information about the location of residential and commercial establishments. When integrated with AID data, Geo-boundaries, and GADM data, which detail the location of public services like clinics, hospitals, and police stations, by overlaying these data sets, local governments can identify areas that are underserved and need additional services. Secondly, understanding proximity of essential services to communities is a key factor in accessibility. Machine learning algorithms can analyze spatial data to calculate the distance from each household or business to the nearest service point. This assists local governments in identifying areas where services are not easily accessible, and subsequently, where service accessibility needs to be improved (Müller et al., 2018; Sumanta, 2022).\n\nThe planning of new services also substantially benefits from spatial data. By identifying areas experiencing rapid growth but with limited access to essential services, local governments can strategically plan and locate new service centers, such as health clinics, to cater to this expanding population. Efficiency in service delivery is another critical area where AI and ML can make a significant difference. These technologies can optimize routes for service delivery vehicles, such as garbage trucks or ambulances, based on real-time traffic data and the location of households or incidents, leading to improved operational efficiency (Akanbi & Agunbiade, 2013).\n\nUnderstanding public sentiment is crucial for any government, and geocoded Afrobarometer data can provide invaluable insights into citizen perceptions of public services. This feedback can help local governments prioritize improvements in areas where citizens express dissatisfaction or concerns (Konte & Vincent, 2021). Lastly, AI and ML can be employed to predict future demand for public services by analyzing trends and patterns in spatial and Afrobarometer data. This foresight allows local governments to plan resources and infrastructure effectively to meet anticipated demand (Burke, Driscoll, Lobell, & Ermon, 2021).\n\nIn conclusion, the strategic application of digital technologies presents a significant opportunity for local governments in Africa to bolster fiscal decentralization and revenue enhancement, particularly through property taxation. These tools can be leveraged to address local economic development challenges, ultimately leading to more sustainable and inclusive growth. However, the successful deployment of these technologies’ hinges on several essential factors. Firstly, the provision of robust digital infrastructure is vital to support the wide-scale implementation and optimal utilization of these technologies. Secondly, it is crucial to build a workforce that possesses the skills and knowledge required to leverage these digital tools effectively. This requires substantial investment in education and training programs, as well as a commitment to ongoing professional development. In addition, a conducive legal and regulatory environment is necessary to foster the growth and application of digital technologies (Sousa & Rocha, 2019). Policymakers must ensure that regulations are adaptable and responsive to the rapidly changing digital landscape, while also safeguarding citizens’ rights and interests. Data privacy and security are paramount, particularly given the sensitive nature of the data involved. As such, robust measures should be put in place to protect data and prevent breaches, which can undermine public trust and impede the uptake of digital services (Romansky, 2021).\n\nFinally, it is important to ensure digital inclusivity, so that all citizens, including those who are marginalized or digitally excluded, can benefit from the improvements in service delivery that these technologies enable. This may involve initiatives to improve digital literacy and access among these groups. Despite the significant potential that digital technologies, AI, and ML offer, these challenges must be acknowledged and addressed to fully harness their benefits. With thoughtful planning, investment, and policy frameworks that support their effective implementation, these tools can make a meaningful contribution to enhancing fiscal decentralization, boosting revenue, and promoting local economic development in Africa (Latif, Qadir, Farooq, & Imran, 2017).\n\n\n6. Conclusion and policy recommendations\n\nThis paper delves into the transformative potential of fiscal decentralization as a catalyst for local economic development across Africa, a subject of growing importance and multifaceted complexity. Through a methodical review of existing literature, the study explores both the challenges and opportunities inherent in fiscal decentralization, with a particular emphasis on the pivotal role of digital technologies. By enhancing our understanding and application of these concepts within the African context, the study concludes that investment in digital infrastructure, skills, and robust regulatory frameworks, coupled with judicious consideration of data privacy and security concerns, can empower subnational governments in Africa. This enables them to harness the power of fiscal decentralization to foster sustainable growth and development.\n\nThis paper contributes a valuable perspective to the existing literature, offering actionable insights and policy recommendations that can guide policymakers, scholars, and practitioners in their concerted efforts to realize the full potential of fiscal decentralization in Africa. Firstly, to successfully implement fiscal decentralization and enhance its impacts on local economic development in Africa, it is crucial that local governments build robust institutional capacities. This involves the provision of training and development programs aimed at enhancing skills in fiscal management, tax administration, and governance. Additionally, the establishment of efficient administrative systems is key to ensuring smooth operations. As part of this capacity-building effort, governments must also invest in the development of reliable digital infrastructure, including internet connectivity, data centers, and the necessary hardware for digital technologies, artificial intelligence (AI), and machine learning (ML) applications.\n\nSecondly, governments should also focus on creating supportive legal and regulatory frameworks. These would clearly define the fiscal responsibilities and rights of local governments and encourage transparency and accountability in their operations. Additionally, leveraging digital technologies, AI, and ML can greatly enhance revenue generation, particularly in the area of property taxation. By improving the accuracy of tax assessments, streamlining tax collection processes, and reducing tax evasion, these technologies can play a pivotal role in revenue enhancement. However, as digital technologies become more integrated into fiscal management and public service delivery, stringent measures to ensure data privacy and security, including the use of secure databases, encryption, and regular cybersecurity audits, must be in place.\n\nLastly, promoting fiscal autonomy is crucial. Central governments should work towards granting local governments the ability to administer their own taxes and make independent decisions about how to allocate and spend their revenues. This would involve establishing fair and efficient intergovernmental fiscal transfer systems to ensure that local governments have the resources they need to fulfill their responsibilities. Consideration should also be given to implementing performance-based grant systems. Under these systems, a portion of intergovernmental transfers would be allocated based on performance indicators such as revenue collection efficiency or service delivery quality. By implementing these policies, local governments in Africa could successfully implement fiscal decentralization and enhance its beneficial impacts on local economic development.\n\nEthical approval and written informed consent were not required.", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\nFigshare: Checklist for Fiscal decentralization in Africa, 10.6084/m9.figshare.25331896.\n\n\nAcknowledgments\n\nThe authors extend their sincere gratitude to the Council on Economic Policies (CEP) for providing a grant to launch this project, which focuses on fiscal decentralization in Africa. Special acknowledgment is also due to Dr. Alexander Barkawi, the founder, and director of CEP. His belief in and support for the initiative have enabled us to lay the foundation for solving local government challenges in Africa. This is being achieved through innovative approaches involving research, digital technology, and data science.\n\n\nReferences\n\nAbdulai A-R, Tundyiridam R, Alhassan AY: Mechanisms and Strategies for Mobilisation of Property Rates in the Kassena-Nankana Municipality of Ghana. Public Policy and Administration Research. 2016; 6(6): 113–123.\n\nAkanbi AK, Agunbiade OY: Integration of a city GIS data with Google Map API and Google Earth API for a web based 3D Geospatial Application. arXiv preprint arXiv:1312.0130. 2013.\n\nAndroutsopoulou A, Charalabidis Y: A framework for evidence based policy making combining big data, dynamic modelling and machine intelligence. Paper presented at the Proceedings of the 11th International Conference on Theory and Practice of Electronic Governance. 2018.\n\nAnshari M, Hamdan M: Enhancing e-government with a digital twin for innovation management. Journal of Science and Technology Policy Management. 2022.\n\nAtkinson D: Preparing for the worst: South African municipalities’ readiness to manage disasters related to potential shale gas mining. International Journal of Disaster Risk Reduction. 2021; 65: 102537. Publisher Full Text\n\nAwasthi R, Nagarajan M, Deininger KW: Property taxation in India: Issues impacting revenue performance and suggestions for reform. Land Use Policy. 2021; 110: 104539. Publisher Full Text\n\nBahl R: Intergovernmental Fiscal Relations & Local Financial Management Program. The World Bank, Background Series. 2000; 3–6.\n\nBahl R: Pillars of Fiscal Decentralization.2008.\n\nBahl RW, Martinez-Vazquez J: Sequencing fiscal decentralization. World Bank Publications; 2006; vol. 3914. .\n\nBahl RW, McCluskey WJ, Franzsen R: Lessons Learned and Prospects for Reform.2022.\n\nBellé N, Ongaro E: NPM, administrative reforms and public service motivation: Improving the dialogue between research agendas. International Review of Administrative Sciences. 2014; 80(2): 382–400. Publisher Full Text\n\nBello DMF, Mackson AM: Revenue Generation, Fiscal Federalism and the National Question in Nigeria. KIU Journal of Humanities, Kampala International University. 2023. 2415-0843.\n\nBhushan A, Samy Y, Medu K: Financing the post-2015 development agenda: Domestic revenue mobilization in Africa. Ottawa: The North-South Institute (Research Report); 2013.\n\nBoukenze B, Mousannif H, Haqiq A: Predictive analytics in healthcare system using data mining techniques. Computer Science & Information Technology. 2016; 1: 1–9.\n\nBozzato S, Pollice F: Perspectives for community-driven tourism in Cape Verde. Revista de Turismo Patrimonio Cultura. 2022. 1695-7121.\n\nBurke M, Driscoll A, Lobell DB, et al.: Using satellite imagery to understand and promote sustainable development. Science. 2021; 371(6535): eabe8628. PubMed Abstract \| Publisher Full Text\n\nBvuma S, Joseph BK: Empowering communities and improving public services through open data: South African local government perspective. Governance Models for Creating Public Value in Open Data Initiatives. 2019; 141–160. Publisher Full Text\n\nChilenga-Butao T: Decentralisation and recentralisation in South Africa’s local government: case studies of two municipalities in Limpopo. Transformation: Critical Perspectives on Southern Africa. 2020; 103(1): 12–35. Publisher Full Text\n\nCollin ME, Di Maro V, Evans DK, et al.: Property Tax Compliance in Tanzania.2022.\n\nCong X, Pandya KV: Issues of knowledge management in the public sector. Electronic Journal of Knowledge Management. 2003; 1(2): 181–188.\n\nCsorba P, Bánóczki K, Túri Z: Land use changes in Peri-Urban open spaces of small towns in Eastern Hungary. Sustainability. 2022; 14(17): 10680. Publisher Full Text\n\nDabla-Norris E: The challenge of fiscal decentralisation in transition countries. Comparative Economic Studies. 2006; 48: 100–131. Publisher Full Text\n\nDąbrowski R, Latos D: Possibilities of the practical application of remote sensing data in real property appraisal. Real Estate Management and Valuation. 2015; 23(2): 68–76. Publisher Full Text\n\nDaughters R, Harper L: Fiscal and political decentralization reforms.2007.\n\nde Visser J , de Visser S : Intergovernmental Fiscal Relations in the Phillipines- Perspectives from South Africa.2022.\n\nDevas N: The challenges of decentralization. Paper presented at the Global Forum on Fighting Corruption: Brasilia, United Kingdom. 2005.\n\nEngdaw B: The effect of administrative decentralization on quality public service delivery in Bahir Dar city administration: the case of Belay Zeleke sub-city. Cogent Social Sciences. 2022; 8(1): 2004675. Publisher Full Text\n\nEngstrom DF, Ho DE, Sharkey CM, et al.: Government by algorithm: Artificial intelligence in federal administrative agencies. NYU School of Law, Public Law Research Paper. 2020; 20–54. Publisher Full Text\n\nGranda JC, Nuño P, Suárez FJ, et al.: E-pSyLon: a synchronous e-learning platform for staff training in large corporations. Multimedia Tools and Applications. 2013; 66: 431–463. Publisher Full Text\n\nHaas AR, Knebelmann J, Nyirakamana C: Five tenets for consideration when undertaking property tax reform in Africa.2021.\n\nHenman P: Improving public services using artificial intelligence: possibilities, pitfalls, governance. Asia Pacific Journal of Public Administration. 2020; 42(4): 209–221. Publisher Full Text\n\nJose J: Essays On Public Debt Management: An Exploration Of State Oversight Of Local Government Debt Issuance.2022.\n\nJoubert A, Murawski M, Bick M: Measuring the big data readiness of developing countries–index development and its application to Africa. Information Systems Frontiers. 2023; 25(1): 327–350. Publisher Full Text\n\nKahn T, Baron A, Vieyra JC: Digital technologies for transparency in public investment. Inter-American Development Bank. 2018; 15: 1–36.\n\nKalonda J, Govender K: Factors affecting municipal service delivery: A case study of Katima Mulilo Town Council, Namibia. African Journal of Public Affairs. 2021; 12(2): 1–26.\n\nKamara RD: Creating enhanced capacity for Local Economic Development (LED) through collaborative governance in South Africa. SocioEconomic Challenges. 2017; 1(3): 98–115. Publisher Full Text\n\nKamil I: Influence Artificial Intelligence Technology For E-filling and Digital Service Tax (DST) in Tax Administration on Tax Compliance. International Journal of Management Studies and Social Science Research. 2022; 4(1): 144–156.\n\nKangave J, Occhiali G, Kamara I: How Might the National Revenue Authority of Sierra Leone Enhance Revenue Collection by Taxing High Net Worth Individuals?2023. Publisher Full Text\n\nKeola S, Andersson M, Hall O: Monitoring economic development from space: using nighttime light and land cover data to measure economic growth. World Development. 2015; 66: 322–334. Publisher Full Text\n\nKhumalo P: Improving the Contribution of Cooperatives as Vehicles for Local Economic Development in South Africa. African Studies Quarterly. 2014; 14(4).\n\nKhumalo P, Netswera MM: The complex nature of coalitions in the local sphere of government in South Africa. African Journal of Democracy and Governance. 2020; 7(3-4): 173–192.\n\nKithatu-Kiwekete A: Improving the revenue capacity of large African cities. Administratio Publica. 2018; 26(4): 6–21.\n\nKonte M, Vincent RC: Mining and quality of public services: The role of local governance and decentralization. World Development. 2021; 140: 105350. Publisher Full Text\n\nKwabena Obeng S: Fiscal decentralization, democracy and government size: Disentangling the complexities. Journal of International Development. 2021; 33(6): 975–1004. Publisher Full Text\n\nLai H-J: Examining civil servants’ decisions to use Web 2.0 tools for learning, based on the decomposed theory of planned behavior. Interactive Learning Environments. 2017; 25(3): 295–305. Publisher Full Text\n\nLambin EF, Meyfroidt P, Rueda X, et al.: Effectiveness and synergies of policy instruments for land use governance in tropical regions. Global Environmental Change. 2014; 28: 129–140. Publisher Full Text\n\nLameck W, Kinemo S: In Search of A Link Between Fiscal Decentralization And Fiscal Autonomy In Service Delivery In Urban Local Government Authorities In Tanzania. Journal of Governance and Development. 2021; 17(2): 23–40. Publisher Full Text\n\nLatif S, Qadir J, Farooq S, et al.: How 5G wireless (and concomitant technologies) will revolutionize healthcare? Future Internet. 2017; 9(4): 93. Publisher Full Text\n\nLee Y-H: The Effects of Intergovernmental Transfers For Urban Development In Korea. Public Budgeting & Finance. 2013; 23(4).\n\nLópez-Guzmán T, Borges O, Castillo-Canalejo AM: Community-based tourism in Cape Verde-a case study. Tourism and Hospitality Management. 2011; 17(1): 35–44. Publisher Full Text\n\nMadhi S, Gray GE, Ismail N, et al.: COVID-19 lockdowns in low-and middle-income countries: Success against COVID-19 at the price of greater costs. SAMJ: South African Medical Journal. 2020; 110(8): 724–726. PubMed Abstract \| Publisher Full Text\n\nManaga A: Unfulfilled promises and their consequences: A reflection on local government performance and the critical issue of poor service delivery in South Africa.2012.\n\nMarconcini M, Metz-Marconcini A, Esch T, et al.: Understanding current trends in global urbanisation-the world settlement footprint suite. GI_Forum. 2021; 1(1): 33–38. Publisher Full Text\n\nMarshall GR: Nesting, subsidiarity, and community-based environmental governance beyond the local level. International Journal of the Commons. 2008; 2(1): 75–97. Publisher Full Text\n\nMartínez-Córdoba P-J, Benito B, García-Sánchez I-M: Efficiency in the governance of the Covid-19 pandemic: political and territorial factors. Global Health. 2021; 17: 1–13. Publisher Full Text\n\nMartinez-Vazquez J: Revenue assignments in the practice of fiscal decentralization. Edward Elgar; 2008.\n\nMartinez-Vazquez J, Searle B: Fiscal equalization: Challenges in the design of intergovernmental transfers. Springer Science & Business Media; 2007.\n\nMartinez J, Qian B, Wang S, et al.: Local Public Finance in China: Expenditure Responsibilities of Local Governments.2006.\n\nMasaki T: The impact of intergovernmental transfers on local revenue generation in Sub-Saharan Africa: Evidence from Tanzania. World Development. 2018; 106: 173–186. Publisher Full Text\n\nMasuku MM, Jili NN: Public service delivery in South Africa: The political influence at local government level. Journal of Public Affairs. 2019; 19(4): e1935. Publisher Full Text\n\nMcCluskey W, Franzsen R, Kabinga M, et al.: The role of information communication technology to enhance property tax revenue in Africa: A tale of four cities in three countries.2018.\n\nMihgo D, Magina FB: The role of open data and digital technology in property management in the developing world. The case of Rwanda. African Journal on Land Policy and Geospatial Sciences. 2022; 5(2): 442–455.\n\nMollah MAH: Administrative decentralization in Bangladesh: Theory and practice. International Journal of Organization Theory & Behavior. 2007; 10(1): 1–34. Publisher Full Text\n\nMonkam N, Mangwanya MG: Fiscal decentralization in Africa. [Dataset]. 2024. Publisher Full Text\n\nMonkam N, Moore M: How property tax would benefit Africa. Africa Research Institute London; 2015.\n\nMosikari T, Stungwa S: Fiscal Decentralization and Economic Growth in South Africa: A South African Perspective. Acta Universitatis Danubius. Œconomica. 2023; 19(1): 95–110.\n\nMothamaha W, Govender K: Exploring the role of knowledge management in improving service operations: The case of the select departments in the City of Johannesburg, South Africa. International Journal of Managerial Studies and Research. 2014; 2(5): 1–8.\n\nMsomi AP, Munapo E, Choga I: The conceptualisation of e-Learning in the public sector. Problems and Perspectives in Management. 2016; 14(4): 41–53. Publisher Full Text\n\nMtasigazya P: The impact of intergovernmental fiscal transfers on local government autonomy and service delivery in Tanzania. International Journal of Teaching, Education and Learning. 2019; 3(2): 68–93. Publisher Full Text\n\nMüller I, Hipondoka M, Winkler K, et al.: Monitoring flood and drought events-Earth observation for multiscale assessment of water-related hazards and exposed elements. Climate Change and Adaptive Land Management in Southern Africa-assessments, Changes, Challenges, and Solutions. 2018; 6(6): 136–143. Publisher Full Text\n\nMunoz L, Mascagni G, Prichard W, et al.: Should governments tax digital financial services? A research agenda to understand sector-specific taxes on DFS.2022. Publisher Full Text\n\nMunyede P, Chikwawawa C, Mazambani D: Enhancing Socio-Economic Rights in the Mashonaland Central Province of Zimbabwe through Fiscal Decentralization: Progress and Challenges. Quest. 2021; 3(2): 277–290.\n\nMutandwa T, Hendriks C: Implementation of Local Government Strategies in Zimbabwe. Administratio Publica. 2022; 30(4): 120–141.\n\nMwangi W: Evaluation of Property Rates Collection and Enforcement in Devolved Systems of Governance in Kenya. Africa Habitat Review. 2019; 13(1): 1601–1613.\n\nNdevu Z, Muller K: A conceptual framework for improving service delivery at local government in South Africa. African Journal of Public Affairs. 2018; 10(4): 181–195.\n\nNengeze M: How Local Authorities Can Exploit the Potential for Effective Property Taxes: A Case Study of Harare.2018.\n\nNkrumah B: Think tanks and democratisation in South Africa. Cosmopolitan Civil Societies: An Interdisciplinary Journal. 2022; 14(1): 17–31. Publisher Full Text\n\nNkuna F: Barriers to revenue collection affecting municipal financial viability: A case of Maruleng local municipality.2021.\n\nObwaka EM, Kwanya T, Mwai N: Knowledge transfer and retention challenges and service delivery in Nairobi City County Government (NCCG), Kenya. Paper presented at the Proceedings of 20th Annual IS Conference. 2019.\n\nOppong F: Fiscal Decentralization and Autonomy of Subnational Entities in Ghana. (PhD), University of Pretoria, Pretoria.2020.\n\nOtu J, Anam B: Internally Generated Revenue and Local Government Performance in Nigeria: Implications for Rural Development. International Journal of Development Strategies in Humanities, Management and Social Sciences. 2019; 9(2): 112–120.\n\nPeixoto T, Fox J: When does ICT-enabled citizen voice lead to government responsiveness?2016.\n\nPhillip M, Ajibade OE: Local Government and Challenges of Revenue Allocation in Nigeria (a study of Yewa South Local Government, ogun state). Journal of Public Administration, Finance and Law. 2016; 3(10): 55–66.\n\nPolitou E, Alepis E, Patsakis C: Profiling tax and financial behaviour with big data under the GDPR. Computer law & security review. 2019; 35(3): 306–329. Publisher Full Text\n\nPrichard W, Nyirakamana C, Stewart-Wilson G: The Progress, Problems, and Potential of Property Taxation in sub-Saharan Africa: A Review of the Literature.2022.\n\nPRISMA: Prisma framework statement. F1000 Res. 2020; 120 KB.\n\nRodríguez-Pose A, Krøijer A: Fiscal decentralization and economic growth in Central and Eastern Europe. Growth and Change. 2009; 40(3): 387–417. Publisher Full Text\n\nRomansky R: Privacy and data protection in the contemporary digital age. International Journal on Information Technologies and Security. 2021; 13(4): 99–110.\n\nRutto A, Minja D, Kosimbei G: Intergovernmental Fiscal Transfers and Decentralization Initiatives in Sub-Saharan Africa: A Case Study of SNGs in Kenya. SDMIMD Journal of Management. 2022; 13: 45–60. Publisher Full Text\n\nSanogo T: Does fiscal decentralization enhance citizens’ access to public services and reduce poverty? Evidence from Côte d’Ivoire municipalities in a conflict setting. World Development. 2019; 113: 204–221. Publisher Full Text\n\nSantoro F, Amine R, Magongo T: Mandating digital tax tools as a response to Covid: evidence from Eswatini.2022.\n\nSaragih AH, Reyhani Q, Setyowati MS, et al.: The potential of an artificial intelligence (AI) application for the tax administration system’s modernization: the case of Indonesia. Artificial Intelligence and Law. 2022; 1–24.\n\nSebele-Mpofu FY: Governance quality and tax morale and compliance in Zimbabwe’s informal sector. Cogent Business & Management. 2020; 7(1): 1794662. Publisher Full Text\n\nShava E, Chamisa SF: Cadre Deployment Policy and its Effects on Performance Management in South African Local Government: A Critical Review. Politeia (02568845). 2018; 37(1). Publisher Full Text\n\nShrestha K, Martinez-Vazquez J, Hankla C: Political decentralization and corruption: Exploring the conditional role of parties. Economic Politics. 2023; 35(1): 411–439. Publisher Full Text\n\nSivarajah U, Irani Z, Weerakkody V: Evaluating the use and impact of Web 2.0 technologies in local government. Government Information Quarterly. 2015; 32(4): 473–487. Publisher Full Text\n\nSmoke P: Accountability and service delivery in decentralising environments: Understanding context and strategically advancing reform. A Governance Practitioner’s Notebook. 2015; pp. 219–232.\n\nSmoke P: Improving subnational government development finance in emerging and developing economies: Toward a strategic approach.2019.\n\nSousa MJ, Rocha Á: Digital learning: Developing skills for digital transformation of organizations. Future Generation Computer Systems. 2019; 91: 327–334. Publisher Full Text\n\nSumanta D: A Review of Urban Heat Island formation over changing climate and its impacts on Urban Land Use and Environments and Adaptation Measures. International Journal of Environment and Geoinformatics. 2022; 9(1): 64–73. Publisher Full Text\n\nTejedo-Romero F, Araujo JFFE, Tejada Á, et al.: E-government mechanisms to enhance the participation of citizens and society: Exploratory analysis through the dimension of municipalities. Technology in Society. 2022; 70: 101978. Publisher Full Text\n\nTetteh EG: Automation system procedure of the Ghana Revenue Authority on the effectiveness of revenue collection: A case study of customs division.2012.\n\nThomas ND, Sevidzem MC, Wiykiynyuy TM: Fiscal Decentralization and Intergovernmental Fiscal Relations in Sub-Saharan Africa: A Critical Literature Survey and Perspectives for Future Research in Cameroon. PanAfrican Journal of Governance and Development (PJGD). 2022; 3(2): 166–193. Publisher Full Text\n\nThusi X, Selepe MM: The Impact of Poor Governance on Public Service Delivery: A Case Study of the South African Local Government. International Journal of Social Science Research and Review. 2023; 6(4): 688–697.\n\nVilakazi SA, Adetiba TC: Political and administrative dichotomy in South Africa: The principle of separation of powers at local government level. Acta Universitatis Danubius. Administratio. 2020; 12(1).\n\nVon Haldenwang C: Electronic government (e-government) and development. The European Journal of Development Research. 2004; 16: 417–432. Publisher Full Text\n\nWagana DM, Iravo MA, Nzulwa JD, et al.: Effect of Financial and Political Decentralization on Service Delivery in County Governments in Kenya.2017.\n\nXusan o‘g‘li DJ: Improving the competitive environment through taxes. Paper presented at the Proceedings of Scientific Conference on Multidisciplinary Studies. 2023.\n\nYigitcanlar T, Agdas D, Degirmenci K: Artificial intelligence in local governments: perceptions of city managers on prospects, constraints and choices. AI & Society. 2023; 38(3): 1135–1150. Publisher Full Text\n\nYigitcanlar T, Wilson M, Kamruzzaman M: Disruptive impacts of automated driving systems on the built environment and land use: An urban planner’s perspective. Journal of Open Innovation: Technology, Market, and Complexity. 2019; 5(2): 24. Publisher Full Text\n\n\nFootnotes\n\n1 This relates to the physical production of goods and services, involving the acquisition and integration of factor inputs (such as capital, labour, raw materials, land, technology, or management) to generate the desired end products.\n\n2 This pertains to executing budget priorities by strategically planning government programs, defining program objectives, conducting service tenders, outsourcing services to the private sector, overseeing and auditing service delivery, and evaluating the effectiveness of implemented programs.\n\n3 Intergovernmental fiscal transfers pertain to the redistribution of financial resources from higher tiers of governance to lower-level tiers, namely from central governments to regional or local governments and they are a key tool for managing the balance of resources and responsibilities between different levels of government (Thomas, Sevidzem, & Wiykiynyuy, 2022).\n\n4 The practice of cadre deployment involves appointing party loyalists to key positions, often not qualified, leading to incompetence, corruption, and political interference (Shava & Chamisa, 2018).\n\n5 The erratic nature of coalition refers to the unstable and unpredictable formation and dissolution of local government (Khumalo & Netswera, 2020).\n\n6 Technologists refers to professionals who specialize in the application of scientific knowledge and technical skills to various fields.\n\n7 Synchronous e-learning refers to as real-time e-learning or live online learning. This mode of online learning entails instructors and learners engaging in learning activities simultaneously (Granda, Nuño, Suárez, & Pérez, 2013)." }	[ { "id": "270654", "date": "29 May 2024", "name": "François Vaillancourt", "expertise": [ "Reviewer Expertise Public economics in particular" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article nicely summarizes the literature on the classical pillars of the decentralization literature with example mainly from Africa. It uses an up to date systematic review of the literature with its methodology described in the methods part of the paper. It then discusses the potential of fiscal decentralization to drive local economic development in Africa. Here we would argue that the discussion of borrowing/debt is incomplete. Payment arrears are one way that local governments take on debt. Such arrears vary in kind between countries (wages, social security funds/superannuation, electricity /street lighting , suppliers). Each kind has different consequences. For example, supplier arrears can lead to private suppliers withdrawing supply or charging higher prices (implicit risk premium and interest charge)to compensate for late /uncertain payment. Electricity arrears ,avoided when prepaid cards are used by the utility ,can lead to cuts in services and thus to the incapacity to access the digital economy Fiscal decentralization challenges impeding local economic development in Africa are then presented. The authors quite correctly note the importance of weak institutional capacity as a prevalent challenge among subnational governments in Africa. The best financial arrangements will come to naught if there is no capacity to manage resources/provide services. Unfortunately, skilled personnel is often reluctant to work at the subnational level in Africa. Finally, the authors put forward recommendations on the use of digital technology to address a subset of issues linked to fiscal decentralization and property taxation in Africa. They correctly note that this will work only if the digital infrastructure is in place. Thus, it is odd that the provision of electricity is not mentioned in the paper .While more easily provided now than twenty years ago in remote areas though solar panels ,it is still lacking in many parts of Sub-Saharan Africa with 50% of the population without it in 2021. (https://data.worldbank.org/indicator/EG.ELC.ACCS.ZS?locations=ZG )\nThus, their specific useful recommendations to maximize local revenue potential by better identifying taxpayers and taxable values apply mainly in larger cities unless local revenues are collected centrally as is done in a fair number of African countries. If they work mainly in larger cities, then their implementation should be accompanied by a strengthening of the equalization dimension of the central government transfers to subnational governments to help those left behind .This would be an improvement on many existing scheme that reward already better off larger/capital cities. Finally let us note that the use of various digital tools to analyze matched data bases presupposes that the various silos of a given department, let alone government, will cooperate; this is often hard to achieve. In conclusion we agree with the authors who state that \"This paper contributes a valuable perspective to the existing literature, offering actionable insights and policy recommendations that can guide policymakers, scholars, and practitioners in their concerted efforts to realize the full potential of fiscal decentralization in Africa.\"\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "270659", "date": "31 May 2024", "name": "Jamie Boex", "expertise": [ "Reviewer Expertise Public finance", "intergovernmental finance", "local government finance", "local administration" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic of the study is an important one, and the initial draft provides a good foundation for a peer-reviewed and approved article. The draft can benefit from revision in a number of different ways.\n1. Introduction The introductory paragraph seems to go into too much detail of the four pillars, rather than setting the scene for the paper.\n\nIt is a priori unclear to what extent the focus is on the role of IT and all four pillars, or whether the focus is exclusively revenue decentralization, and/or specific LED functions.\n2.Methods This sections adds little value, beyond stating that you did a thorough literature review.\n3. FD and potential for LED This section leads the reader to think about LED, but really the section is about the assignment of functions and expenditure responsibilities.\n4. FD challenges The section title is misleading.\nOther than RSA and Kenya, weak political and admin decentralization are the #1 and #2 reasons for weak FD in Africa. I suggest you lead with that.\nThere should be a discussion on the negative impact of IGFT on OSR incentives and performance.\nSection 5. Leveraging digital technology Too much emphasis is given to AI, Machine learning and block chain. The benefits of digital technology--including the ability of IT to improve service delivery processes and offer better value for money in public service delivery; greater transparency; and more effective revenue collection-- could be presented in a clearer and more structured manner, with consistent, concrete examples.\nSection 6. Conclusions The minimum efficient scale of digital solutions is high. National governments in Africa are increasingly using digital platforms, but individual LGs do not have the scale to efficiently develop (or purchase) their own built-from-scratch IT solutions. Instead, they should \"contract-in\" skills and services from IT firms based on existing platforms (think: parking apps, online platforms for paying registration fees, for issuing local permits, etc.). Unfortunately, the market for municipal IT services in Africa is still small, because most LGs still work in a traditional (paper-based) public sector manner, and not in a results-based, evidence-based, client-oriented manner.\nGiven that there is currently no market for local digital solutions, the emergence of a market for local digital solution will require simultaneous action on both the demand and supply. Such systems change is difficult to accomplish. The paper omits any discussion on how to achieve the systems-change needed for digital solutions to become accessible to LGs.\nOverall, the language in the paper should be more nuanced. Statements about the benefits of fiscal decentralization should be qualified (e.g., \"Assuming political and administrative decentralization are effective, ...\".\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "270657", "date": "12 Jun 2024", "name": "Felix Oppong", "expertise": [ "Reviewer Expertise Fiscal decentralization and taxation." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMethodology The methodology applied to the research seem appropriate for this type of work. However, Figure 1 does not mirror the description of the methodology. While the authors initially downloaded papers from 246 sources, and 14 websites, the paper notes that about 108 sources were relevant. These papers included peer-reviewed academic journals and conference proceedings to dissertations, policy briefs, and digitally accessible materials. Figure 1 in the end shows only 30 studies and 30 reports. If the paper is using stratified random sampling technique (which I think is appropriate), it would be great to include the details in Figure 1 or at least ensure that it reflects the description. Figure 1 also indicates that out of 108 reports assessed, 136 of them were excluded. Authors should correction the chart to mirror the narrative.\nLiterature Review\nPresentation of the literature: Authors did not follow their own format in the section 3 (background: understanding the potential of fiscal decentralization to drive local economic development in Africa), which gives an indication of how they intend to proceed in the paper as follows: “The four pillars we will discuss include the distribution of expenditure responsibilities, the assignment of revenue sources, the allocation of intergovernmental fiscal transfers or grants, and the regulations surrounding subnational borrowing, budget deficits, and the accrual of subnational debt”. Authors should re-order the literature review section along the lines of the sentence.\nLiterature on digital tools for fiscal decentralization vs. title of the paper: The literature review is globally adequate. The paper uses current and relevant literature to argue it points while discussing empirical literature and identifying constraints facing selected African countries. Authors must address the following comments.\n\nSection 3 to 3.5 do not have strong connection with challenges with the use of digital technologies which is central to the paper. In each section discussing the four pillars of fiscal decentralization and challenges of decentralization, it would be useful create linkages necessitating the need for digital tools. As it stands, the first eleven pages of the paper seem somewhat disconnected with the title of the paper and does not engage the reader gradually to comprehend the title until section 5.\n\nCountry cases in the section 3.5 require referencing.\n\nSection 5: Leveraging digital technology for fiscal decentralization and property taxation in Africa: The paper starts full discussion on digital technology in this section. The section covered important areas such as application of evolving digital technology ( including IA powered solutions), automated processes, digital platforms, use of big data, etc. These are well written.\n\nThe paper should note clearly that many of the digital technologies are evolving even in advanced economies and that African countries require time to roll them out. Also, some of these digital tools are applied by the central governments as such the systems may already be in place at the center, regional capital or metropolitans. In some cases, there may be need for expansion of the coverage to SNG while in other cases, the central government may not have started applying specific tools due to legal arrangements and cost factors. Discussion of factors that impede rapid deployment of digital tool will be great. For instance, Telecom agreements are needed for fiber optic cables to be laid or cell Tower to be set up to enable mobile money platforms to be accessible to SNG. The lack of expansion of critical infrastructure to local levels could hamper the extension of certain digital tools. Section 5 explains what technological tools are available. Section 5.3 could benefit from “when” and “how” to use these tool to improve fiscal decentralization for SNGs.\n\nConclusion\nThe paper draws relevant conclusions. Countries are at different stages of development and may not be in the possible to quickly put in place a provision of robust digital infrastructure. That said, many African Countries beginning to deploy digital tools for revenue collection at the level of Central government. Thus, the conclusion and policy recommendation are appropriate.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-279
https://f1000research.com/articles/13-278/v1	16 Apr 24	{ "type": "Systematic Review", "title": "Exogenous foods that activate the NRF2 protein: Systematic review", "authors": [ "Ambrocio Teodoro Esteves Pairazaman", "Emma Caldas Herrera", "Jesus Collanque Pinto", "Flor Lidia Bustamante Fustamante", "José Rincón Chavez", "Carmela Gelida Barboza Justiniano", "Pamela Belen Esteves Cardenas", "Patricia Mariane Grados Alva", "Elmer Oyarce Alvarado", "Emma Caldas Herrera", "Jesus Collanque Pinto", "Flor Lidia Bustamante Fustamante", "José Rincón Chavez", "Carmela Gelida Barboza Justiniano", "Pamela Belen Esteves Cardenas", "Patricia Mariane Grados Alva", "Elmer Oyarce Alvarado" ], "abstract": "Background The activation of the Nuclear factor erythroid 2-related factor 2 (NRF2) signaling pathway, whether through natural compounds, diet, or supplements, plays a crucial role in protecting against oxidative stress and promoting health in various aspects. The objective of this research was to identify studies on exogenous foods that activate the NRF2 protein in the scientific literature.\n\nMethods A literature review aimed at identifying manuscripts on NRF2 activation with exogenous foods and its human benefits was conducted. The systematic review spanned English and Spanish articles from MEDLINE, PubMed, SciELO, and Scopus repositories until August 2023. All authors participated in search, analysis, and selection. Inclusion criteria prioritized NRF2-activating foods and their benefits, with exclusion criteria for irrelevant articles in other languages. Stringent filters were applied in stages—initial title search, abstract review, and thorough reading of remaining articles—to minimize bias and ensure relevance to the study’s objective.\n\nResults A total of 25 articles were analyzed, which discussed the adaptive mechanism of NRF2 and its role in hormone dose response, the effects of certain foods and health benefits associated with NRF2 activation\n\nConclusions The studies support the notion that NRF2 activation plays a fundamental role in promoting health in various spheres, underscoring the relevance of factors such as diet, natural components, and antioxidant supplementation in defending against oxidative stress and its implications for overall well-being. For future research on this topic, it is important to analyze how the population stands regarding the consumption of exogenous foods that activate NRF2, to understand both the consumption, quantity, and frequency of certain foods and whether they are doing so correctly.", "keywords": [ "NRF2", "activation", "antioxidant", "food", "protein" ], "content": "Introduction\n\nAging is a complex process that involves a combination of genetically programmed development and degenerative changes caused by the accumulation of stress. It is not entirely clear whether cellular senescence is the sole factor associated with aging.1,2 Theories of aging, such as programmed degeneration, evolutionarily favored aging, or cumulative aging, implicate the formation of free radicals. Some older organisms produce more reactive oxygen species (ROS) than younger organisms. Under healthy living conditions, cumulative changes in lifespan limits have resulted in an average life expectancy at birth of around 85 years, with the maximum reaching 122 years. These boundaries have expanded over the last 2,000 years due to progressive improvements in living conditions. Life expectancy at birth has grown from around 30 years in ancient Rome to over 80 years in today’s developed countries. Surprisingly, life expectancy has nearly doubled in the last century.3 Considering this, it can be said that oxidative stress increasingly plays a fundamental role in aging and various age-associated physiopathological conditions.4\n\nSkin degeneration can be divided into two conditions: intrinsic and extrinsic. Intrinsic aging is described as natural aging, while extrinsic aging is caused by environmental factors such as ultraviolet rays, tobacco, wind, and exposure to harmful substances. When cells are stimulated by various external factors, several ROS reactions are triggered in the body.5 The human body requires a significant amount of energy to maintain homeostasis and autonomous function. Cellular homeostasis is maintained by using mitochondria to generate large amounts of adenosine triphosphate (ATP). However, during this process, mitochondria inadvertently produce ROS, disrupting normal cellular function. This occurs mainly when unpaired electrons leave the electron transport chain (ETC) and react with molecular oxygen to form superoxide. This ROS radical is commonly eliminated by various antioxidant enzymes, including reduced glutathione, vitamins C and E, bilirubin, and urate. Non-catalytic antioxidant proteins such as thioredoxin, glutaredoxin, and metallothionein, as well as enzymes like superoxide dismutase, catalase, peroxidase, and glutathione peroxidase, play important roles. Glutathione serves as a primary antioxidant to reduce oxidative stress caused by ROS.6,7\n\nThe primary transcription factor responsible for initiating the response to oxidative stress is called factor 2, which is closely related to Nuclear factor erythroid 2-related factor 2 (NRF2). This protein consists of 605 amino acids, and it is within NRF2 that we find erythroid 2 factor, a human transcription factor that regulates the expression of various key components for mitochondrial function and aids in cellular cytoprotection with its effects.8\n\nUnder normal circumstances, NRF2 is retained within the cytosol through interaction with its inhibitory binding partner Kelch-like ECH-associated protein 1 (Keap1), and NRF2 activity is thereby inhibited.9 However, when it dissociates from Keap1, NRF2 engages in antioxidant protein activity with a protective function, inhibiting oxidative stress. NRF2 also possesses the ability to repair damaged mitochondrial function, reduce endoplasmic reticulum stress to prevent an inflammatory response, and enhance neuronal network regeneration, thereby reducing causes of cellular oxygen and glucose deprivation. This injury has a significant protective effect on cerebral ischemia-reperfusion in animals.10\n\nNRF2 mediates the antioxidant defense network and efficiently interacts with other transcription factors, not only synergizing with these proteins to enhance biopersistence through a dose-dependent graded process but also adjusting the quantitative dose-response characteristics of hormetic responses to subtoxic or below-threshold doses of various stressors that directly and immediately disrupt cellular homeostasis.11\n\nTherefore, the primary objective of this study was to investigate the fundamental role of exogenous foods in activating the NRF2 protein and how the genetic expression of the human body subsequently diminishes the signs of progressive internal and external aging through the human genome. All of this occurs with the activation of antioxidants that help combat oxidative stress, which is the predominant factor in aging and various forms of physiopathology commonly associated with aging.12,13\n\n\nMethods\n\nTo develop the research, a scientific search related to the topic of exogenous foods that activate the NRF2 protein in scientific production was conducted. This method aims to identify, interpret, and evaluate various studies conducted by researchers on a specific topic or field,14 with the intention of “providing the researcher and the reader with clarifying information on a particular subject”.15 Based on this, the research question for the review was formulated: What are the exogenous foods that activate the NRF2 protein addressed in research articles?\n\nThis study involved a thorough review of the scientific literature related to exogenous foods that activate the NRF2 protein and their effects within the human body. To carry out this review, the procedures described in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement16,36 were followed, specifically designed to ensure rigorous systematic reviews.\n\nThe first step in the systematic review process was to conduct initial searches in January 2023 in the MEDLINE (RRID:SCR_002185), PubMed (RRID:SCR_004846), SciELO, and Scopus (RRID:SCR_022559) databases. All databases were searched until 30 August 2023. These searches yielded a total of 34,212 manuscripts to be analyzed on the research topic.\n\nThe search was conducted, taking into account works published from 2020 to 2023, in the MEDLINE, PubMed, SciELO, and Scopus databases, resulting in a total of 34,212 works found.\n\nThe combination of terms that yielded the best results in the search engines was as follows: (“alimentos activadores del NRF2”; “NRF2-activating foods”; “NRF2” AND “foods” AND “medicine” “Alimentos” AND “NRF2”), or the search strategy was adapted according to the specific requirements of each database.\n\nSpecifically, 29,080 results were obtained from the five databases. Before proceeding to the article selection, inclusion and exclusion criteria were defined.\n\nInclusion criteria\n\n• Empirical studies and systematic reviews addressing foods that activate the NRF2 protein, their antioxidant properties, direct activation benefits, among other relevant aspects.\n\n• Studies published in Spanish and English.\n\n• Studies published in the period from 2020 to 2023 up to the cutoff date of our review (February 2023).\n\nExclusion criteria\n\n• Studies that did not specifically address foods that activate NRF2 and their benefits.\n\n• Studies that solely focused on NRF2 benefits without addressing the topic of foods that may help in its activation.\n\n• Studies that were not accessible in full text.\n\nThe selection of studies was carried out in three stages: a first stage based on reading the titles, a second stage based on reading the abstracts, and a third stage based on a thorough review of the articles chosen in the first stage. The selection was independently performed by five researchers, and disagreements were resolved through consensus.\n\nUltimately, 25 articles met the inclusion criteria and were chosen for a systematic review.\n\nSystematic reviews were conducted with the aim of identifying data related to food-mediated NRF2 protein activation, focusing on its antioxidant properties and direct benefits. The outcomes sought are listed and defined below:\n\n• Antioxidant Properties of Foods.\n\n• Measurement of the antioxidant capacity of foods that activate NRF2.\n\n• Search for data on antioxidant capacity in different studies and analyses.\n\n• Direct Benefits of NRF2 Activation.\n\n• Type of food, frequency of consumption, dosage.\n\n• We assumed inclusion of outcomes consistent with each outcome domain in each study, unless otherwise stated in the specific research methods.\n\n• In the absence of clear information, studies were considered not to address the variable in question.\n\nThe procedure for determining the suitability of an article began with a review of the titles of each research project, where it was assessed whether the article addressed the topic. After this first filter, all results were read and evaluated for their agreement with the search variable. Finally, a thorough review of the entire content of the manuscript was carried out for inclusion in the article. The filtering process was carried out by nine of the authors, and each author individually reviewed the registered and retrieved documents. It is essential to note that the distribution of tasks was carried out equally, considering the number of articles among the authors. Although each article was subject to individual review and analysis, in the end, all writers collaborated to create a comprehensive compilation.\n\nEach author conducted a thorough review of the content of each manuscript, assessing in detail the variable “activation of NRF2 by exogenous foods”. The methodology employed, data collected and preliminary interpretations were considered. Individual analysis facilitated a thorough exploration of each manuscript, ensuring a diversity of perspectives and experiences in the interpretation of the data.\n\nSystematic data collection was carried out for each article, including information on authors, year, abstract, type of research and key findings. After this phase, all papers that included the study variable in their abstracts or findings were analyzed in detail. Priority was given to selecting data from those articles that specifically addressed foods that activate NRF2.\n\nIn order to ensure the cohesion and integration of the various studies, a collaborative review phase was carried out. During this stage, the different methodologies and findings were compiled and compared. Constructive discussions and debates were encouraged to resolve potential disagreements and ensure that the final interpretation was robust and well-supported. The process concluded with the creation of a final compilation incorporating the data and conclusions drawn by consensus from the various analyses.\n\nThe data were analyzed according to each author’s individual criteria and filtered according to their relevance to the results. It is important to note that this process was shared with all authors, culminating in a final consensus for selection. This method was used to assess the reliability of the papers analyzed.\n\n\nResults\n\nWe analyzed 25 articles that met the inclusion criteria (Figure 1), indicating that we included all research that talked about foods or supplements that activate the NRF2 protein, as well as their benefits and properties that they have in people’s bodies. All works that address the aforementioned topic were taken into account, regardless of the methodology used, population and/or instrument.\n\nAccording to the 25 articles analyzed, it was found that (Table 1):\n\nThe analyzed studies underscore the significance of the NRF2 signaling pathway in safeguarding against oxidative stress and its crucial role in various facets of health and cellular protection. This adaptive pathway is pivotal in responding to hormonal doses, supporting essential hormonal properties. The conservation of NRF2 and its moderately stimulating responses are key factors amplifying its assimilation efficiency, as indicated by Calabrese and Kozumbo.11\n\nPrevious research has illuminated the impact of NRF2 protein activation on health promotion in diverse areas. Hongyan, et al.,29 illustrated that resveratrol can delay ovarian aging and enhance reproductive health. Conversely, Pistol, et al.,30 explored the beneficial effects of grape seed flour by-products in neutralizing prooxidant effects, suggesting significant health implications for oxidative stress prevention. Chan, et al.,31 emphasized the positive effects of fermented pomegranate extract on the skin, potentially applicable in skincare and overall health. Liang, et al.,32 addressed the importance of diet and salinity in the health of transgenic tilapia fry, underscoring the relevance of adequate protein and salinity levels in maintaining health through improved antioxidant and immune capacity. Additionally, Bykowska, et al.,34 examined foods associated with higher birth rates, highlighting NRF2 protein activation as a beneficial factor. Collectively, these studies offer valuable insights into how NRF2 activation contributes to health promotion in various domains.\n\nAuthors such as Lin et al.17 and Zhang et al.19 emphasize the NRF2 signaling pathway in the antioxidant response and cellular protection. They demonstrate how curcumin and extracts from medicinal plants like Alpinia officinarum can activate this pathway, reinforcing antioxidant defenses in the body. These results suggest that natural compounds can be valuable tools in preventing oxidative stress.\n\nJi et al.1 and Martemucci et al.3 explore therapeutic approaches for diseases related to cellular degeneration and aging. They discuss cellular reprogramming and the inclusion of antioxidants in the diet as strategies to counteract the harmful effects of oxidative stress and degeneration.\n\nAbrescia et al.22 discuss the role of polyunsaturated fatty acids in cellular signaling, intertwining with research on dietary antioxidants. These fatty acids, found in foods like fish, exhibit antioxidant properties and activate the NRF2 pathway, supporting the idea that diet plays a crucial role in protection against oxidative stress.\n\nSupplementation with antioxidants, such as vitamin E and curcumin, is addressed in several studies (Farshbaf et al., 24) and (George et al., 6). These antioxidants show beneficial effects in improving oxidative stress biomarkers, suggesting their utility in protecting against oxidative damage.\n\nThe use of exogenous foods with antioxidant properties is highlighted in research such as that of Li et al.8 and Zhao et al.28 Both Herpetospermum pedunculosum seeds and dietary resveratrol activate the NRF2 signaling pathway, alleviating oxidative stress and emphasizing the relevance of food choices in oxidative stress prevention.\n\nRegarding reproductive health, studies by Steiner et al.35 and Keshani et al.33 explore the effects of antioxidants and genetically modified foods on fertility. Although improvements in fertility parameters are not always observed, some of these compounds activate the NRF2 pathway, suggesting implications for other aspects of health.\n\nQian et al.18 conducted research focused on the protective effects of Ginkgo biloba seeds in relation to oxidative stress. Findings indicated that these seeds had the ability to modify NRF2 expressions and inhibit oxidative stress, highlighting the possibility that natural compounds could significantly impact the activation of this pathway and cellular protection.\n\nIslam et al.20 explored the beneficial effects of Clerodendrum viscosum, a medicinal plant in Ayurveda. Their study demonstrated how this plant could strengthen the antioxidant system by stimulating the NRF2 pathway, suggesting its potential in promoting health and neuronal protection, especially in environments exposed to harmful substances such as lead.\n\nIn the context of mitigating cerebral ischemia/reperfusion injury, Sun et al.10 investigated the activation of NRF2. Results indicated that activated NRF2 had a protective effect by preventing inflammatory reactions, inhibiting nerve cell apoptosis, and improving nerve function, emphasizing the crucial role of this pathway in cerebral protection.\n\nLiu et al.21 evaluated the effects of polysaccharides derived from algae on oxidative stress and inflammatory response. Their study demonstrated how these polysaccharides improved antioxidant capacity and reduced the inflammatory response by suppressing NF-κB p65 signaling, suggesting their utility in reducing oxidative stress and inflammation. On the other hand, Felgus et al.23 focused on the health benefits associated with blueberry consumption, particularly in mitigating oxidative stress. Their review highlighted how blueberry phytochemicals possessed antioxidant and anti-inflammatory properties, supporting the health benefits of this food.\n\nShirvani et al.26 conducted research on oregano supplementation in soldiers subjected to extreme physical conditions. Their study suggested that oregano could reduce muscle damage and increase antioxidant capacity, which could be beneficial for improving physical readiness in high-stress situations. Meanwhile, Kobayashi et al.27 established an interesting connection between caffeine and age-related oxidative stress prevention in periodontal tissues and alveolar bone loss in rats. Their study emphasized how coffee consumption could positively regulate the NRF2 signaling pathway, supporting the idea that certain foods and beverages could have protective effects.\n\nZhao et al.28 investigated the effects of dietary resveratrol on muscle quality in broiler chickens under heat stress. Results suggested that resveratrol could enhance muscle antioxidant capacity by activating the NRF2 pathway, highlighting its utility in protection against oxidative stress.\n\nLastly, the importance of physical activity and antioxidant supplementation in overall health is discussed. Studies like that of Mohammadrezaei et al.25 highlight how the combination of aerobic exercise and the consumption of certain foods can improve antioxidant capacity and overall health.\n\n\nDiscussion\n\nThe analyzed studies underscore the fundamental relevance of the NRF2 signaling pathway in protection against oxidative stress and its profound impact on various aspects of health and cellular defense. This adaptive pathway emerges as an essential pillar in hormone response and support of basic hormonal functions, as indicated by Calabrese and Kozumbo.11 Furthermore, the preservation of NRF2 and its moderate stimulating responses have been observed as crucial components that enhance its assimilation efficiency.\n\nParticularly, significant results from various studies have been highlighted. Hongyan, et al.29 revealed how resveratrol has the ability to delay ovarian aging and improve reproductive health, suggesting a key role of NRF2 in reproductive health. On the other hand, Pistol, et al.30 explored the benefits of grape seed flour by-products in neutralizing prooxidant effects, pointing to significant implications for health and oxidative stress prevention. Additionally, Chan, et al.31 emphasized how fermented pomegranate extract may have positive effects on the skin and possibly on overall skin-related health.\n\nThe study by Liang, et al.32 underscores the relevance of diet and salinity in the health of transgenic tilapia fry, emphasizing the importance of maintaining adequate levels of protein and salinity to enhance antioxidant and immune capacity. Furthermore, Bykowska, et al.34 examined the relationship between NRF2 protein activation and women’s fertility through foods associated with higher birth rates.\n\nAdditionally, previous studies have demonstrated how natural compounds such as curcumin and extracts from medicinal plants can activate the NRF2 pathway, strengthening antioxidant defenses and suggesting the relevance of incorporating natural foods in oxidative stress prevention. Therapeutic approaches to address diseases related to cellular degeneration and aging, such as cellular reprogramming and the inclusion of antioxidants in the diet, have also been explored.\n\nPolyunsaturated fatty acids found in foods like fish have also been shown to possess antioxidant properties and the ability to activate the NRF2 pathway, emphasizing the importance of diet in protection against oxidative stress. Antioxidant supplementation, such as vitamin E and curcumin, has shown beneficial effects in improving oxidative stress biomarkers.\n\nRegarding reproductive health, the effects of antioxidants and genetically modified foods have been explored, highlighting that some of these compounds activate the NRF2 pathway, which could have implications beyond fertility.\n\nFinally, the relationship between caffeine and age-related oxidative stress prevention has been highlighted, as well as the potential of resveratrol in enhancing antioxidant capacity in various conditions, including thermal stress.\n\n\nConclusions\n\nTaken together, these studies support the notion that NRF2 activation through food intake plays a crucial role in promoting health in a variety of areas, emphasizing the importance of diet, natural compounds, and antioxidant supplementation in protection against oxidative stress and its implications for overall health.\n\n\nAuthor roles\n\nAmbrocio Teodoro Esteves Pairazaman: Conceptualization, Investigation, Supervision, Funding acquisition, Visualization and Writing – original draft\n\nEmma Caldas Herrera: Methodology, Visualization and Writing – Review & Editing\n\nJesus Collanque Pinto: Resources, Validation and Writing – Review & Editing\n\nFlor Lidia Bustamante Fustamante: Formal analysis, Visualization and Writing – Review & Editing\n\nJosé Rincón Chavez: Formal analysis, Visualization and Writing – Review & Editing\n\nCarmela Gelida Barboza Justiniano: Visualization and Formal Analysis\n\nPamela Belen Esteves Cardenas: Formal analysis and Writing – Review & Editing\n\nPatricia Mariane Grados Alva: Investigation, Methodology, Validation, Visualization, Writing – Original Draft Preparation and Writing – Review & Editing\n\nElmer Oyarce Alvarado: Methodology, Visualization and Writing – Review & Editing", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nZenodo: Exogenous foods that activate the NRF2 protein: Systematic review. https://zenodo.org/doi/10.5281/zenodo.8400672. 36\n\n• PRISMA_2020_checklist.docx\n\n• Figure 1. docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nJi S, Xiong M, Chen H, et al.: Cellular rejuvenation: molecular mechanisms and potential therapeutic interventions for diseases. Sig Transduct Target Ther. 2023; 8: 116. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSalminen A: Feed-forward regulation between cellular senescence and immunosuppression promotes the aging process and age-related diseases. Ageing Res. Rev. 2021; 67: 101280. PubMed Abstract \| Publisher Full Text Reference Source\n\nMartemucci G, Portincasa P, Di Ciaula A, et al.: Oxidative stress, aging, antioxidant supplementation and their impact on human health: An overview. Mech Ageing Dev. 2022; 206: 111707. PubMed Abstract \| Publisher Full Text\n\nYazar İ, Sarıkaya B, Koyuncu İ, et al.: Evaluation of oxidative stress in degenerative rotator cuff tears. J. Shoulder Elb. Surg. 2022; 31(10): e490–e497. Publisher Full Text Reference Source\n\nLiu T, Xia Q, Lv Y, et al.: ErZhiFormula prevents UV-induced skin photoaging by NRF2/HO-1/NQO1 signaling: An in vitro and in vivo studies. J. Ethnopharmacol. 2023; 309(309): 115935. Publisher Full Text Reference Source\n\nGeorge M, Tharakan M, Culberson J, et al.: Role of NRF2 in aging, Alzheimer’s and other neurodegenerative diseases. Ageing Res. Rev. 2022; 82: 101756. PubMed Abstract \| Publisher Full Text\n\nGao L, Wang Y, Liu Z, et al.: Identification of a small molecule SR9009 that activates NRF2 to counteract cellular senescence. Aging Cell. 2021; 20(10): e13483. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi J, Lu Q, Peng M, et al.: Water extract from Herpetospermum pedunculosum attenuates oxidative stress and ferroptosis induced by acetaminophen via regulating NRF2 and NF-κB pathways. J. Ethnopharmacol. 2023; 305: 116069. Publisher Full Text Reference Source\n\nZhu L, He S, Huang L, et al.: Chaperone-mediated autophagy degrades Keap1 and promotes NRF2-mediated antioxidative response. Aging Cell. 2022; 21(6): e13616. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSun Y, Yang X, Xu L, et al.: The Role of NRF2 in Relieving Cerebral Ischemia-Reperfusion Injury. Curr. Neuropharmacol. 2023; 21(6): 1405–1420. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCalabrese E, Kozumbo W: The hormetic dose-response mechanism: NRF2 activation. Pharmacol. Res. 2021; 167: 105526. PubMed Abstract \| Publisher Full Text Reference Source\n\nZweig J, Caruso M, Brandes M, et al.: Loss of NRF2 leads to impaired mitochondrial function, decreased synaptic density and exacerbated age-related cognitive deficits. Exp. Gerontol. 2020; 131: 110767. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhu H, Li X, Qiao M, et al.: Resveratrol Alleviates Inflammation and ER Stress Through SIRT1/NRF2 to Delay Ovarian Aging in a Short-Lived Fish. J. Gerontol. A Biol. Sci. Med. Sci. 2023.30; 78(4): 596–602. Publisher Full Text Reference Source\n\nPardal J, Ochoa C: Revisiones sistemáticas. Revista ORL. 2017; 8(4): 197–203. Publisher Full Text\n\nPardal J, Pardal B: Anotaciones para estructurar una revisión sistemática. Revista ORL. 2020; 11(2): 155–160. Publisher Full Text\n\nPRISMA: 2020. Reference Source\n\nLin X, Bai D, Wei Z, et al.: Curcumin attenuates oxidative stress in RAW264.7 cells by increasing the activity of antioxidant enzymes and activating the NRF2-Keap1 pathway. PLoS One. 2019. 21; 14(5): e0216711. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nQian Y, Yan L, Wei M, et al.: Seeds of Ginkgo biloba L. inhibit oxidative stress and inflammation induced by cigarette smoke in COPD rats through the NRF2 pathway. J. Ethnopharmacol. 2023. 30; 301: 115758. PubMed Abstract \| Publisher Full Text Reference Source\n\nZhang X, Liu A, Zhang Y, et al.: A diarylheptanoid compound from Alpinia officinarum Hance ameliorates high glucose-induced insulin resistance by regulating PI3K/AKT-NRF2-GSK3β signaling pathways in HepG2 cells. J. Ethnopharmacol. 2022. 15; 295: 115397. PubMed Abstract \| Publisher Full Text Reference Source\n\nIslam J, Shila TT, Islam Z, et al.: Clerodendrum viscosum leaves attenuate lead-induced neurotoxicity through upregulation of BDNF-Akt-NRF2 pathway in mice. J. Ethnopharmacol. 2023. 25; 304: 116024. PubMed Abstract \| Publisher Full Text Reference Source\n\nLiu W, Zhuang D, Zhao Y, et al.: Seaweed-Derived Polysaccharides Attenuate Heat Stress-Induced Splenic Oxidative Stress and Inflammatory Response via Regulating NRF2 and NF-κB Signaling Pathways. Mar. Drugs. 2022. 27; 20(6): 358. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbrescia P, Treppiccione L, Rossi M, et al.: Modulatory role of dietary polyunsaturated fatty acids in NRF2-mediated redox homeostasis. Prog. Lipid Res. 2020; 80: 101066. PubMed Abstract \| Publisher Full Text Reference Source\n\nFelgus L, Howard L, Adams S, et al.: The Effects of Blueberry Phytochemicals on Cell Models of Inflammation and Oxidative Stress. Adv. Nutr. 2022. 1; 13(4): 1279–1309. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFarshbaf A, Ostadrahimi A, Mirghafourvand M, et al.: Clinical Efficacy of Curcumin and Vitamin E on Inflammatory-Oxidative Stress Biomarkers and Primary Symptoms of Menopause in Healthy Postmenopausal Women: A Triple-Blind Randomized Controlled Trial. J. Nutr. Metab. 2022. 9; 2022: 1–12. Publisher Full Text Reference Source\n\nMohammadrezaei A, Kavakeb A, Abbasalizad M, et al.: Effects of hemp seed alone and combined with aerobic exercise on metabolic parameters, oxidative stress, and neurotrophic factors in young sedentary men. Food Bioche. 2022; 46(12): e14417. PubMed Abstract \| Publisher Full Text\n\nShirvani H, Bazgir B, Shamsoddini A, et al.: Oregano (Origanum vulgare) Consumption Reduces Oxidative Stress and Markers of Muscle Damage after Combat Readiness Tests in Soldiers. Nutrients. 2022. 28; 15(1): 137. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKobayashi T, Maruyama T, Yoneda T, et al.: Effects of Coffee Intake on Oxidative Stress During Aging-related Alterations in Periodontal Tissue. In Vivo. 2020; 34(2): 615–622. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao Y, Li Z, Wang X, et al.: Resveratrol Attenuates Heat Stress-Induced Impairment of Meat Quality in Broilers by Regulating the NRF2 Signaling Pathway. Animals (Basel). 2022. 25; 12(15): 1889. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHongyan Z, Xiaowen L, Mengxue Q, et al.: Resveratrol Alleviates Inflammation and ER Stress Through SIRT1/NRF2 to Delay Ovarian Aging in a Short-Lived Fish. The Journals of Gerontology: Series A. 2023; 78(4): 596–602. Publisher Full Text Reference Source\n\nPistol G, Marin D, Bulgaru V, et al.: Grape seed meal by-product is able to counteract oxidative stress induced by lipopolysaccharide and dextran sulphate in IPEC cells and piglets after weaning. PLoS One. 18(4): e0283607. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChan L, Tseng Y, Liu C, et al.: Fermented pomegranate extracts protect against oxidative stress and aging of skin. J. Cosmet. Dermatol. 2021; 21(5): 2236–2245. PubMed Abstract \| Publisher Full Text\n\nLiang H, Wu L, Hamunjo M, et al.: Culture salinity modulates NRF2 antioxidant signaling pathway and immune response of juvenile Genetically Improved Farmed Tilapia (GIFT) (Oreochromis niloticus) under different dietary protein levels. Fish Shellfish Immunol. 2021; 117: 220–227. PubMed Abstract \| Publisher Full Text Reference Source\n\nKeshani P, Hossein M, Reza M, et al.: The Effect of Genetically Modified Food on Infertility Indices: A Systematic Review Study. Scie Word Jour. 2020; 1–7. Publisher Full Text Reference Source\n\nBykowska A, Kolay E, Kaluzna M, et al.: Emerging Trends in Research on Food Compounds and Women’s Fertility: A Systematic Review. Appl. Sci. 2020; 10: 4518. Publisher Full Text Reference Source\n\nSteiner A, Hansen K, Barnhart K, et al.: The effect of antioxidants on male factor infertility: the Males, Antioxidants, and Infertility (MOXI) randomized clinical trial. Fertil. Steril. 2020; 113(3): 552–560.e3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEsteves A, Caldas E, Collanque J, et al.: Exogenous foods that activate the NRF2 protein: Systematic review. [Dataset]. Zenodo. Publisher Full Text" }	[ { "id": "290805", "date": "28 Jun 2024", "name": "Gian Luigi Russo", "expertise": [ "Reviewer Expertise Keywords : phytochemicals", "polyphenols", "botanicals", "disease prevention", "health", "cancer", "chemoprevention", "antioxidant", "protein kinases", "cell division cycle", "apoptosis", "senescence", "autophagy." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI read with great attention and interest the work by Ambrocio Teodoro Esteves Pairazaman et al. The scope of the systematic review is to assess the role of foods in activating the NRF2 system of antioxidant response. Although the topic is of great interest, leading me to accept the current revision, I must admit that, in my opinion, the authors fail to achieve their objective. If the main question to be answered was: “What are the exogenous foods that activate the NRF2 protein addressed in research articles?” (page 3 of 15), this is not clearly answered in the article. While I am not an expert in systematic reviews, it seems the main issue lies in the method used to select the 25 articles that met the inclusion criteria. Notably, about 30% of these articles are reviews, not original research. Additionally, the articles include studies where single compounds were tested alongside others using extracts, making it difficult to discern a functional relationship between specific food agents and their effects on the NRF2 pathway. The Results section does little to aid comprehension, as it is limited to brief descriptions of each article retrieved. Instead, it was expected that the authors would attempt to identify common modes of action triggered by specific classes of compounds in particular food groups that activate the NRF2 pathway. The functional relationship (if any) between the measurement of the antioxidant capacity of foods and the activation of NRF2 remains unclear (page 4 of 15). Finally, the article does not sufficiently address the concentrations of the putative agents used to stimulate NRF2. This is crucial since NRF2 activation is not always or exclusively associated with beneficial effects. Overall, after reading the article, I, and presumably other readers, are left with the unresolved question of which foods and their portions should be consumed to maintain an activating level of NRF2 activity. Other comments: - The Discussion section largely duplicates the Results and needs revision. - A clear definition of “exogenous” food should be provided. - An explanation of why only studies published in Spanish and English were considered, excluding other languages, should be given.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? No\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-278
https://f1000research.com/articles/12-24/v1	09 Jan 23	{ "type": "Research Article", "title": "Role of apoptotic inhibitors, viability, and differentiation in low oxygen tension of mesenchymal stem cells cultured in a rat model of ovarian failure", "authors": [ "Erma Safitri", "Hery Purnobasuki", "Muhammad Thohawi Elziyad Purnama", "Shekhar Chhetri", "Hery Purnobasuki", "Muhammad Thohawi Elziyad Purnama", "Shekhar Chhetri" ], "abstract": "Background: Stem cell therapy shows applications potential for malnutrition-induced ovarian failure in rat models. However, it is ineffective because of the lack of viability and differentiation of transplanted stem cells, resulting in low adaptation and survival rates. We aimed to determine whether stem cells cultured under low oxygen (O2) tension improves the adaptability and viability of stem cells, as well as ovarian failure. Methods: After four days of culturing mesenchymal stem cells (MSCs) in 21% oxygen (normoxia) as the T2 group and 1% oxygen (low O2 or hypoxia) as the T1 group, 200 million bone marrow-derived MSCs per rat were transplanted into female rats with ovarian failure (15 rats per treatment group). A total of 15 fertile and 15 infertile rats were categorized as the C+ and C− groups, respectively. Results: The slight increase in cells expressing HSP70 (C+, T2, T1, and C− groups were 0.5a±0.53, 1.7a±0.82, 6.2b±1.5, and 9.6c±1.3, respectively), decrease in cells expressing caspase-3 as an apoptotic inhibitor (C+, T2, T1, and C− groups were 0.2a±0.42, 0.6a±0.52, 4.8b±1.03, and 7.3c±1.42, respectively), and increase in cells expressing VEGF-1 (C+, T2, T1, and C− groups were 10.8c±1.55, 8.7b±0.48, 0.4a±0.52, and 0.2a±0.42, respectively) and GDF-9 (C+, T2, T1, and C− groups were 5.8c±1.47, 4.6b±0.97, 0.5a±0.53, and 0.3a±0.48, respectively) were used as markers for viability and differentiation in ovarian tissue, indicating that MSCs cultured under low O2 tension were more effective than those cultured under normoxic conditions as a treatment for female rats with ovarian failure. Furthermore, infertile female rats treated with MSCs cultivated under low O2 tension had an enhanced ovarian tissue shape, as indicated by the increasing Graafian follicle count (C+, T2, T1, and C− groups were 8.9c±0.74, 4.5b±0.71, 0.5a±0.53, and 0.4a±0.52, respectively). Conclusions: MSCs cultured under low O2 tension are an effective treatment for malnourished rats with ovarian failure.", "keywords": [ "malnutrition", "ovarian failure", "stem cells", "good health and well being" ], "content": "Introduction\n\nStem cell transplantation has been explored as a therapy for various diseases such as stroke, 1 Alzheimer’s disease, 2 diabetes mellitus, 3 Parkinson’s, 4 myocardial infarction, 5 HIV, 6 testicular failure, 7 , 8 and other degenerative diseases such as ovarian failure. 9 As an important organ in female reproduction, the ovary produces ovum and female hormones. 10 MSC transplantation derived from rabbit bone marrow, 11 rat bone marrow, 7 , 9 rat adipose tissue, 12 or umbilical cord blood 13 has shown promising results for tissue repair via the proliferation and development of endogenous stem cells into germ cells. 7 , 9 , 14\n\nHowever, the lack of viability and differentiation of implanted stem cells results in poor adaptivity and a low survival rate, indicating that the therapy is ineffective. The low survivability and function of MSCs might be related to a higher incidence of apoptosis during culture and after transplantation. This finding indicates that the milieu of damaged tissues is not conducive to stem cell adaptation survival; hence, stem cell transplantation is not a feasible option. Recently, researchers cultivating stem cells under low oxygen tension have observed cell stress, although one study has found that the stress situation activates HSP27 as a function of anti-apoptosis via caspase-9 suppression. 15\n\nThe success of stem cell transplantations is limited by their weak adaptivity and differentiation. The low efficacy of MSC transplantation might be due to apoptosis occurring during cell growth. 15 , 16 Consequently, high doses of stem cells via regular boosters are necessary for effective therapy, which increases the therapy cost. 17 In vitro stem cell cultivation must be adapted to a niche environment, such as the microenvironment of bone marrow, to avoid apoptosis. Low O2 tension is an example of a niche habitat for stem cells in bone marrow. 18 Low O2 tension caused by in vitro culture reduces apoptosis, viability, and differentiation of stem cells, all of which promote ovarian function in ovulation production via folliculogenesis and oogenesis. The expression of HSP70 19 and caspase-3 20 in ovarian tissue inhibits apoptosis, whereas that of VEGF-1 and GDF-9 promotes viability and differentiation. 21\n\nThis study aimed to determine the role of HSP70 and caspase-3 as apoptotic inhibitors, as well as VEGF-1 and GDF-9 as viability and differentiation markers, respectively, in MSCs cultivated under low O2 tension for malnutrition-induced ovarian failure in female rats.\n\n\nMethods\n\nThis research, including experiments with animals, was approved by the ethical clearance committee of the Animal Care and Use Committee of the Veterinary Medicine Faculty, Universitas Airlangga with number 239-KE. Experiments were performed in adherence with the guideline manual by the ethical committee. All efforts were undertaken to ameliorate animal suffering.\n\nBone marrow stem cells were extracted by aspirating the iliac crest 7 , 9 of three-month-old male rats. 22 The aspirate was placed in heparinized tubes (Z181099, Sigma Aldrich®, Burlington, Massachusetts, USA), which was then transported to the lab and kept at 4°C. 7 , 9 , 23 The aspirate was transferred to 15-mL sterile tubes (SIAL0790-500EA, Sigma Centrifuge tubes, Sigma Aldrich, Burlington, Massachusetts, USA), cleaned two times with 5 mL of sterile phosphate-buffered saline (PBS; MFCD00131855, Sigma Aldrich, Burlington, Massachusetts, USA), and then filled to a final volume of 10 mL. The same amount of Ficoll (F9378, Sigma Aldrich, Burlington, MA, USA) was added after diluting the sample in a separate 15-mL tube. Centrifugation (Sorvall MX Series Floor Model Micro-Ultracentrifuge, Thermo Fisher, Grand Island, NY, USA) was performed at 1,600 rpm for 15 min at room temperature. The mononucleated cells were collected in a 15-mL tube after centrifugation in a form of a “buffy coat” that had accumulated on the Ficoll–PBS surface. In PBS, the cells were resuspended in a 15-mL total volume. The tube (CLS6791 Sigma, Corning LSE Benchtop Shaking Incubator with Platform, Sigma Aldrich, Burlington, MA, USA) was inverted gently and shaken five times to homogenize the suspension.\n\nFor another 10 min, the suspension was centrifuged. The cell pellet was resuspended in 6 mL of an alpha-modified essential medium after the supernatant and floating cells were removed from the experiment (α-MEM; M0894; Sigma Aldrich, Burlington, MA, USA). Mononucleated cells were plated in a 10 cm2 plate (Falcon™, Thermo Fisher Scientific, Pittsburgh, PA, USA) with approximately 2×107 cells and incubated at 37°C in a humidified atmosphere containing 5% CO2 (BioSpherix, Canada/USA) for 24 h to allow cell adherence. Medium and non-adherent cells were removed after 24 h. The plate was returned to the incubator after the adhering cells had been rinsed two times with 5 mL of PBS and 10 mL of fresh α-MEM media. An inverted microscope was used to monitor the culture every day. The medium was replaced every four days, followed by washing with 10 mL of PBS before adding 10 mL of fresh α-MEM media. The culture was maintained until a convergence of about 75%–80% confluence was achieved. The cells were moved to various dishes after confluence to grow subcultures. 7 The cells were separated into two low-O2-tension treatments of 1% after three rounds in a hypoxic chamber (BioSpherix, Canada/USA) inside a 5% CO2 incubator. A separate treatment was the use of 21% O2 concentration (normoxic chamber) over four days. MSCs were observed and characterized by using a microscope before being transferred into an ovary.\n\nMSC characterization between low O2 and normoxic culture conditions was performed before being transferred into the ovary based on morphological analysis of cells using an inverted microscope (Phase Contrast, MXD-400, Nanjing BW Optics & Instrument Co., Ltd). HSP70 and caspase-3 were identified via real-time polymerase chain reaction (PCR; MxPro software, PCR, [Cat No. 401513]; Brilliant II QPCR Low ROX Master Mix [Cat No. 600806], Agilent 2100 Bioanalyzer system [Cat No. G2939AA], Macherey-Nagel GmbH & Co [Düren, Germany]). Apoptosis was detected using immunofluorescence (Apoptag Fluorescein In Situ Apoptosis Detection Kit, S7110, Sigma Aldrich, Burlington, MA, USA). 15\n\nReal-time PCR was performed using the following method. The MSC-containing media were aspirated, rinsed two times with 1 mL of PBS, and then added with 500 μL of RNAiso/well. Afterward, 100 μL of chloroform was poured into a small tube containing scraped-off cells. Then, the tube was repeatedly shaken. Centrifugation was performed to separate the supernatant (250–300 μL) for 15 min at 12,000 rpm and 4°C. Only RNA molecules remained in the tube after the supernatant was removed; thus, 500 μL of 75% ethanol vortex was added until the pellet floated. At 12,000 rpm and 4°C, the samples were centrifuged for 5 min. After the supernatant was removed from the tube, it was dried for 5–10 min before adding 25 μL of Aqua bidest. The RNA concentration suitable for spectrophotometric measurement and purification was 1.7–2.1 μL in 1 μL of the tested sample. 15\n\nThe RNA sample was then added to 11 μL of Aqua bidest, and 9 μL of the combined component was placed into a new tube and mixed with 11 μL of RNA samples. Thereafter, the mixture was incubated in a PCR machine followed by pre-denaturation at 37°C for 15 min, denaturation at 65°C for 10 min, annealing at 65°C for 10 min, and final extension at 65°C for 2 h. All stages were repeated for 40 cycles. This identification was used a primary sequence template CD44f (5′-TCC CAG TAT GAC ACA TAT TGC-3′) and CD44r (5′-CAC CTT CTT CGA CTG TTG AC-3′) (Oligo Macrogen, Seoul, Korea). Real-time PCR identification was prepared for 20 e-DNA samples for 30 min.\n\nFemale rats used in this study were fasted for five days but given unlimited access to water, creating a rat model with ovarian failure. 21 , 24 Female rats aged 12 to 14 weeks and weighing 250 to 300 g served as the study's model animals. In the experimental animal facility of the Faculty of Veterinary Medicine, Universitas Airlanggas, the rats were housed in separate plastic cages with sufficient ventilation.\n\nThe transplanted MSCs were evaluated against negative and positive control rats, as well as female rats with ovarian failure. The T1 group included 15 infertile female rats that received 200 million stem cells per rat from a four-day normoxic culture (21% O2 concentration). 7 , 9\n\nThe T2 group included 15 infertile female rats that received 200 million stem cells per rat from a four-day low O2 culture (1% O2 concentration). 7 , 9 0.1 mL of PBS injection was given to 15 healthy female rats in the fertile positive control group. A total of 15 infertile female rats were injected with 0.1 mL of PBS as part of the negative control group (infertile rat).\n\nOvarian tissue was collected from the ovaries of female rats 10 days after surgical excision (allowing for two estrous cycles). 21\n\nHistopathological preparations using hematoxylin and eosin (HE) stain (B8438, Sigma Aldrich, Burlington, MA, USA) allowed researchers to detect an improvement in ovarian tissue. HSP70 expression (with monoclonal antibody HSP 70, catalog number MA3-007, Thermo Fisher Scientific, Waltham, MA USA) as anti-apoptosis was assessed by immunohistochemistry (IHC). Caspase-3 expression (with caspase-3 monoclonal antibody, E-8 7272 for IHC staining, Santa Cruz Biotechnology, LI-COR, Bioscience, Santa Cruz, CA, USA), as a pro-apoptotic factor, was inhibited. In addition, VEGF-1 expression (with a mouse monoclonal antibody, cone OTI4E3 [formerly 4E3], True MAB, OriGene, Beijing, China) served as a marker of the viability of stem cells, whereas GDF-9 (with a GDF-9 monoclonal antibody, sc-514933, Santa Cruz Biotechnology, LI-COR, Bioscience, Santa Cruz, CA, USA) served as a marker of the differentiation of stem cells into progenitor germ cells to improve ovarian failure and infertility.\n\nHistopathological observation of ovarian tissue in the presence of a Graafian follicle and regeneration of tissue were performed through light microscopy. 25\n\nA 10% formalin solution was used to fix the tissues of the ovaries. Subsequently, the ovaries were dehydrated using a series of progressively increasing alcohol concentrations, cleaned with xylol, and fixed in paraffin. Routine staining was performed on thin sections and placed on slides. 26\n\nA light microscope with 400× magnification was used to conduct histopathological evaluation. Each slide’s five fields of view were evaluated. Based on an existing histological description, a Graafian follicle was observed and identified, and seminiferous tubular regeneration was performed. 21\n\nThe expression of HSP70, caspase-3, VEGF-1, and GDF-9 was examined by IHC. Samples were prepared for histological examination by making an incision transversely from the paraffin blocks of ovarian tissue. IHC used monoclonal antibodies to analyze the expression of HSP70 (catalog number MA3-007, HSP 70 monoclonal antibody, Thermo Fisher Scientific, Waltham, MA, USA), caspase-3 (caspase-3 E-8 7272 monoclonal antibody for IHC staining, Santa Cruz Biotechnology, LI-COR, Bioscience, Santa Cruz, CA, USA), VEGF-1 (mouse monoclonal antibody, cone OTI4E3 [formerly 4E3], True MAB, OriGene, Beijing, China), and GDF-9 (sc-514933, GDF-9 monoclonal antibody, Santa Cruz Biotechnology, LI-COR, Bioscience, Santa Cruz, CA, USA). Observations were performed using a light microscope with 200× magnification. Each slide’s five fields of view were evaluated to determine the score of tissue with brownish chromogen as a result of HSP70, caspase-3, VEGF-1, and GDF9-9. The IHC scoring system 27 assigned an IHC score of A×B (A=width of expression percentage; B=intensities of chromogen color; Table 1).\n\nThe expression of HSP70, caspase-3, VEGF-1, and GDF-9 and the Graafian follicle count with a 99% confidence level (= 0.01) and 0.05 significance threshold of difference (p<0.05) were statistically analyzed using SPSS (v. 17 for Windows XP; SPSS Inc, Chicago, IL, USA). The comparative steps for hypothesis testing included normality data test, Kolmogorov–Smirnov test, homogeneity of variance test, analyses of variance, and Tukey’s significant difference post hoc test with 5% least significant difference.\n\n\nResults\n\nData were collected from 60 female rats. The data were divided into four groups of treatment: (1) fertile female (normal rat) as the positive control group; (2) infertile female treated with PBS as the negative control group; (3) infertile female with stem cells transplanted from the four-day normoxic culture (21% O2 concentration) as the T1 group (first treatment); (4) infertile female with stem cells transplanted from the four-day low-O2 culture (1% O2 concentration) as the T2 group (second treatment). The study results revealed that MSC transplantation from the hypoxic precondition culture improved ovarian function by decreasing the damage level and increasing fertility score. The expression level of HSP70, VEGF-1, and GDF-9 was upregulated, whereas the expression level of caspase-3 was decreased; the regeneration of ovarian tissue achieved a normal histopathological figure as evidenced by the development of a follicle into a Graafian follicle.\n\nCharacteristics of MSCs between low-O2 and normoxic cultures were observed before being transferred into the ovaries to assess cell morphology, HSP27 and caspase-3 expression, and apoptosis. MSC characterization was performed using an inverted microscope after the third passage of normoxic (O2 21%) and low-O2 (O2 1%) cultures on the second day. The cells exhibited a larger cell size, fewer cell deaths, and slower proliferation rate in the low-O2 culture, whereas the cells showed a higher rate of proliferation, more cell deaths, and smaller cell sizes in the normoxic culture (Figure 1).\n\nMSCs (red arrow) and cell death (yellow arrow). Magnification at 400×.\n\nReal-time PCR analysis of HSP27 and caspase-3 expression revealed considerably and significantly increased HSP27 and decreased caspase-3 under low oxygen tension (O2 1%; p<0.01) compared with those under the normoxic culture as a control (Figures 2 and 3).\n\nApoptosis was detected through IHC under normoxic and low-O2 conditions. The positive expression of apoptosis reached 50% of cells cultured under a normoxic condition, whereas only 5% of cells cultured under low O2 culture in vitro until 72 h exhibited apoptotic cells (Figure 4).\n\n(A) Positive expression of apoptosis in normoxia (red arrow) and number of apoptotic cells reaching 25%. (B). Low-O2 culture in vitro for 72 h show a small number of apoptotic cells (5%, red arrow). Magnification at 400×.\n\nThe IHC score for HSP70 expression in ovarian tissue from four treatments is shown in Figures 2, 5 and Table 2. As shown in Table 2, the average score of HSP70 expression (brown) was 0.5a ± 0.53 for the positive (fertile) control group, 1.7a±0.82 for the T2 group, 6.2b±1.5 for the T1 group, and 9.6c±1.3 for the negative (infertile) control group.\n\na–d Different superscripts in the same column were significantly different (p<0.05).\n\nThe IHC score for caspase-3 expression in ovarian tissue from four treatments is shown in Figures 3, 6 and Table 2. As shown in Table 2, the average score of caspase-3 expression (brown) was 0.2a±0.42 for the positive (fertile) control group, 0.6a±0.52 for the T2 group, 4.8b±1.03 for the T1 group, and 7.3c±1.42 for the negative (infertile) control group.\n\nThe IHC score of VEGF-1 expression in ovarian tissue from four treatments is shown in Figure 7 and Table 2. As shown in Table 2, the average score of VEGF-1 expression (brown) was 10.8c±1.55 for the positive (fertile) control group, 8.7b±0.48 for the T2 group, 0.4a±0.52 for the T1 group, and 0.2a±0.42 for the negative (infertile) control group.\n\nThe IHC score of the GDF-9 expression in ovarian tissue from four treatments is shown in Figure 8 and Table 2. As shown in Table 2, the average score of the GDF-9 expression (brown) was 5.8c±1.47 for the positive control group (fertile rats), 4.6b±0.97 for the T2 group, 0.5a±0.53 for the T1 group, and 0.3a±0.48 for the negative control group (infertile rats).\n\nThe microscopic examination from five different angles showed that the T2 group had a repaired tissue ovary. As shown in Figure 9, an improvement in ovarian tissue regeneration and Graafian follicle count was detected via microscopic examination with 400× magnification using HE staining of rat ovarian tissue from the four treatment groups. The positive (fertile) control group exhibited a Graafian follicle without hemorrhage, congestion, hemosiderin, or deposition of fibrin in the ovaries. The T2 group exhibited the regeneration of intact ovaries despite hemorrhage in some areas; however, a Graafian follicle had developed. The T1 group showed ovarian congestion and severe hemorrhage, although follicles were developed. Moreover, no Graafian follicle was observed. The negative (infertile) control group exhibited ovarian congestion, severe hemorrhage, and hemosiderin because of blood cell lysis (brownish yellow) with fibrin deposition, which indicated the presence of chronic congestion (pink colour); no follicles or Graafian follicle had developed.\n\nA. Positive (fertile) control group showed Graafian follicle ( ), with an average count of 8.9c±0.74; B. T2 group, ovaries begin to regenerate and become intact despite the presence of hemorrhage () in some areas, but a Graafian follicle () was observed with an average count of 4.5b±0.71; C. T1 group, ovarian congestion (), severe hemorrhage (), and growing follicles () were observed, but no Graafian follicle was found (0.5a±0.53); D. Negative (infertile) control group, ovarian congestion (), severe hemorrhage (), and visible hemosiderin () caused by blood cell lysis (brownish yellow) with fibrin deposition () were observed, indicating that chronic congestion occurred (pink) without growing follicles or Graafian follicle (0.4a±0.52).\n\nA Graafian follicle count for ovarian tissue from each of the four treatments was conducted using HE staining (Figure 9 and Table 2). As shown in Figure 9, the Graafian follicle count obtained by microscopic examination at 400× magnification using HE staining of rat ovarian tissue from each of the four treatments were as follows: the positive (fertile) control group displayed an average count of 8.9c±0.74; the T2 group displayed an average count of 4.5b±0.71; the T1 group showed growing follicles but no Graafian follicle (=0.5a±0.53); the negative (infertile) control group showed no growing follicles nor Graafian follicle (=0.4a±0.52).\n\n\nDiscussion\n\nLow O2 tension is a crucial element in the stem cell microenvironment, 15 which is important for stem cells self-renewal, viability, and proliferation stability. In this research, the effect of low O2 on cell proliferation was observed on the basis of morphological analysis of MSCs. After the third passage on the second day of culturing under low O2, cells exhibited a larger cell size, fewer cell deaths, and a slower proliferation rate; meanwhile, cells in the normoxic culture exhibited a smaller size, higher cell deaths, and faster proliferation rate (Figure 1). This research was consistent with a previous study, 28 which reported that the slow proliferation of stem cells is necessary for the inhibition of senescence cells or rapidly aging cells. Another study has reported that rapid proliferation is needed to achieve cell confluence and prevent cell deaths. 15\n\nThe results of this research indicated that low O2 can inhibit apoptosis. Based on real-time PCR, the expression of HSP27 and caspase-3 was detected. This result indicated significantly increased HSP27 and decreased caspase-3 expressions in cells in vitro cultured with low oxygen tension (O2 1%, p<0.05) compared with those in cells cultured under normoxic conditions, which served as the control (Figures 2 and 3). This research was consistent with a previous study, 15 which reported that low O2 had a significant effect on apoptotic resistance, as indicated by the expression of HSP27. The study indicated that low O2 could reduce apoptosis by increasing HSP27 expression and decreasing caspase-3 expression. Caspase-3 is a marker of apoptosis; thus, a decrease in caspase-3 indicated that low O2 could reduce apoptosis. 20\n\nFurthermore, IHC of cells cultured under low-O2 (O2 1%) conditions until 72 h exhibited a small number of apoptotic cells (5%) compared with those cultured under a normoxic condition (O2 21%), which showed an apoptotic cell number of 25% (Figure 4). The study results were supported by several studies that stated that under low-O2 (O2 1%) conditions, the stem cells decreased the level of apoptosis. 21 , 22 The incidence of apoptosis was between 2.45% and 2.55% under low O2 for 24, 48, and 72 h compared with a number of cells that were cultured under normoxic (O2 21%) conditions, in which the apoptotic cell number reached 12.5%. 23 , 24 In vitro culture of stem cells required the same treatment as those maintained in vivo because stem cells require a hypoxic condition (a low concentration of O2) to maintain self-renewal, 25 viability, 26 and slow proliferation based on the location and type of the stem cells. 27 , 28\n\nA low-O2 culture of stem cells maintained the proliferation rate 25 and viability 26 and achieved self-renewal because stem cells require a low-O2 concentration. 29 – 31 Hematopoietic stem cells require an O2 concentration of 0%–5%; 24 adipose stem cells require an O2 concentration of 5%; 32 neural stem cells require an O2 concentration of 1%–5%; 33 cord blood requires an O2 concentration of 3%, 34 and MSCs require an O2 concentration of 0.5%–3%. 35\n\nIn nearly every type of tissue that makes up the body of multicellular creatures, stem cells may be considered as an undifferentiated cell. 36 However, in this study, endogen stem cells cannot repair ovarian tissues under chronic conditions because of severe malnutrition. Therefore, stem cell transplantation from an in vitro culture that simulates endogenous stem cells under low oxygen conditions is a potential therapy option. This research investigated an in vitro culture of stem cells under 1% oxygen. 37\n\nStem cells have two unique characteristics: first, stem cells can renew or regenerate themselves by replicating identically through cell division. Secondly, stem cells can differentiate from other cells. Stem cells can develop into various types of mature cells, such as nerve, heart muscle, skeletal muscle, and pancreatic cells; 38 female gametes; 39 and male gametes. 17 This research focuses on female gamete cells. Low O2 is important for stem cells to maintain their differentiation ability, and plasticity. 40 , 41 Therefore, a low-O2 culture can promote the survival, strong attachment, and integration of stem cells into the microenvironment of original cells to achieve successful therapy.\n\nThis study reported that MSCs culture can improve the fertility of female rats with malnutrition-induced. The success of the therapy was determined on the basis of six parameters: (1) increased expression of HSP70 as a chaperone molecule for the repair of cell protein and inhibition of apoptosis, (2) decreased expression of caspase-3 for the inhibition of apoptosis, (3) increased expression of VEGF-1 as a marker of viability, (4) increased expression of GDF-9 as a marker of differentiation, (5) regeneration of ovarian tissue as evidenced by the intact structure of ovarian tissue and the development of follicles, and (6) improvement of the Graafian follicle count.\n\nBased on the result of this study, the first parameter for successful therapy was the IHC average score of the HSP70 expression in ovarian tissue from the four treatment groups (Figure 5 and Table 2). HSP70 expression increased under T2 treatment (O2 1%). Although this increase was inconsistent with that of the positive control group (fertile rats), this increase improved ovarian failure caused by malnutrition, as evidenced by the increase of follicle growth and Graafian follicle count. The chaperone protein HSP70 must be produced at optimal levels to heal injured cells (not exceeding the levels necessary for cell repair)\n\nHSP70 is a protein that is strongly expressed when exposed to oxidative stressors such reactive oxygen species. This study found that malnutrition caused oxidative stress. Overexpressed HSP70 could be found in damaged cells. 42 The expression of HSP70 as a chaperone molecule promotes the activity of endogenous stem cells to improve the development of follicles and Graafian follicle. Both follicle types contain the ovum and estrogen hormone which are important for female reproduction. Previous studies on male rats have shown that male gametes, also known as spermatogonia stem cells, which are found in mouse testicles, can develop into progenitor cells after transplantation. 17 In this study, the expression of HSP70 in T2 (O2 1%) improved the development of follicles and Graafian follicle of the ovaries, which was significantly different from the result of the negative control (infertile rats), but these advancements were still not on par with the positive control (fertile rats).\n\nThe second parameter for successful therapy was based on the average IHC score of caspase-3 expression (Figure 6 and Table 2). The caspase-3 expression decreased under T2 treatment (O2 1%). The decrease was consistent with that of the positive (fertile) control group, which led to an improvement in ovarian damage caused by malnutrition, as evidenced by an enhancement in follicular growth and Graafian follicle count. Oxidative stress caused by malnutrition triggers apoptosis via an inherent route in the mitochondrial component of cells. The intrinsic route requires mitochondrial activity because of the activation and release of the caspase protein into the cytosol caused by oxidative stress. A protease, namely caspase, can disassemble protein chains. In this study, malnutrition-induced oxidative stress could be due to cytochrome binding to apoptotic protease-activating factor-1 (APAF-1) released from the mitochondria; then procaspase-9 can activate caspase-9. 43 Caspase-9, which serves as an apoptosis initiator, is dimerized, which triggers feedback by inhibiting BCL-2 release and then binds to procaspase-3 to activate caspase-3. Then, as an executor, caspase-3 aids in the activation of cytoplasmic and endonuclease, which may fragment nuclear DNA and break down cytosol proteins in cells. The production of apoptotic bodies, which contain intracellular organelles, express phosphatidylserine, and cause phagocytosis, is the ultimate stage of fragmentation, thereby causing cell failure as a constituent of the tissue. 44\n\nThe third parameter for successful therapy is based on the viability of transplanted stem cells, which is assessed on the basis of VEGF-1 expression (Figure 7 and Table 2). VEGF-1 expression increased under T2 treatment (O2 1%). Although this increase was not consistent with the positive control group (fertile rat), it could improve ovarian damage caused by malnutrition, as evidenced by the increase in follicular growth and Graafian follicle count. VEGF-1 as a marker of viability of transplanted stem cells is expressed in ovarian tissue. 21\n\nThe fourth parameter for successful therapy is based on the expression of GDF-9 (Figure 8 and Table 2). GDF-9 expression increased under T2 treatment (O2 1%). Although this increase was not consistent with the positive control group (fertile rats), it could improve ovarian damage caused by malnutrition. The growth of ovarian cortical cells is induced by the progenitor cell marker GDF-9, which is produced from germline stem cells. 21 , 45 Stem cells rapidly develop into cells that are required to respond to damage and strengthen the immune response. 46 The oocyte produces GDF-9, a growth factor that is a member of the TGF-ß family. GDF-9 is essential for folliculogenesis and fertility. 47 In addition, progenitor germ cells can address issues with folliculogenesis caused by malnutrition by repairing damaged follicles and can restore molecular communication in ovarian follicles by increasing the synthesis of SCF and GDF-9. 21 Oogenesis can activate homing directly through the activation of cells that have been repressed and indirectly through the stimulation of the microenvironment (niche) of injured cells. 48\n\nThe fifth and sixth parameters for determining the success of therapy are based on the regeneration of ovarian tissue and improvement of the Graafian follicle count (Figure 9 and Table 2). In the positive (fertile) control group, the Graafian follicle developed. In the T2 group (O2 1%), the ovaries began to regenerate and appeared intact, and a Graafian follicle was observed despite hemorrhage in some areas. In the T1 group (O2 1%), ovarian congestion and severe hemorrhage were observed, and no Graafian follicle was found despite the presence of follicles. In the negative (infertile) control group, ovarian congestion and severe hemorrhage were observed, and blood cell lysis produced hemosiderin, which is brownish-yellow and deposits fibrin, indicating the occurrence of chronic congestion (pink colour), with no development of follicles or the Graafian follicle.\n\nOvarian tissue regeneration showed an intact ovarian tissue structure with the development of follicles and a Graafian follicle. This result indicated the effectiveness of the therapy using stem cells cultured under low O2 tension (1%). In this study, the regeneration of the ovarium was observed microscopically with HE staining. 49 Microscopic observation showed stem cell therapy cultured under low-O2 tension (1%, T2) achieved ovarian tissue repair. Improvements were found on the basis of the formation of follicles and a Graafian follicle and the regeneration of ovarian tissue. The positive control group (fertile rat), which did not experience ovarian failure and maintained a normal condition with developing follicles and a Graafian follicle, was contrasted with these advances (Figure 9). The degenerative ovarian tissue of the negative (infertile) control group of rats was compared with the aberrant characteristics of the damaged ovarian tissue. The latter demonstrated chronic congestion with ovarian congestion, severe hemorrhage, and hemosiderosis (yellow brown) caused by hemolysis of red blood cells with fibrin deposition (Figure 9).\n\n\nConclusions\n\nOvarian treatment with MSCs cultured under low-O2 tension could improve ovarian failure caused by malnutrition in female rats based on increased HSP70 expression and decreased caspase-3 expression as apoptotic inhibitors, increased VEGF1 and GDF-9 expression as markers of viability and differentiation, regeneration of ovarian tissue, and improved count of Graafian follicle.", "appendix": "Data availability\n\nFigshare: Graafian follicle count data sets, as well as HSP70, Caspase-3, VEGF-1, and GDF-9 results. https://doi.org/10.6084/m9.figshare.20440575. 50\n\nThis project contains the following underlying data:\n\n- Data availability.xlsx (Graafian follicle number data and Caspase-3, GDF-9, HSP70 and VEGF scores)\n\nFigshare: ARRIVE Checklist MSCs therapy. https://doi.org/10.6084/m9.figshare.20440509. 51\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe Faculty of Veterinary Medicine, Universitas Airlangga, provided the research facilities, and the chairman and staff of LIPJPHKI helped with the grammar check and Prof. Dr. R. Heru Prasetyo, dr., MS., SpParK, for his assistance in this research. The author would like to express his gratitude to all of them.\n\n\nReferences\n\nLindvall O, Kokaia Z: Recovery and rehabilitation in stroke: Stem cells. Stroke. 2004; 35(11): 2691–2694. Publisher Full Text\n\nBlurton-Jones M, Kitazawa M, Martinez-Coria H, et al.: Neural stem cells improve cognition via BDNF in a transgenic model of Alzheimer disease. PNAS. 2009; 106(32): 13594–13599. PubMed Abstract \| Publisher Full Text\n\nVolarevic V, Arsenijevic N, Lukic ML, et al.: Concise review: Mesenchymal stem cell treatment of the complications of diabetes mellitus. Stem Cells. 2011; 29(1): 5–10. PubMed Abstract \| Publisher Full Text\n\nKenichiro H, Noritoshi N, Takashi I, et al.: Adrenomedullin enhances therapeutic potency of mesenchymal stem cells after experimental stroke in rats. Stroke. 2005; 6(36): 853–858.\n\nShah VK, Shalia KK: Stem cell therapy in acute myocardial infarction: A pot of gold or Pandora's box. Stem Cells Int. 2011; 2011: 536758. Publisher Full Text\n\nKitchen SG, Zack JA: Stem cell-based approaches to treating HIV infection. Curr. Opin. HIV AIDS. 2011; 6(1): 68–73. PubMed Abstract \| Publisher Full Text\n\nSafitri E, Hariadi M: Comparison of biotechnological culture of hypoxia-conditioned rat mesenchymal stem cells with conventional in vitro culture of normoxia-conditioned rat mesenchymal stem cells for testicular failure therapy with low libido in rats. Vet World. 2019; 12(6): 916–924. PubMed Abstract \| Publisher Full Text\n\nZhao X, Wan W, Zhang X, et al.: Spermatogonial stem cell transplantation in large animals. Animals. 2021; 11(4): 918. PubMed Abstract \| Publisher Full Text\n\nSafitri E, Purnobasuki H, Purnama MTE, et al.: Effectiveness of forest honey (Apis dorsata) as therapy for ovarian failure causing malnutrition. F1000Res. 2022; 11(512): 512. Publisher Full Text\n\nHafez ESE, Hafez B: Reproduction in farm animal. Philadelphia:Lippincott Williams & Wilkins;7th ed2010.\n\nLiu H, Wei LK, Jian XF, et al.: Isolation, culture and induced differentiation of rabbit mesenchymal stem cells into osteoblasts. Exp. Ther. Med. 2018; 15(4): 3715–3724. PubMed Abstract \| Publisher Full Text\n\nCakici C, Buyrukcu B, Duruksu G, et al.: Recovery of fertility in azoospermia rats after injection of adipose-tissue-derived mesenchymal stem cells: The sperm generation. Biomed. Res. Int. 2013; 10(12): 1–18.\n\nScaradavou A, Smith KM, Hawke R, et al.: Cord blood units with low CD34+ cell viability have a low probability of engraftment after double unit transplantation. Biol. Blood Marrow Transplant. 2010; 16(4): 500–508. PubMed Abstract \| Publisher Full Text\n\nMonsefi M, Fereydouni B, Rohani L, et al.: Mesenchymal stem cells repair germinal cells of seminiferous tubules of sterile rats. Iran J. Reprod. Med. 2013; 11(7): 537–544. PubMed Abstract\n\nMulyani SWM, Setiawati EM, Safitri E, et al.: The role of heat shock protein 27(HSP 27) as inhibitor apoptosis in hypoxic conditions of bone marrow stem cell culture. Dent. J. 2014; 47(1): 41–44.\n\nGalleu A, Riffo-Vasquez Y, Trento C, et al.: Apoptosis in mesenchymal stromal cells induces in vivo recipient-mediated immunomodulation. Sci. Transl. Med. 2017; 9(416): 7828.\n\nSafitri E, Utama S, Widiyatno TV, et al.: Auto-regeneration of mice testicle seminiferous tubules due to malnutrition based on stem cells mobilization using honey. Asian Pac. J. Reprod. 2016; 5(1): 31–35. Publisher Full Text\n\nSzablowska-Gadomska I, Zayat V, Buzanska L: Influence of low oxygen tension on expression of pluripotecy genes en stem cells. Acta Neurobiol. Exp. 2011; 71: 86–93. PubMed Abstract\n\nPrasetyo RH, Safitri E: Effects of honey to mobilize endogenous stem cells in efforts intestinal and ovarian tissue regeneration in rats with protein energy malnutrition. Asian Pac. J. Reprod. 2016; 5(3): 198–203. Publisher Full Text\n\nSamik A, Safitri E: Mycotoxin binders potential on histological of ovary mice exposed by zearalenone. Vet World. 2017; 10(31): 353–357. PubMed Abstract \| Publisher Full Text\n\nSafitri E, Widiyatno TV, Prasetyo RH: Honeybee product therapeutic as stem cells homing for ovary failure. Vet World. 2016; 9(11): 1324–1330. PubMed Abstract \| Publisher Full Text\n\nJosé VSS, Monnerat G, Guerra B, et al.: Bone-marrow–derived mesenchymal stromal cells (MSC) from diabetic and nondiabetic rats have similar therapeutic potentials. Arq. Bras. Cardiol. 2017; 109(6): 579–589. PubMed Abstract \| Publisher Full Text\n\nEleotério RB, Sepúlveda RV, Reis ECC, et al.: Isolation, expansion and differentiation of mesenchymal stromal cells from rabbits’ bone marrow. Pesqui. Vet. Bras. 2016; 36(5): 423–430. Publisher Full Text\n\nPrasetyo RH: Infeksi Parasit Usus Oportunistik. 1st ed.Surabaya Indonesia:Airlangga University Press;2015.\n\nPalermo R: Differential actions of FSH and LH during folliculogenesis. Reprod. Biomed. Online. 2007; 15(3): 326–337. Publisher Full Text\n\nRazi M, Najafi G, Feyzi S, et al.: Histological and histochemical effects of Gly-phosate on testicular tissue and function. Iran J. Reprod. Med. 2012; 10(3): 181–192. PubMed Abstract\n\nNowak M, Madej J, Dziegiel P: Intensity of COX2 expression in cells of soft tissue fibrosarcomas in dogs as related to grade of tumour malignancy. Bull. Vet. Int. Pulawy. 2007; 51: 275–279.\n\nTsai CC, Chen YJ, Yew TL, et al.: Hypoxia inhibits senescence and maintains mesenchymal stem cell properties though down-regulation of E2A-p21 by HIF-TWIST. Blood J. Hematol. 2011; 117(2): 459–469.\n\nSafitri E: Effect of low oxygen tension on transcriptional factor OCT4 and SOX2 expression in New Zealand rabbit bone marrow-derived mesenchymal stem cells. Vet. World. 2020; 13(11): 2469–2476. PubMed Abstract \| Publisher Full Text\n\nArrieta CN, Silberstain SL: The science behind the hypoxic niche of hematopoietic stem and progenitors. Am. Soc. Hematol. 2014; 2014: 542–547. Publisher Full Text\n\nSimsek T, Kocabas F, Zheng J, et al.: The distinct metabolic profile of hematopoietic stem cells reflects their location ina hypoxic niche. Stem Cells. 2010; 7(9): 380–390.\n\nZhang CC, Sadek HA: Hypoxia and metabolic properties of hematopoietic stem cells. Antioxid. Redox Signal. 2014; 20(12): 1891–1901. PubMed Abstract \| Publisher Full Text\n\nMantymaa A: The effects of hypoxic conditions on the chondrogenic differentiation of adipose stem cells. Institute of Medical Technology: University of Tampere;2010. Master’s Thesis.\n\nMannello F, Medda V, Tonti GA: Hypoxia and neural stem cells: from invertebrates to brain cancer system cells. Int. J. Dev. Biol. 2011; 55(6): 569–581. PubMed Abstract \| Publisher Full Text\n\nYan F, Yao Y, Chen L, et al.: Hypoxic preconditioning improves survival of cardiac progenitor cells: Role of stromal cell derived factor-1α–CXCR4 axis. PLoS One. 2012; 7(7): e37948–e37948. PubMed Abstract \| Publisher Full Text\n\nRosová I, Dao M, Capoccia B, et al.: Hypoxic preconditioning results in increased motility and improved therapeutic potential of human mesenchymal stem cells. Stem Cells. 2008; 26(8): 2173–2182. PubMed Abstract \| Publisher Full Text\n\nHu X, Yu SP, Fraser JL, et al.: Transplantation of hypoxia-preconditioned mesenchymal stem cells improves infarcted heart function via enhanced survival of implanted cells and angiogenesis. J. Thorac. Cardiovasc. Surg. 2008; 135(4): 799–808. PubMed Abstract \| Publisher Full Text\n\nZakrzewski W, Dobrzyński M, Szymonowicz M, et al.: Stem cells: Past, present, and future. Stem Cell Res. Ther. 2019; 10(1): 68. Publisher Full Text\n\nPrasetyo RH, Hestianah EP: Honey can repairing damage of liver tissue due to protein energy malnutrition through induction of endogenous stem cells. Vet. World. 2017; 10(6): 711–715. PubMed Abstract \| Publisher Full Text\n\nChow DC, Wenning LA, Miller WM, et al.: Modeling pO(2) distributions in the bone marrow hematopoietic compartment. II. Modified Kroghian models. Biophys. J. 2001; 81(2): 685–696. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMa T, Grayson WL, Fröhlich M, et al.: Hypoxia and stem cell-based engineering of mesenchymal tissues. Biotechnol. Prog. 2009; 25(1): 32–42. PubMed Abstract \| Publisher Full Text\n\nNiu P, Liu L, Gong Z, et al.: Overexpressed heat shock protein 70 protects cells against DNA damage caused by ultraviolet C in a dose-dependent manner. Cell Stress Chaperones. 2006; 11(2): 162–169. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBratton SB, Salvesen GS: Regulation of the Apaf-1– caspase-9 apoptosome. J. Cell Sci. 2010; 123(19): 3209–3214. PubMed Abstract \| Publisher Full Text\n\nGuerrero AD, Schmitz I, Chen M, et al.: Promotion of caspase activation by caspase-9-mediated feedback amplification of mitochondrial damage. J. Clin. Cell Immunol. 2012; 03(3): 1000126. Publisher Full Text\n\nCarabatsos MJ, Elvin J, Matzuk MM, et al.: Characterization of oocyte and follicle development in growth differentiation factor-9-deficient mice. Dev. Biol. 1998; 204(2): 373–384. PubMed Abstract \| Publisher Full Text\n\nDussaubat C, Brunet JL, Higes M, et al.: Gut pathology and responses to the microsporidium nosemaceranae in the honey bee Apis mellifera. PLoS One. 2012; 7(5): 1–12. Publisher Full Text\n\nFilho FLT, Baracat EC, Lee TH, et al.: Aberrant expression of growth differentiation factor-9 in oocytes of polycystic ovary syndrome. J. Clin. Endocrinol. Metab. 2001; 87: 1337–1344.\n\nLee HJ, Salesniemi K, Niikura Y, et al.: Bone marrow transplantation generates immature oocytes and rescues long-term fertility in a preclinical mouse model of chemotherapy-induced premature ovarian failure. J. Clin. Oncol. 2007; 25(22): 3198–3204. PubMed Abstract \| Publisher Full Text\n\nDan S, Haibo L, Hong L: Review: Pathogenesis and stem cell therapy for premature ovarian failure. OA Stem Cells. 2014; 2(1): 1–8.\n\nSafitri E, Purnobasuki H, Purnama MTE, et al.: ARRIVE checklist MSCs therapy. Figshare. Dataset. 2022. Publisher Full Text\n\nSafitri E, Purnobasuki H, Purnama MTE, et al.:Datasets for Graafian follicle number, and scores of HSP70, Caspase-3, VEGF-1 and GDF-9. figshare. Dataset.2022. Publisher Full Text" }	[ { "id": "192203", "date": "26 Sep 2023", "name": "Deepa Bhartiya", "expertise": [ "Reviewer Expertise I have worked on ovarian stem cells", "MSCs", "oogenesis from stem cells in vivo" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors have studied the effects of transplanting MSCs (cultured in normal or hypoxic conditions) in rat ovaries with POF induced by fasting for 4 days. The article is not written nicely. It is not clear whether the cells were transplanted directly in the ovaries or via tail vein.\nThe concept of culturing MSCs in hypoxic conditions is not new. It is well known in literature and should be mentioned in the Introduction.\nResults are broadly described on the effects of hypoxia on MSCs and effect of MSCs on POF ovaries. These should be written under distinct subheadings to avoid confusion. No scale bars on the images. Legends mention A, B etc and the figures are not marked. CD44 markers are mentioned in Methods – but no results are described. Results in Fig 4 are not clear.\n\nIf the authors think hypoxia improves the quality of transplanted MSCs, it would be best to study conditioned medium from the two conditions (normal and hypoxic conditions) and show the difference in cytokines/ growth factors released. Transplanted MSCs provide paracrine support. It is the resident stem cells/ primordial follicle reserve that will grow when MSCs are transplanted. Hypoxic conditions led to increased HSP27, decreased Caspase expression and reduced apoptosis in the MSCs. Fig 1 – it is mentioned that yellow arrows mark cell death, but that may not be true. These could be a sub-population of stem cells that get enriched in hypoxic conditions. MUSE cells!\nThere is increased vasculature (Fig 9) in T1 and Negative (infertile) group. VEGF expression results in Fig 7 are not convincing. Will not Fig 7 C & D should show more VEGF? Which cells in Fig 7 A & B express VEGF? It is expressed by endothelial cells – not sure if the cells shown positive in Fig 7 A & B are endothelial cells. Using VEGF as a marker for viability may not be appropriate. It marks angiogenesis – not viability.\n\nSame is the case with GDF9 expression in Fig 8. It is a stem cells and oocyte marker. Not sure what cells are shown positive in the Fig.\n\nDiscussion is nothing but description of results again. All the results should be shifted to the results section and discussion should be overall. It needs to discussed how MSCs help to regenerate. Fasting resulted in the loss of follicles. How they get restored on transplantation of MSCs cultured in hypoxic conditions. Authors may refer to Bhartiya et al., (2022)1\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "205142", "date": "26 Sep 2023", "name": "Zezheng Pan", "expertise": [ "Reviewer Expertise Female reproduction" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI regret that this article cannot be aindexed due to the problems stated below.\nThis study demonstrated the protective effect of hypoxic conditions on the cell viability and differentiation capacity of bone marrow mesenchymal stem cells and confirmed the promising therapeutic potential of MSCs cultured in low O2 in rat model of malnutrition-induced ovarian failure. These works are a little innovative in providing the possibility of overcoming the original limitations of stem cell transplantation therapy for ovarian failure. This report falls short in terms of content presentation, experimental results demonstrability, legend labelling, and control group settings. Specifically, the following points:\nMisstatements: In abstract, \"Apoptotic inhibitor\" should be replaced with \"Apoptosis indicator\". In introduction, there's a misrepresentation in “Low O2 tension caused by in vitro culture reduces apoptosis, viability, and differentiation of stem cells\".\n\nThe setting of T1 and T2 experimental groups in abstract does not match the later text.\n\nCaspase 3 promotes apoptosis and is not an inhibitor of apoptosis.\n\nThere is no experimental content related to \"fertility score\" mentioned in the results.\n\nThe experimental results in Figure 1 cannot well prove the relationship between cell size, death and proliferation rate and the oxygen levels in the culture environment, you can add EDU, TUNEL and other related experiments and quantify the results after statistical analysis to increase the persuasive power of the experiment.\n\nFigure 2 and Figure 3 are missing units in the vertical coordinates (e.g., initial copy number of samples), and the normoxic environment group should be set as a control.\n\nFigure 4 does not contain the arrows depicted in the legend, the normoxic incubation group does not specify the incubation time, and the experimental data lacks statistical analysis.\n\nThe presentation of the result graphs needs to be adjusted by stitching related pictures together (e.g., Figure 3 with Figure 6)\n\nFertility test, oestrus evaluation or related hormone expression level measurement could be added to enhance the persuasiveness of the conclusion.\n\nThe title is not clearly expressed and does not accurately reflect the research content of the article; it is recommended that the title be replaced.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-24
https://f1000research.com/articles/12-1215/v1	26 Sep 23	{ "type": "Research Article", "title": "Access to health services and its influence on adherence to treatment of arterial hypertension during the COVID-19 pandemic in a Hospital in Callao, Peru: A cross-sectional study", "authors": [ "Oriana Rivera-Lozada", "Isabel Cristina Rivera-Lozada", "Cesar Antonio Bonilla-Asalde", "Isabel Cristina Rivera-Lozada" ], "abstract": "Background: Access to health services compromises therapeutic adherence in patients with arterial hypertension (HTN), which is a risk factor for cardiovascular disease and premature death. The aim of the research is to determine the influence of access to health services on adherence to antihypertensive treatment during the COVID-19 pandemic. Methods: We included a cross-sectional analytical study. A survey was applied to 241 hypertensive patients at the Daniel Alcides Carrión Hospital, Callao-Peru. Data were analyzed using SPSS software. Absolute and relative frequencies were reported and the chi-square test was applied with a statistical significance level of p<0.05. In addition, multiple logistic regression analysis was performed using the Stepwise method. Results: Our results show that non-adherence to treatment is associated with health expenses (ORa: 1.9 CI 95% 1.7-2.2), not receiving care due to lack of a doctor (ORa: 2.8 CI 95% 1.5-3.2), having difficulty with schedules (ORa: 3.7 CI 95% 2. 3-5.5), fear of receiving care at the hospital (ORa: 4.5 CI 95 % 2.7-6.8), trust in health personnel (ORa: 7.5 CI 95% 2.3-10.5) and considering that the physician does not have enough knowledge (ORa: 3.1 CI 95% 2.4-7.8).\n\nConclusion: Therapeutic adherence was associated with physician availability for care, difficulty with schedules, fear of being seen in the hospital, trust in health personnel, and waiting time.", "keywords": [ "adherence", "COVID-19", "arterial hypertension", "health services" ], "content": "Introduction\n\nNon-communicable diseases (NCDs) are the cause of 71% (41 million) deaths per year worldwide, with cardiovascular diseases being the leading cause.1 Arterial hypertension (HTN) is one of the main risk factors for the development of cardiovascular disease and is the leading cause of premature death worldwide, making it a threat to public health2 despite the fact that early detection, treatment and adequate control make it possible to reduce its morbidity, mortality and complications.3 This mainly affects middle- and low-income countries, complicating the achievement of the Sustainable Development Goals (SDGs), especially the reduction of premature deaths from NCDs by 33% by 2030.4\n\nIn Peru, according to the Demographic and Family Health Survey 2020 -ENDES 2020 - the prevalence of arterial hypertension in the population aged 15 years and older is 16.4%, with notorious differences between males (21.3%) and females (12%),5 where 68% of the population with the disease received treatment.6 In this sense, hypertension control involves risk identification, appropriate treatment, lifestyle changes and adherence to treatment.7\n\nAdherence was defined according to the World Health Organization (WHO): “The degree to which a person's behavior - taking medication, following a dietary regimen, and making lifestyle changes - corresponds to the agreed-upon recommendations of a health provider”.8 Currently, adherence to treatment is an important point for the successful control of HTN.9 However, Latin America registered heterogonous percentages associated mainly to low incomes and limitations to access to health care.10 Guzman-Tordecilla et al.11 reported medication adherence range between 46-94%. In the case of Peru, previous studies report that less than 50% of the population has optimal blood pressure levels and adherence to treatment. This situation makes them vulnerable to the development of complications such as acute myocardial infarction, stroke, among others.12–15\n\nIn this sense, non-adherence to pharmacological treatment is a serious public health problem for the control of arterial hypertension, thus challenging health systems to improve their range of services.16 In a current context of lessons learned from the COVID-19 pandemic, it is necessary to build services networks that answer to the needs of care and facilitate access to establishments with equity and quality, guaranteeing comprehensive health care in order to contribute to universal access of the population to establishments and that these act efficiently to face prevalent health problems, such as hypertension, thus protecting people’s lives. Health services must be actively involved and implement innovative strategies to ensure and effective and quick answer to recover the space lost during the COVID-19 pandemic.17\n\nLikewise, the control of hypertension can be affected by the limitations of health systems and the patient's personal factors.7 The literature mentions that access to health services can be explained thanks to facilitating elements and personal, geographic, economic, and health system barriers, among others.18,19 Our paper considers Tanahashi's definition of access to health care: “the interaction between specific aspects of service provision and the population that is influenced both by the characteristics of the health system and by the population's resources and capacities to recognize needs and seek care”.9\n\nDue to the great global impact of HTN and its complications, in addition to the partial or total interruption in access and provision of health services for non-communicable diseases in the world caused by the COVID-19 pandemic,20 it is more necessary than ever to ensure access to care for patients with HTN, since there has been a neglect of diseases other than those caused by the coronavirus from the beginning of 2020.21 This is a challenge for weak health systems and for countries with limited resources, as it implies having policies that guarantee quality and equitable care that favors adherence to treatment and control of the disease.22\n\nPeru is a country with an economy in transition that is facing important structural challenges, as well as epidemiological, demographic, technological and health risk changes, leading to the increase of chronic noncommunicable diseases that emphasize health inequities and health impacts on vulnerable populations.23 If we add the slowdown in health interventions to the situation described above as a result of the COVID-19 pandemic, all this raises challenges to the health system, where the approach to arterial hypertension and other chronic noncommunicable diseases becomes a sentinel indicator from the perspective of public health and the management of health services, becoming an expression of the good or bad that might result from the control strategies applied by the health system.24\n\nEven though several factors that contribute to nonadherence to antihypertensive treatment have been postulated,25–27 it is important to develop studies to determine the influence of the determinants of access to health services on adherence to treatment, in order to prevent complications of the disease, in addition to having an impact on improving the Peruvian health system. Therefore, the aim of the present study was to determine the influence of access to health services on adherence to antihypertensive treatment during the COVID-19 pandemic.\n\n\nMethods\n\nA cross-sectional study was carried out between September-December 2021 in patients with a medical diagnosis of HTN who were seen in the cardiology and internal medicine clinics at the Daniel Alcides Carrion National Hospital in Peru. The inclusion criteria involved people over 18 years old, totally independent of their care, with at least 6 months of treatment, reading ability, and who would agree to sign the informed consent. Patients with metabolic comorbidities that require treatment, patients with complications of HTN, patients unable to answer the survey for medical reasons, and patients who did not prefer to participate in the study were excluded. The study took as reference a population of 1200 patients, an expected adherence to the therapeutic regime of 50%, 95% confidence interval, a design effect of 1 and losses due to non-response of 20%, resulting in a sample size of 291, 241 of which met the inclusion criteria. The sampling was systematic.\n\nThe survey included sociodemographic aspects and questions on access to health services according to the Tanahashi model,9 which considers four stages in the access process to obtain quality coverage: availability, accessibility, acceptability, contact, and effective coverage. Treatment adherence was measured using the Morisky-Green test, which included the following questions: 1. Do you ever forget to take your medication? 2. Are you careless at times about taking your medication? 3. When you feel better, do you sometimes stop taking your medication? 4. Sometimes, if you feel worse when you take the medication, do you stop taking it? We consider patients with HNT treatment adherence as those who answer the questions in the established order NO/YES/NO/NO.12 The instruments were subjected to a reliability analysis, for which a pilot test was performed and a Cronbach’s Alpha of 0.88 was obtained for the Tanahashi model instrument, and a K-R of 0.85 for the Morisky-Green test.\n\nData were collected in Excel 2010 format and analyzed using SPSS 21.0 software. Descriptive analysis included frequency distribution for sociodemographic, adherence variables, and dimensions of health care access. For the bivariate analysis, contingency tableswere performed and p-values were calculated using the chi-square test. The level of statistical significance was established with a value of p<0.05.\n\nNext, a multiple logistic regression analysis was performed, using the Stepwise method, where the indicators that showed a value of p<0.05 in the bivariate analysis were added step by step. The regression equations were elaborated until no more indicators were found to contribute to the model. The advantage of this method lies in the continuous evaluation of the predictors included in the model, so that the indicator that is explained by the remaining one is eliminated.\n\nThis study was conducted following the guidelines of the Declaration of Helsinki 1964 and its subsequent amendments. In addition, the study was approved by the Research Ethics Committee of the Hospital Daniel Alcides Carrion oficio N 2131 2021-HNDAC of the Callao region, Peru. All the participants in the study signed the informed consent form before their participation and their identity was anonymized for the elaboration of the database, so their integrity was not violated.\n\n\nResults\n\nA total of 241 adult patients with a diagnosis of hypertension were analyzed, of whom 65.15 % (n=157) were female and 72.61 % (n=175) were 60 years of age or older. In addition, 52.28% (n=126) were married or cohabitant. Likewise, only 4.15% (n=10) had a university education. On the other hand, 21.99% (n=53) were not affiliated to the Public Health Insurance Scheme (SIS), 26.14% (n=3) indicated that they spent on medical consultations and 64.73% (n=156) spent on medicines. The bivariate analysis of the sociodemographic characteristics according to adherence is shown in Table 1.\n\n1 p-value estimated by chi-square test, with a significance level of p<0.05.\n\nRegarding the characteristics and availability of health services, 66.8 % (n=161) responded that they did not receive care because the physician was not available. In addition, when asked about the timely care received, 32.78% (n=79) reported not having received timely care for their consultations or examinations (29.88%, n=72). Finally, 46.89 % (n=113) responded that they did not receive any information about their disease. The bivariate analysis of the characteristics and availability of health services according to adherence is shown in Table 2.\n\n1 p-value estimated by chi-square test, with a significance level of p<0.05.\n\nRegarding accessibility, 24.48% (n=59) reported a travel time of more than 40 minutes, and the most frequently used means of transportation was the bus (78.42%, n=189). A total of 82.57% (n=199) responded that they considered that the health personnel were trained to provide care. Likewise, 58.51% (n=141) responded that they had had difficulties with administrative procedures, where the most common problem was the availability of the service (50.62%, n=122), while the least common was the lack of authorization of the service (0.41%, n=1).\n\nOn the other hand, it was found that 55.19 % (n=133) considered inadequate the time they had to wait from the time they requested their appointment until they received care. Similarly, 49.8% (n=120) reported having waited more than 60 minutes to be seen on the day of their appointment and 39% (n=94) reported not having received timely care. Regarding the economic aspect, it was found that the median loss in soles for attending a consultation was 30.00 (RIQ=20). On the other hand, 33.2% (n=80) mentioned that they pay for the consultation or service received and 13.28% (n=32) have missed their appointment or care due to monetary limitations. Finally, 82.57% (n=199) bought medicines for their treatment and 46.47% (n=112) expressed not having complied with taking such medicine due to economic precariousness. Table 3 shows the bivariate analysis of the accessibility of health services according to adherence.\n\n1 p-value estimated by chi-square test, with a significance level of p<0.05.\n\nRegarding the acceptability of health services, it was found that 88.38 % (n=213) reported that they did not feel afraid of being treated at the hospital and 96.68 % (n=233) did not feel discriminated against or rejected because of their illness. Likewise, 93.78 % (n=226) considered that the doctor had sufficient knowledge for their recovery, while 82.16 % (n=198) trusted the health personnel in general. Finally, 16.6 % (n=40) rated it as excellent, while 2.9 % (n=7) rated the medical treatment as bad. Table 4 shows the bivariate analysis of the acceptability of health services according to adherence.\n\n1 p-value estimated by chi-square test, with a significance level of p<0.05.\n\nIt was found that 34.02% (n=82) rated the quality of care as fair or very poor, while 5.81% (n=14) rated it as excellent or very good. Likewise, the quality of treatment received was perceived as fair or very poor by 8.71% (n=21) and as excellent by 27.39% (n=66) of the respondents. In addition, 70.95 % (n=171) reported that the staff answered their questions, 95.85 % (n=231) had their disease explained to them and 97.51 % (n=235) received an explanation of the indicated treatment. It was found that 92.95 % (n=224) were satisfied with the explanation provided by the health staff. Table 5 shows the bivariate analysis of the variables according to adherence.\n\n1 p-value estimated by chi-square test, with a significance level of p<0.05.\n\nMultiple logistic regression analysis according to adherence to antihypertensive treatment in the study sample.\n\nThe multiple logistic regression model found an association between adherence to antihypertensive treatment and consultation costs (ORa: 1.9, CI 95% 1,7:2,2), not receiving care because the physician was not available (ORa: 2,8, CI 95% 1,5:3,2), and fear of receiving care at the hospital (ORa: 4,5 CI 95 % 2,7:6,8). Table 6 shows all the associations found.\n\n1 p-value estimated by chi-square test, with a significance level of p<0.05.\n\n\nDiscussion\n\nIn this study, non-adherence to antihypertensive treatment reached 92.94%, this predominance of non-adherence to treatment in hypertensive patients was also reported in a study on therapeutic adherence in patients with chronic diseases, where Bertoldo et al.28 found that 38% of patients did not comply with treatment, highlighting hypertensive patients with 75% non-adherence. However, this high percentage found does not coincide with the general acceptance of therapeutic adherence which is between 50 and 70% and differs from the 37.4 % adherence reported by Quintana et al.29 or the 43.9% reported by Martinez30 using, in both cases, the same instrument.\n\nLikewise, it differs from Peruvian studies where the Morisky-Green test was also used, such as that of Carhuallanqui et al.31 who found 37.9% adherence and that of Fernández-Arias14 who found 57.4% adherence in hypertensive patients. However, the low adherence rate coincides with that found by Rosas-Chávez32 in an observational study, where they determined a 15% adherence rate, although it is still above the percentage found in the present study, this low adherence is a sample of the heterogeneity of this phenomenon in Peru, probably related to cultural, demographic and educational factors, considering that both studies were carried out in different hospitals in Lima and Callao.\n\nOn the other hand, in the United States, lack of adherence to antihypertensive treatment affects approximately 75% of patients, which implies that they do not achieve optimal blood pressure control. In addition, studies carried out in recent years show that about 50% of hypertensive patients are unable to comply with a hygienic-health regimen and to adhere correctly to pharmacological treatment, especially when these measures last for more than 1 year.33\n\nLikewise, the evidence reviewed suggests that sociodemographic characteristics such as gender and age, among others, seem to be related to adherence.25 This does not coincide with the findings of this study, since none of the sociodemographic characteristics studied was significantly associated with adherence, with the exception of family income (p=0.004), where the results showed a greater number of adherent patients (9.5%) among those with an income of between 751 and 1500 dollars. Despite the above, the percentage remains low; and expenditure on medications (p=0.002) where 100% non-adherence was found among those who do not spend on medications, probably due to the fact that those who spend on their health tend to take better care of themselves. The findings of Ruiz-Alejos et al.26 and Martínez et al.26 show that arterial hypertension predominates in the male gender, in contrast to this study, which found a predominance in the female sex (65.15%).\n\nOn the other hand, in order to study the reasons for this low adherence to antihypertensive treatment, Tanahashi suggested the need to focus attention on access to health services to identify the population that does not have access or has difficulty in doing so and to redirect actions towards them to improve primary care coverage.34 This is all the more important because of the asymptomatic nature of hypertension and, therefore, in many cases it is detected as a finding in a routine examination and most patients are unaware that they suffer from hypertension,35 so early detection of hypertension is crucial in Peru and relies mainly on routine blood pressure control in patients who come for consultation. However, this is not consistent with what was found in this study, because although 82.99% of patients had their blood pressure checked at the time of consultation, it was not found that receiving such control was significantly associated with adherence (p=0.168). It also differs from what was reported by Gabert et al.,27 in that study, which also refers to the scarcity or deterioration of resources and personnel to carry out an adequate diagnosis, as in the present study, since the unavailability of the physician to provide care (p<0.001), as well as the availability of the services (p=0.001), not knowing the location of some services such as the laboratory (p=0.024) and the hygienic state of the environments where care was received (p=0.004) were associated with therapeutic adherence.\n\nIn addition, adherence may also be compromised by the patient's confidence in receiving care and his or her relationship with the health care provider,36 demonstrating that fear of receiving care in the hospital is associated with adherence (p<0.001).\n\nIt is important to mention the importance of patient follow-up after the first visit to control the progression of the disease and reduce the possible risk factors that the patient presents, taking into account the cardiovascular risk, which should also be evaluated at the first visit. Carrying out the aforementioned can be complicated by the availability of patients who work or fulfill obligations that demand a large part of their day,37 this coincides with what was found in this study, since the timetable difficulty was associated with adherence (p<0.001) as well as the waiting time to receive an appointment (p=0.018) and to be seen on the scheduled day (p=0.014).\n\nOther authors, such as Gabert27 and Owolabi38 raised the availability and accessibility of adequate medications as important barriers to the management of hypertension, similar to what has been found in other studies on access to treatment in other chronic diseases, all of which coincides with the results of this study that identified as factors associated with adherence the means of transportation (p<0.001) and difficulty with administrative procedures (p=0.002). As consequence, in this study, not having received timely care was related to adherence (p=0.009).\n\nLikewise, the family plays a fundamental role in compliance with the therapeutic regimen, providing support in seeking care and, in many cases, assuming a leadership role during treatment.29 However, no significant association was found between therapeutic adherence and family or acquaintance support (p=0.428), This could be explained by the lack of specificity of the question in the Morisky-Green test, since it does not have a question directed to this point and the closest questions are marital status and a question related to the difficulty of a family member or neighbor knowing about the patient's health, which leaves little or no information available to study this possible relationship.\n\nThe limitations of the present study include: First, the methodologic design of our study does not allow us to estimate a causal relationship. Second, we used a nonprobabilistic sampling method. This limits generalizing the conclusion because our sample could not be representative. Finally, our results cannot be extrapolated to different populations.\n\nDespite these limitations, the present study provides a first scope of the influence of access to health services on adherence, which will contribute evidence for larger studies.\n\n\nConclusions\n\nThe adherence to antihypertensive treatment evaluated in our study sample is associated with family income, medicine expenses, availability of the physician for care, means of transportation, difficulty of dates and schedules, fear of being treated in the hospital, trust in health staff, availability of services, waiting time, and receiving timely care.", "appendix": "Data availability\n\nZenodo: Access to health services and its influence on adherence to treatment of arterial hypertension during the COVID-19 pan-demic in a Hospital in Callao, Peru: A Cross-Sectional Study, https://doi.org/10.5281/zenodo.8299902. 39\n\nThis project contains the following underlying data:\n\n- DATABASE_.xlsx (dataset)\n\nZenodo: Access to health services and its influence on adherence to treatment of arterial hypertension during the COVID-19 pan-demic in a Hospital in Callao, Peru: A Cross-Sectional Study, https://doi.org/10.5281/zenodo.8299902. 39\n\nThis project contains the following extended data:\n\n- Survey (a copy of the questionnaire)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nRoth GA, Abate D, Abate KH, et al.: Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980–2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet. 2018; 392: 1736–1788. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStanaway JD, Afshin A, Gakidou E, et al.: Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: a systematic analysis for the Global Burden of Disease Stu. Lancet (London, England). 2018; 392: 1923–1994. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Hypertension. WHO; 2021. (accessed on 15 April 2022). Reference Source\n\nPrograma de las naciones unidas para el desarrollo: Objetivos de Desarrollo Sostenible. PNUD; 2020. (accessed on 07 June 2022). Reference Source\n\nBadara S, Nina D, Sania N, et al.: Prevention and management of chronic disease: a litmus test for health-systems strengthening in low-income and middle-income countries. Lancet (London, England). 2010; 376: 1785–1797. Publisher Full Text\n\nInstituto Nacional de Estadistica e Informatica: Enfermedades no transmisibles y transmisibles 2020. INEI; 2020. (accessed on 02 April 2022). Reference Source\n\nHernández-Vásquez A, Santero M: New 2017 ACC/AHA hypertension guideline: Implications for a Latin American country like Peru. Eur. J. Prev. Cardiol. 2019; 26: 668–670. PubMed Abstract \| Publisher Full Text\n\nOrganizacion Mundial de la Salud: Adherencia a los tratamientos a largo plazo - Pruebas para la acción. OMS; 2004. (accessed on 30 April 2022). Reference Source\n\nWorld Health Organization: Cardiovascular diseases (CVDs). WHO; 2021. (accessed on 05 March 2022). Reference Source\n\nGarcía-Reza C, Landeros ML, Zeitoune RCG, et al.: Rol socioeconómico y la adhesión al tratamiento de pacientes con hipertensión arterial - contribución de enfermería. CUIDARTE. 2012; 3: 280–286. Publisher Full Text\n\nGuzman-Tordecilla D, Bernal García A, Rodríguez I: Interventions to increase the pharmacological adherence on arterial hypertension in Latin America: a systematic review. Int. J. Public Health. 2020; 65: 55–64. PubMed Abstract \| Publisher Full Text\n\nRuiz E, Ruiz H, Guevara L, et al.: Factores de riesgo cardiovascular en mayores de 80 años. Horiz Med (Barcelona). 2015; 15: 26–33. Publisher Full Text\n\nZavala-Loayza JA, Benziger CP, Cárdenas MK, et al.: Characteristics Associated With Antihypertensive Treatment and Blood Pressure Control: A Population-Based Follow-Up Study in Peru. Glob. Heart. 2016; 11: 109–119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFernández-Arias M, Acuña-Villaorduna A, Miranda J, et al.: Adherence to pharmacotherapy and medication-related beliefs in patients with hypertension in Lima, Peru. PLoS One. 2014; 9: e112875. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSarki AM, Nduka CU, Stranges S, et al.: Prevalence of Hypertension in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis. Medicine (Baltimore). 2015; 94: e1959. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMalta DC, Gomes CS, Stopa SR, et al.: Inequalities in health care and access to health services among adults with self-reported arterial hypertension: Brazilian National Health Survey. Cad Saude Publica. 2022 May 20; 38(Suppl 1): e00125421. PubMed Abstract \| Publisher Full Text\n\nBasu S: Non-communicable disease management in vulnerable patients during Covid-19. Indian J. Med. Ethics. 2020 Apr-Jun; 05(2): 103–5. NS. Publisher Full Text\n\nMaimaris W, Paty J, Perel P, et al.: The influence of health systems on hypertension awareness, treatment, and control: a systematic literature review. PLoS Med. 2013; 10: e1001490. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhatib R, Schwalm JD, Yusuf S, et al.: Patient and healthcare provider barriers to hypertension awareness, treatment and follow up: a systematic review and meta-analysis of qualitative and quantitative studies. PLoS One. 2014; 9: e84238. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOrganización Mundial de la Salud: La COVID-19 afecta significativamente a los servicios de salud relacionados con las enfermedades no transmisibles. OMS; 2020. (accessed on 20 June 2022). Reference Source\n\nOrganización Mundial de la Salud/Organización Panamericana de la Salud: La COVID-19 afectó el funcionamiento de los servicios de salud para enfermedades no transmisibles en las Américas. OMS; 2021. (accessed on 18 June 2022). Reference Source\n\nAdauy H, Angulo P, Sepúlveda J, et al.: Barreras y facilitadores de acceso a la atención de salud: una revisión sistemática cualitativa. Rev Panam Salud Pública. 2013; 33: 223–229. Publisher Full Text\n\nHerrera-Añazco P, Pacheco-Mendoza J, Valenzuela-Rodríguez G, et al.: Autoconocimiento, adherencia al tratamiento y control de la hipertensión arterial en el Perú: una revisión narrativa. Rev. Peru. Med. Exp. Salud Pública. 2017; 34(3): 497–504. Publisher Full Text\n\nTzelios C, Contreras C, Istenes B, et al.: Using digital chatbots to close gaps in healthcare access during the COVID-19 pandemic. Public Health Action. 2022 Dec 21; 12(4): 180–185. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlfian SD, Annisa N, Fajriansyah F, et al.: Modifiable Factors Associated with Non-adherence to Antihypertensive or Antihyperlipidemic Drugs Are Dissimilar: a Multicenter Study Among Patients with Diabetes in Indonesia. J. Gen. Intern. Med. 2020; 35: 2897–2906. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRuiz A, Carrillo R, Bernabé A: Artículo Original Prevalencia E Incidencia De Hipertensión Arterial En Perú: Revisión Sistemática Y Metaanálisis Prevalence and Incidence of Arterial Hypertension in Peru: a Systematic Review and. Rev. Peru. Med. Exp. Salud Publica. 2021; 38: 521–529. PubMed Abstract \| Publisher Full Text\n\nGabert R, Ng M, Sogarwal R, et al.: Identifying gaps in the continuum of care for hypertension and diabetes in two Indian communities. BMC Health Serv. Res. 2017; 17: 846. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBertoldo P, Ascar G, Campana Y, et al.: Cumplimiento terapéutico en pacientes con enfermedades crónicas. Rev. Cuba. Farm. 2013; 47.\n\nQuintana C, Fernandez-Britto E: Adherencia terapéutica farmacológica antihipertensiva en adultos de atención primaria y factores relacionados con su incumplimiento. Rev. Cuba. Investig. Biomed. 2009; 28.\n\nde Murga Gustavo , Sujo M, Estevez A: Adherencia farmacológica en pacientes hipertensos. Rev. Cuba. Med. Gen. Integr. 2020; 36: 982.\n\nCarhuanllanqui R, Diestra-Cabrera G, Tang-Herrera J, et al.: Adherencia al tratamiento farmacológico en pacientes hipertensos atendidos en un hospital general. Rev. Medica Herediana. 2010; 21: 21. Publisher Full Text\n\nRosas-Chavez G, Romero-Visurraga CA, Ramirez-Guardia E, et al.: El grado de alfabetización en salud y adherencia al tratamiento en pacientes con hipertensión arterial en un hospital nacional de Lima, Perú. Rev. Peru. Med. Exp. Salud Publica. 2019; 36: 214–221. PubMed Abstract \| Publisher Full Text\n\nTagle R, Acevedo M: Objetivos terapéuticos en hipertensión arterial: metas de presión arterial en los diversos subgrupos de hipertensos. Rev. Médica Clínica Las Condes. 2018; 29: 21–32. Publisher Full Text\n\nTanahashi T: Health service coverage and its evaluation. Bull. World Health Organ. 1978; 56: 295–303. PubMed Abstract\n\nOrganizacion Mundial de la Salud: Hipertensión. OMS; 2021. (accessed on 18 May 2022). Reference Source\n\nVan Der Laan DM, Elders PJM, Boons CCLM, et al.: Factors associated with antihypertensive medication non-adherence: A systematic review. J. Hum. Hypertens. 2017; 31: 687–694. PubMed Abstract \| Publisher Full Text\n\nMINSAP: Programa del médico y enfermera de la familia. 1st ed. La Habana, Cuba: Publisher; 2011.\n\nOwolabi M, Olowoyo P, Miranda JJ, et al.: Gaps in Hypertension Guidelines in Low- and Middle Income Versus High Income Countries: a Systematic Review. Hypertens. 2016; 68: 1328–1337. (accessed on 11 June 2022). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRivera-Lozada O, Rivera-Lozada IC, Bonilla-Asalde CA: Access to health services and its influence on adherence to treatment of arterial hypertension during the COVID-19 pan-demic in a Hospital in Callao, Peru: A Cross-Sectional Study. [Dataset]. 2023. Publisher Full Text" }	[ { "id": "210111", "date": "17 Nov 2023", "name": "Hans Contreras Pulache", "expertise": [ "Reviewer Expertise Public health", "epidemiology." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI consider this work to be adequately supported, with a noteworthy level of methodological detail. Furthermore, it is likely that this study will become a fundamental reference for education and research in Peru (given its original focus on the subject matter). To further enrich the discussion, I suggest adding a paragraph in the discussion section that alludes to the low prevalence of treatment adherence (less than 10%) and the implications this has for future designs, specifically what parameters would be recommended for consideration regarding sample size calculations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "210110", "date": "22 Feb 2024", "name": "Salomon Huancahuire-Vega", "expertise": [ "Reviewer Expertise public health" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting work on the influence of access to health services on adherence to antihypertensive treatment during the COVID-19 pandemic in a Peruvian hospital. This work is well planned, uses good instruments to measure the variables, and reports important data to take into consideration so that patients can have better adherence to treatment. However, there are some aspects of the manuscript that remain unclear and imprecise, and that must be clarified and corrected: 1. In the summary, results section, 6 characteristics associated with adherence are mentioned. It is understood from the description that these associations were obtained from the regression analysis; however, in Table 6 (logistic regression) 8 associations are mentioned. Why not mention the two missing ones? (considers the environment clean, difficulty with procedures) 2. Similarly, in the results section (multiple logistic regression analysis) (page 10) only three associations are mentioned. 3. In the conclusion of the abstract and the manuscript, waiting time is mentioned as an element associated with treatment adherence, however, this result is not shown in the regression analysis. 4. In the methodology section, according to the calculation of the sample size mentioned, this was not achieved. Why was this not achieved? This should be mentioned as a limitation of the study. 5. The description of the dimensions of the instrument used to measure access to health services indicates: availability, accessibility, acceptability, contact, and effective coverage. However, there are no results for the last dimension. 6. In the results section it is mentioned that 4.5% of participants had a university education, however, table 1 indicates 57.26% 7. The report of results in tables 2 – 5 focuses on percentages according to the responses to each question of the instruments. It would be more interesting and the information in these tables would be better utilized if their description focused on the significance obtained from the bivariate analysis. 8. Why was the characteristic “expenses in the consultation” included in the multiple regression analysis if this characteristic did not show a significant association in the bivariate analysis (table 1)? 9. The data in Table 6 show the adjusted OR values. It would be interesting to show the raw ORs and mention which characteristics were considered to make the adjusted analysis. 10. The discussion section should focus in more detail on those elements or characteristics that were shown to have an influence on treatment adherence (from the regression analysis), rather than the prevalence of treatment adherence. 11. It would be interesting to add to the discussion what the implications of the results of this study would be, as well as mention other limitations of the study. For example, since the study was done during a pandemic, it was important to have information on how many of the participants had the infection. 12. The conclusion of the work mentions “family income”, “means of transportation” and “waiting time” as elements associated with adherence, however, this is not reported in the results section. These inaccuracies must be corrected in the different sections of the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1215
https://f1000research.com/articles/13-115/v1	19 Feb 24	{ "type": "Research Article", "title": "Morphometry of the thyroid cartilage, epiglottis and piriform sinus: An anatomical study", "authors": [ "Rajanigandha Vadgaonkar", "Ashwin R. Rai", "Chettiar Ganesh Kumar", "B.V. Murlimanju", "Mangala M. Pai", "Latha V. Prabhu", "Amit Agrawal", "Rajanigandha Vadgaonkar", "Ashwin R. Rai", "Chettiar Ganesh Kumar", "Mangala M. Pai", "Latha V. Prabhu", "Amit Agrawal" ], "abstract": "Background The larynx is a complex organ for voice production, and respiration consists of a series of cartilages, membranes, muscles, and joints with a considerable range of flexibility and mobility. Understanding the laryngeal framework is important for various professionals, including phoneticians, speech therapists, oncologists, and oto-rhino-laryngologists. The goal was to measure the piriform sinus, epiglottis, and thyroid cartilage in our sample population.\n\nMethods This study included 22 adult embalmed cadavers available in the Department of Anatomy. Dimensions were measured using a digital Vernier caliper.\n\nResults The mean height of the thyroid laminae was 27 ± 1.4 mm at the right side and 25.5 ± 1.4 mm at the left side. Mean width of the thyroid lamina was 27.1 ± 1.3 mm at the right side and 27.4 ± 0.9 mm at the left side. The mean thickness of thyroid cartilage was found to be 4.4 ± 0.4 mm and 3.9 ± 0.5 mm over the right and left sides. The mean length, width and thickness of the epiglottis were 29.1 ± 0.5 mm, 22.2 ± 0.6 mm and 2.6 ± 0.3 mm correspondingly. The height, width and thickness of the right piriform sinus were 25 ± 0.5 mm, 14.2 ± 0.5 mm and 12.6 ± 0.5 mm, the same parameters were 25.3 ± 1.3 mm, 15.1 ± 0.7 mm and 13.3 ± 0.4 mm for the left side.\n\nConclusions The morphometric data reported in this study are enlightening for clinicians involved in laryngeal and endoscopic procedures. Some of the parameters showed statistically significant differences between the right and left sides (p<0.05). However, the limitation is that the smaller sampler size being studied in this anatomical research, and the data will only be accurate with a larger sample size.", "keywords": [ "endoscopy", "morphometry", "otorhinolaryngology", "piriform sinus" ], "content": "Introduction\n\nThe larynx is a complex organ for voice production and respiration, which is supported by a series of cartilages, membranes, muscles, and joints. They bring about movement of vocal cords with a considerable range of mobility.1 Apart from the phonating mechanism, it also serves as a sphincter or watch dog of the lower respiratory tract. Knowledge of laryngeal anatomy is important for various professionals, such as phoniatricians, speech therapists, oncologists, and otorhinolaryngologists. Understanding the laryngeal framework is mandatory for constructing biomechanical models for voice disorders that require accurate laryngeal dimensions. The thyroid cartilage forms a bulky structure in front of the laryngeal wall that protects the highly vibrating vocal cords located directly behind it. Because of its strength and power of resistance, it provides valuable protection to the laryngeal architecture. It has two quadrilateral laminae that are fused anteriorly in the lower two thirds leaving a ‘V’ shaped laryngeal notch superiorly. The fused anterior borders form a subcutaneous thyroid angle (laryngeal prominence) that is more prominent in males than in females. Being a hyaline cartilage, its ossification is not uncommon to the extent that, in old age, the cartilage may fracture on lateral compression or may compress backward against the vertebral column, as in strangulation or hanging. Injury to this cartilage warrants immediate attention, as subsequent laryngeal edema may lead to respiratory impairment.1\n\nThe epiglottis is shaped like a leaf, projecting into the lumen of the pharynx, posteroinferior to the tongue, and hyoid bone. It is an elastic cartilage belonging to the larynx. In animals, the epiglottis serves the additional function of olfaction as well.2 It develops from the 4th pharyngeal arch.3,4 There is scant information in the literature about the dimensions of the epiglottis in adults. However, cadaveric studies are scarce, particularly in the Indian population. The morphometric data of the epiglottis are clinically important as there are changes in the dimensions of the epiglottis in epiglottitis.\n\nAnatomically, the piriform sinus is a hidden area, the malignancies of which would initially cause fewer symptoms, and the patient often presents late to the hospital. It has richer lymphatic drainage, which drains into the jugulodigastric lymph nodes. Malignancy in the piriform sinus can cause distant metastasis with a higher frequency. The piriform sinus is a part of the hypopharynx; however, it is more studied along with the larynx. The piriform sinus is pear shaped space form the cavity of laryngopharynx along with the ventricle of larynx.5 They are thought to add to the acoustic uniqueness of the voice.6 However, they are important because of the capacity to store the food and liquid for the temporary period.7 If there is any obstruction in the food passage, due to the irritation in the laryngopharynx, pooling of saliva occurs in the piriform fossa, which is known as ‘Jackson’s sign’. During food swallowing, particles such as chicken and fish bones could be impacted within the piriform sinus and may lead to dysphagia. This is an indication for endoscopic removal under general anesthesia.8 The management of entrapped foreign bodies by endoscopic removal requires clinical training and skill. Inadvertent removal of the foreign body and inappropriate manipulation can cause injury to the internal laryngeal nerve, which is present deep in the piriform sinus. Injury to this nerve can cause anesthesia of the larynx above the level of the vocal cords, and may lead to the entry of food particles inside the larynx. If this continues, food particles may pass to the trachea and lungs, the accumulation of which can manifest as aspiration pneumonia. It has been reported that, the dimensions of piriform fossae have impact in the pitch of the voice particularly in the singers.5 Due to all these implications, the anatomical knowledge of piriform sinus is essential to the anaesthesiologist and otorhinolaryngologist.\n\nData on the dimensions of the thyroid cartilage, epiglottis, and piriform fossa are essential for anesthesiologists during laryngoscopy and endotracheal intubation. However, they are scarce in scientific literature. Few studies have measured the thyroid cartilage, piriform fossa, and epiglottis in our sample population. In this context, the goal of this study was to determine the dimensions of the thyroid cartilage, epiglottis, and piriform sinus in embalmed cadavers of an Indian sample population.\n\n\nMethods\n\nThis anatomical study comprised of 22 adult embalmed human cadavers; the sample size was calculated as described in literature.9 A digital Vernier caliper (Mitutoyo, Japan, 0-150 mm 500-196) was used to perform the measurements. height, width, and thickness of the thyroid cartilage, epiglottis, and piriform fossa were also measured. The measurements were taken at their maximum diameter, and for the thyroid cartilage and piriform fossa, readings were taken separately over the right and left sides. Specimens were excluded if there were any associated pathological changes. The data are presented as mean ± standard deviation, and the side-based comparison of the right and left sides was performed using the paired t-test. The most recent version of the SPSS (version 27) software was used for statistical analysis. Sex-based comparisons and age-wise segregation were not performed in the present study.\n\nThe measurements performed in the thyroid cartilage, epiglottis of the larynx, and piriform fossa in the present study are shown in the represented diagrams (Figures 1, 2, and 3, respectively).\n\na. Photograph of the ventral view of thyroid cartilage showing the measurement of height (AB) and width (CD); b. dorsal aspect of the thyroid cartilage showing the measurement of thickness (EF).\n\nThe measurements are represented as AB: length of the epiglottis, CD: with of the epiglottis, EF: thickness of the epiglottis.\n\nThe measurements performed in this study are represented as AB: supero inferior diameter of the piriform sinus, CD: medio lateral diameter of the piriform sinus, EF: antero posterior diameter of the piriform sinus.\n\nThis study was approved by the institutional ethics committee of our institution (Approval Committee Name: Institutional Ethics Committee, Kasturba Medical College, Mangalore, Approval Number: IEC KMC MLR: 02/2022/61, dated 17.02.2022). We confirm that consent was obtained from the body donors to conduct medical research on their bodies upon death. The protocol for this anatomical study has already been published with the dx.doi.org/10.17504/protocols.io.ewov1q5dpgr2/v1.\n\n\nResults\n\nThe morphometric data of the thyroid cartilage obtained in the present study are presented separately for the right and left sides in Table 1. The mean height of the thyroid laminae was 27 ± 1.4 mm on the right side and 25.5 ± 1.4 mm on left side. The mean width of the thyroid lamina was 27.1 ± 1.3 mm on right side and 27.4 ± 0.9 mm on the left side. The mean thickness of thyroid cartilage was found to be 4.4 ± 0.4 mm and 3.9 ± 0.5 mm on right and left sides. The height and thickness were greater on the right side than on the left side. The difference was statistically significant (p<0.05). There was no statistically significant difference observed with respect to the width (p>0.05). The dimensions of the epiglottis obtained in this study are listed in Table 2. The mean length, breadth and the thickness of the epiglottis were 29.1 ± 0.5 mm, 22.2 ± 0.6 mm and 2.6 ± 0.3 mm respectively.\n\n Significance, p > 0.05.\n\nThe dimensions of the piriform fossa obtained in the present study are given separately for the right and left sides in Table 3. The height, width and thickness of the right piriform sinus were 25 ± 0.5 mm, 14.2 ± 0.5 mm and 12.6 ± 0.5 mm respectively. The same parameters were 25.3 ± 1.3 mm, 15.1 ± 0.7 mm and 13.3 ± 0.4 mm for the left side. It was statistically observed that the width and thickness were greater on the left side than on the right side (p < 0.05). No significant difference was observed in the height of the piriform fossa between the right and left sides (p > 0.05).\n\n* Significance, p > 0.05.\n\n\nDiscussion\n\nThe knowledge of laryngeal anatomy has a range of applications including in clinical practice when we examine a patient to make a diagnosis, and whenever he carries out treatment in the form of a manipulation or an operation as well as for professionals (such as singers) when a speech therapist can explore the relevant anatomy for voice training.10 The increasing frequency of surgical, radiological, and electrophysiological procedures performed over the larynx has led to the importance of anatomical dimensions of the larynx and its cartilages.9,11 It cannot be overstated that morphometric data are essential, and there is depth knowledge that can facilitate procedures such as intubation, stenting, and endoscopic procedures of the upper aerodigestive tract.12 The measurements of cartilages of the larynx are also essential to manage the subglottic and post-intubation stenosis of the lower respiratory tract.13 The morphometry of the cartilages of the larynx can also be enlightening in the planning of surgical interventions of the larynx. It also has implications for placing the electrodes during the electromyography of the larynx and the interpretation of CT and MRI scans of the larynx.9\n\nStudies on laryngeal cartilage measurements have proven to be a boon in the fields of laryngeal anthropometry, physiology, imaging, and surgery. Hajiiannaou et al.14 reported that a rotated thyroid cartilage with a dislocated superior cornu protruding in the pyriform fossa of the same side may lead to globus pharyngeus, dysphagia, and odynophagia, thereby stressing the importance of laryngeal symmetry. Eckel et al.9 reported the average height of thyroid lamina to be 27.4 ± 2.47 mm over the right and 27.6 ± 2.32 mm over the left side in adult male cadavers. In the same study the average measurements in females were 22.2 ± 2.85 mm over the right side and 22.1 ± 2.67 mm over the left side, which was seen to be a little less. In a study conducted by Zrunek et al.,15 there was a 10% to 30% increase in the dimensions of laryngeal cartilage in males when compared to females. Park et al.16 reported that the dimensions of the thyroid cartilage can assist in sex determination. Similar findings have also been reported by Ajmani et al.17 and Lang et al.18 In a study done by Jain and Dhall,11 most of the dimensions of the thyroid and cricoid cartilage were higher in males than in females. They also reported obliquity of the thyroid laminae in both the sagittal and horizontal planes, thereby contributing to the increased angulation in females. They also observed asymmetry in the thyroid angle in 25% of the specimens, which deviated on either the right or left side. Kaur et al.,19 in a study conducted in 30 cadaveric adult larynges, reported similar findings of increased parameters among men. The present study compared the data of the right and left thyroid cartilages. However, sex-based comparisons were not performed in our study.\n\nThe dimensions of the epiglottis are essential for anesthesiologists and ear nose throat surgeons. The length and width of epiglottis in an infant has been reported to be 13.15 ± 0.44 mms and 8.92 ± 0.3 mms respectively.20 The ultrasound thickness of epiglottis measured 2.4 ± 0.2 mm in a Chinese population.21 According to American sonographic research by Werner et al.,22 the epiglottic thickness was 2.39 ± 0.15 mm. The present study from the cadaver specimen reported a mean thickness of 2.6 ± 0.3 mm, which is similar to these reports. Werner et al.22 endorsed that the epiglottis is thicker in the male than in other structures of the body. The present study could not perform a gender-based comparison, which is a limitation of this study.\n\nMorphometric dimensions of the piriform fossa are educative to doctors of anesthesiology and laryngeal surgery because this is the location of entrapment of foreign particles such as fish and chicken bones during eating. The foreign body must be removed endoscopically, as this may cause infection and difficulty in swallowing. The morphology of the piriform fossa is also important to determine its acoustic properties.23 In this perspective, dimensions of the piriform sinus will help in the manufacture of the flexible fiber optic endoscopic instruments, which can match to that particular population. The present study provides morphometric data for the piriform sinus on the right and left sides. The length, width, and thickness are also provided. However, the data of the present study cannot be considered as a morphological database of our sample population, as the sample size was small. However, this sample size cannot represent the population subgroup of the entire country.\n\n\nConclusions\n\nThe present anatomical research presents the morphometric data of the thyroid cartilage, epiglottis, and piriform fossa in cadaveric samples of our sample population, which will help compare them with other populations. These data will guide the manufacture of endoscopic devices and endotracheal tubes with respect to our sample population. However, the limitation of this study is the small sample size; the data will only be accurate with a larger sample size.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Morphometry of the thyroid cartilage, epiglottis and piriform sinus, an anatomical study’, https://doi.org/10.6084/m9.figshare.24455329.v1\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nAnson BJ, McVay CB: Surgical Anatomy. 5th ed.WB Saunders; 1971; 255.\n\nNegus VE: The evidence of comparative anatomy on the structure of the human larynx. Proc. R. Soc. Med. 1937; 30(11): 1394–1396. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAdamiec E, Dzięciołowska-Baran E, Czerwiński F, et al.: Prenatal development of the human trachea. Folia Morphol. (Warsz). 2002; 61(2): 123–125. PubMed Abstract\n\nFayoux P, Marciniak B, Devisme L, et al.: Prenatal and early postnatal morphogenesis and growth of human laryngotracheal structures. J. Anat. 2008; 213(2): 86–92. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDelvaux B, Howard D: A new method to explore the spectral impact of the piriform fossae on the singing voice: benchmarking using MRI-based 3D-printed vocal tracts. PLoS One. 2014; 9(7): e102680. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKitamura T, Honda K, Takemoto H: Individual variation of the hypopharyngeal cavities and its acoustic effects. Acoust. Sci. Technol. 2005; 26(1): 16–26. Publisher Full Text\n\nStandring S: Gray’s anatomy: the anatomical basis of clinical practice. 40th ed.London: Churchill Livingstone/Elsevier, London; 2008.\n\nGuo YC, Tai SK, Tsai TL, et al.: Removal of unapproachable laryngopharyngeal foreign bodies under flexible videolaryngoscopy. Laryngoscope. 2003; 113(7): 1262–1265. PubMed Abstract \| Publisher Full Text\n\nEckel HE, Sittel C, Zorowka P, et al.: Dimensions of laryngeal framework in adults. Surg. Radiol. Anat. 1994; 16(1): 31–36. Publisher Full Text\n\nDavis EDD: The applied anatomy and physiology of the pharynx and oesophagus. Ann. R. Coll. Surg. Engl. 1948; 3(3): 139–153. PubMed Abstract\n\nJain M, Dhall U: Morphometry of the thyroid and cricoid cartilages in adults on C.T. scan. J. Anat. Soc. Ind. 2010; 59(1): 19–23. Publisher Full Text\n\nRandestad A, Lindholm CE, Fabian P: Dimensions of the cricoid cartilage and the trachea. Laryngoscope. 2000; 110(11): 1957–1961. PubMed Abstract \| Publisher Full Text\n\nAjmani ML: A metrical study of the laryngeal skeleton in adult Nigerians. J. Anat. 1990; 171: 187–191. PubMed Abstract\n\nHajiioannou JK, Florou V, Kousoulis P: Superior thyroid cornu anatomical variation causing globus pharyngeous and dysphagia. Case Rep. Med. 2010; 2010: 142928.\n\nZrunek M, Happak W, Hermann M, et al.: Comparative anatomy of human and sheep laryngeal skeleton. Acta Otolaryngol. 1988; 105(1-2): 155–162. PubMed Abstract \| Publisher Full Text\n\nPark DK, Kim DI, Lee UY, et al.: Morphometric analysis of the Korean thyroid cartilage for identification of sex: metric study. Korean J. Phys. Anthropol. 2003; 16(3): 129–136.\n\nAjmani ML, Jain SP, Saxena SK: A metrical study of laryngeal cartilages and their ossification. Anat. Anz. 1980; 148(1): 42–48. PubMed Abstract\n\nLang J, Fischer K, Nachbaur S: Uber Masse, Form und Formvarianten der Cartilagines thyreoidea et cricoidea [Measurements, form and form variants of the thyroid and cricoid cartilages]. Gegenbaurs Morphol. Jahrb. 1984; 130(5): 639–657.\n\nKaur R, Kumar R, Laxmi V: The morphology and morphometry of adult human thyroid cartilage - a cadaveric study in North Indian population. CIB. Tech. Journal of Surgery (Online). 2014; 3(1): 18–26.\n\nSavkovic A, Delic J, Isakovic E, et al.: Age characteristics of the larynx in infants during the first year of life. Period. Biol. 2010; 112(1): 75–82.\n\nChau CW, Chan HH, Wong CP, et al.: Sonographic measurement of the epiglottis in normal Chinese adults. Hong Kong J. Emerg. Med. 2010; 17(5): 429–434.\n\nWerner SL, Jones RA, Emerman CL: Sonographic assessment of the epiglottis. Acad. Emerg. Med. 2004; 11(12): 1358–1360. PubMed Abstract \| Publisher Full Text\n\nDang J, Honda K: Acoustic characteristics of the piriform fossa in models and humans. J. Acoust. Soc. Am. 1997; 101(1): 456–465. PubMed Abstract \| Publisher Full Text" }	[ { "id": "252283", "date": "28 Mar 2024", "name": "Deise Maria Furtado de Mendonça", "expertise": [ "Reviewer Expertise Clinical Anatomy and Medicine" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWe conducted a thorough review of the manuscript titled \"Morphometry of the thyroid cartilage, epiglottis, and piriform sinus: An anatomical study.\" The study aimed to determine the dimensions of the thyroid cartilage, epiglottis, and piriform sinus in embalmed cadavers from an Indian sample population. The paper offers a detailed morphological and morphometric analysis and establishes significant clinical correlations.\nThe findings are valuable for professionals in various fields, including otolaryngologists, oncologists, intensive care physicians, anesthesiologists, speech therapists, and phoniatricians, as well as for comparisons with studies in other populations. The results are succinct, and the discussion section effectively places the findings in the context of existing literature.\nUnfortunately, a comparative analysis between males and females was not feasible, as acknowledged by the authors themselves as a study limitation. Nevertheless, the absence of this comparison does not diminish the significance of the presented data.\nSome minor points for improvement include: - Correcting the word \"width\" in the description of Figure 2. - The conclusions should address the differences between the right and left sides in terms of length, width, and thickness, and clinically discuss the implications of these measurements.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11375", "date": "19 Jun 2024", "name": "B.V. Murlimanju", "role": "Author Response", "response": "We thank the reviewer for the expert opinion. As per the suggestion, the conclusions were revised. The typographical error was corrected." } ] } ]	1	https://f1000research.com/articles/13-115
https://f1000research.com/articles/13-276/v1	15 Apr 24	{ "type": "Case Report", "title": "Case Report: Adenoid cystic carcinoma of tongue", "authors": [ "Dolly Rai", "Deepankar Shukla", "Nitin Bhola", "Deepankar Shukla", "Nitin Bhola" ], "abstract": "Surgery is the primary treatment approach for head and neck cancers, while radiotherapy is considered for advanced tumors in higher T-stages and as an adjunct therapy for cases with positive histopathological margins. Some authors argue that radiotherapy represents the sole option for managing advanced and unresectable cancers. This report focuses on the impact of concurrent chemoradiotherapy in patients diagnosed with adenoid cystic carcinoma (ACC) of the tongue. ACC is a malignant tumor originating from the salivary glands, characterized by slow progression, perineural invasion, and a likelihood of local recurrence. It accounts for approximately 10% to 15% of all head and neck malignancies, primarily affecting the minor salivary glands in the palate. The incidence rate of ACC in the base of the tongue is 8.8%. Our case report involves a patient diagnosed with ACC of the tongue, specifically presenting a lesion on the left side of the base of the tongue. The treatment modality employed was concomitant chemo-radiotherapy, and a follow-up assessment was conducted one month after completing the treatment. The objective of this report is to enhance prognostic outcomes and improve the quality of life for the patient undergoing chemoradiotherapy as a treatment for ACC involving the base of the tongue.", "keywords": [ "Adenoid cystic carcinoma", "tongue", "treatment. Radiotherapy", "Chemotherapy" ], "content": "Introduction\n\nAdenoid cystic carcinoma (ACC) is a relatively uncommon tumor of the salivary glands that originates from epithelial cells. It represents approximately 5% to 10% of all malignant salivary gland tumors and accounts for 10% to 15% of all tumors in the head and neck region.1 31% of these tumors are found in the minor salivary glands, particularly in the palate. However, they can also occur in the major salivary glands such as the submandibular and parotid glands.2 ACC can also develop in other areas of the head and neck region, including the tracheobronchial tree, esophagus, lacrimal gland, and tongue. The occurrence of ACC in the base of the tongue is relatively rare.\n\nACC exhibits a wide age distribution, commonly affecting individuals in their fifth and sixth decades of life, with a higher prevalence in females.3 This type of cancer typically progresses slowly and is characterized by the infiltration of nerves, the potential for distant spread, and a significant likelihood of local recurrence.4 Prognostic factors encompass the stage of the disease, the location of the tumor, the presence of a solid growth pattern, the size of the lesion, the status of surgical margins, and the occurrence of intraneural and/or perineural invasion. Histologically, ACC manifests in three distinctive patterns: cribriform, tubular, and solid. Notably, the solid variant carries a particularly unfavorable prognosis, whereas the cribriform variant is associated with a more favorable outcome. The tubular type, in comparison to all three variants, is expected to demonstrate the most favorable prognosis.5\n\nThe tumor’s neurotropism is indicated by its gradual advancement and extensive infiltration around nearby nerves.6 Perineural invasion can occur through either the spaces surrounding the nerves or within the nerves themselves. Lymphatic dissemination is rare, although there have been instances of tumor spreading through the bloodstream. Metastases to the lungs and bones are probable. The occurrence of ACC in the base of the tongue is 8.8%, whereas it is only 2.9% in the anterior two-thirds of the tongue.7\n\nAdvanced ACC lesions located at the base of the tongue commonly exhibit significant infiltration with perineural invasion. The preferred treatment approach for such cases involves extensive surgical excision, which unfortunately has an impact on swallowing and speech abilities. Since ACC is a tumor that demonstrates resistance to radiation, radiotherapy is considered as an adjunctive therapy for advanced lesions. However, several authors have reported unfavorable outcomes for radiation treatment of advanced and inoperable ACC tumors. In fact, the local control rates in these cases are documented to be below 50%.7 Conversely, the efficacy of chemotherapy in achieving conclusive results remains inconclusive. Despite the frequent use of definitive chemoradiotherapy, the therapeutic outcomes have been unsatisfactory. This discussion presents a case of ACC affecting the tongue, along with a concise overview of the relevant literature concerning its clinical, pathological, and therapeutic implications.\n\n\nCase report\n\nA 75-year-old male from Yavatmal, as shown in Figures 1 and 2, arrived at the Department of Oral and Maxillofacial Surgery, Sharad Pawar Dental College seeking treatment for a painful ulcer that has not healed on the posterior region of the left side of his tongue for approximately two months. The patient has a documented case of hypertension for the past ten years and has been taking 5 mg tablet of Amlodipine once daily. Additionally, the patient has a habit of chewing tobacco four to five times a day for approximately 25 years. The patient had no relevant family medical history. For about a year, the patient has experienced a burning sensation when consuming hot and spicy foods. Furthermore, the patient is having difficulties with chewing and swallowing, and has been experiencing earaches on the same side for the past two months. There is no record of any nerve-related sensations such as tingling or numbness.\n\nThe facial appearance exhibits no noticeable imbalances, and the lips are well-formed and move smoothly and synchronously. During examination, a palpable lymph node is detected on the left side of the jaw, measuring approximately 2 x 1 cm. It has an oval shape, firm texture, and is fixed in place, but does not cause any pain. Intraoral evaluation reveals that the patient has a mouth opening of 24 mm, and both the upper and lower jaws are missing teeth. In the posterior region of the tongue on the left side, there is a single painful ulcerous and proliferative lesion. Its dimensions are approximately 3 cm in size, extending from the posterior one-third of the tongue towards the posterior end, although the full extent cannot be determined. It stretches from the midline to the lateral border of the left side of the tongue. The lesion appears reddish-pink in color, with edges that are turned outward, an irregular surface, and poorly defined borders. Palpation of the lesion reveals tenderness, firmness, and a hardened texture.\n\nThe patient has received an incisional biopsy (Figure 3) indicating adenoid cystic carcinoma with a tubular pattern. The pattern of invasion (POI) was 03, with the worst POI being 04. The depth of invasion (DOI) could not be determined due to the absence of surface epithelium. The lymphocytic response score was 03. Muscle invasion was detected, while lymph-vascular and perineural invasion were not present. Salivary gland invasion was observed.8 Direct video laryngoscopy was performed to visualize the posterior extent of the lesion (Figure 4).\n\nAfter conducting the biopsy, a magnetic resonance imaging (MRI) examination of the tongue was performed. The results revealed an area of modified signal intensity on the left half of the tongue, appearing brighter on FatSat and exhibiting similar brightness on T1-weighted and T2-weighted images. The dimensions of this area were measured to be 4.9 x 4.6 x 2.1cm, involving the intrinsic muscles of the tongue along with the genioglossus, hyoglossus, palatoglossus, and styloglossus on the left side. The lesion extended from the dorsum, reaching the alveolar ridge on the sides and crossing the midline septum posteriorly with an invasion depth of 2.9cm. The lingual tonsil and uvula were affected posteriorly, leading to the obliteration of the left side of the oropharynx. Fortunately, the mylohyoid muscle below appeared to be unaffected. Additionally, multiple lymph nodes of various sizes, ranging from sub-centimeter to centimeter, were detected in the submental, bilateral submandibular, and upper jugulodigastric regions. The largest lymph node measured 1 x 0.7cm and was observed in the right submandibular region (see Figures 5 and 6).\n\nThe high-resolution computed tomography (HRCT) thorax examination revealed the presence of numerous fibrotic changes beneath the pleura, accompanied by localized thickening of the pleura in both the upper and lower lobes. Additionally, a few lymph nodes exhibiting a sub-centric appearance were observed in the paratracheal, pre-vascular, and aorta-pulmonary regions. Based on these findings, the preliminary diagnosis made was carcinoma originating from the base of the tongue, categorized as pT3N2cM0, stage IV A.\n\nThe patient was recommended to undergo a surgical procedure involving the complete removal of the lesion and a significant portion of the tongue, with wide surgical margins. However, the patient expressed unwillingness to undergo any surgical intervention. As a result, the chosen treatment approach for this case was definitive chemoradiotherapy. This was planned within one month of the patient’s initial admission. This involved receiving a total dose of 70 Gy/weekly of radiation therapy, delivered in 35 fractions to both the face and neck regions using the intensity modulated radiation therapy (IMRT) technique. The patient has completed 30 fractions of radiotherapy and has also received 6 cycles of weekly injections of cisplatin, each at a dosage of 50 mg. The patient is currently undergoing treatment and has been in good health for the past month since the treatment started (refer to Figures 7 and 8).\n\n\nDiscussion\n\nAdenoid cystic carcinoma (ACC) is a locally aggressive tumor characterized by its infiltrative growth pattern and perineural invasion. Despite undergoing rigorous surgical resection, ACC has a high recurrence rate and tends to metastasize late. The five-year survival rate for patients with ACC is approximately 70%.9 While the lung is the most common site of distant metastasis, occurrences in the bone, liver, kidney, and prostate have also been reported.10\n\nIn a study conducted by Luna-Ortiz et al.,11 out of 68 patients with head and neck ACC, eight patients (seven females and one male) were diagnosed with ACC of the tongue, accounting for 11.7% of all head and neck ACC cases. Specifically, six cases were located at the base of the tongue, while two were in the oral tongue. Generally, the clinical history of ACC in the tongue presents as asymptomatic, with gradual submucosal tumor growth. The diagnosis is often delayed, ranging from 6 months to 8 years from the initial onset of symptoms.12 In the current study, there was an 8-month delay in diagnosing ACC in the tongue. Tumors affecting the oral tongue tend to be detected earlier due to their impact on normal functioning, whereas tumors in the base of the tongue are typically identified at later stages.\n\nRegional lymph node metastases of adenoid cystic carcinoma (ACC) in the head and neck region are infrequent, occurring in only 6 to 10% of cases.13 One possible explanation for this rarity is that the two primary sites for ACC, namely the parotid gland and the palate/maxilla, have a low tendency to spread to the lymph nodes. A retrospective study conducted by Min et al.,9 involving 616 patients with ACC in the head and neck area, revealed that lesions located at the base of the tongue, mobile tongue, and floor of the mouth exhibited the highest rates of cervical lymph node metastasis (19.2%, 17.6%, and 15.3%, respectively).\n\nChen et al.14 identified several independent predictors of local recurrence in ACC. These included the absence of postoperative irradiation (P=0.007), T4 disease (P=0.0001), perineural invasion (P=0.008), and extensive involvement of nerves (P=0.02). According to Chen et al.,14 the optimal approach for successfully treating resectable ACC of the head and neck involves surgery combined with adjuvant radiation therapy at doses exceeding 60 Gy. In cases of advanced malignancies or partially resectable disease, radiotherapy alone can be employed as a standalone treatment. It is important to note that minor salivary gland ACCs located outside the major salivary glands are less amenable to surgical resection and have a lower likelihood of being cured solely through radiation therapy.15 The choice between radiotherapy alone and surgery plus radiotherapy is influenced by selection bias, as individuals with early-stage lesions are more likely to undergo surgery, while those with advanced, unresectable cancers are more inclined to receive radiotherapy as their primary treatment option.\n\nAccording to Miglianico et al.,16 although there was an improvement in local-regional control, surgery alone did not significantly enhance survival rates compared to combined modality therapy. The limited survival advantage may be attributed to the high occurrence of distant metastases. Some studies propose the use of adjuvant chemotherapy alongside radiotherapy or in combination with surgery due to the high risk of hematogenous spread. However, there is insufficient convincing evidence supporting the benefits of adjuvant chemotherapy,17 and its utilization for patients with ACCs is restricted. Concurrent chemoradiotherapy can be considered as an option for individuals with advanced disease or for organ preservation purposes, but its effectiveness in treating ACC is currently under further investigation.\n\nThe ongoing RTOG 1008 clinical trial is examining whether the addition of cisplatin to standard postoperative radiotherapy improves survival in tumors of major salivary glands with high-risk factors, including pathological staging of T3-4, N1-3, or T1-2, N0, as well as a close or positive surgical margin.18 This randomized phase II/III study includes high-grade ACC (defined as >30% solid component). While awaiting these results, some limited retrospective studies suggest the use of concurrent chemo-radiotherapy in specific patients with unfavorable pathological characteristics in salivary gland cancers.19 It is possible to draw insights from the treatment approaches employed for other head and neck malignancies and consider combining radio-sensitizing chemotherapy to enhance tumor control in certain scenarios. In such cases, it is recommended to seek a multidisciplinary consultation with medical oncology.\n\nAdvanced ACC can remain dormant over an extended period, commonly exhibiting lung metastases. The tumor stage serves as a significant prognostic indicator for both overall survival and cancer recurrence. The collective five-year survival rate for ACC varies from 64% to 89%, while the ten-year survival rate ranges from 37% to 77%.20\n\n\nConclusion\n\nAdenoid cystic carcinoma is an uncommon type of cancer that typically originates in the salivary glands but can also develop in other areas of the body, such as the breast, lung, or trachea. ACC is characterized by its slow growth and has the ability to spread to nearby tissues and organs, posing challenges for effective treatment. The symptoms experienced by individuals with ACC depend on the location of the tumor and may include pain, difficulty swallowing, and changes in voice or facial appearance. The standard treatment approach for ACC usually involves surgical removal of the tumor, followed by radiation therapy or chemotherapy to eliminate any remaining cancer cells. The prognosis for ACC varies depending on the cancer stage and the overall health of the patient. The patient has been showing a good response to the chosen modality and has reported a better quality of life.\n\nIn patients with ACC, the primary therapeutic objective is to achieve control over the cancer in the surrounding area, maintain normal bodily functions, and prevent the development of distant metastases. Early detection by the surgeon is crucial due to the slow-growing nature of these tumors and their tendency to invade extensively. Our aim is to enhance both prognostic outcomes and quality of life for affected individuals. For the majority of patients, concurrent radiation therapy remains the preferred treatment option. However, effective treatments for malignancies are scarce, and managing metastatic disease remains challenging. Consequently, survival rates have not shown significant improvement in recent years.\n\n\nConsent\n\nWritten and oral informed consent was obtained from patient for the publication of his clinical details and images. Additional informed consent was obtained from relatives of the patient for whom identifying information is included in this manuscript.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nKhan AJ, DiGiovanna MP, Ross DA, et al.: Adenoid cystic carcinoma: A retrospective clinical review. Int. J. Cancer. 2001; 96: 149–158. Publisher Full Text\n\nTriantafillidou K, Dimitrakopoulos J, Iordanidis F, et al.: Management of adenoid cystic carcinoma of minor salivary glands. J. Oral Maxillofac. Surg. 2006; 64: 1114–1120. Publisher Full Text\n\nWaldron CA: el-Mofty SK, Gnepp DR: Tumors of the intraoral minor salivary glands: a demographic and histologic study of 426 cases. Oral Surg. Oral Med. Oral Pathol. 1988; 66: 323–333. PubMed Abstract \| Publisher Full Text\n\nHuang M, Ma D, Sun K, et al.: Factors influencing survival rate in adenoid cystic carcinoma of the salivary glands. Int. J. Oral Maxillofac. Surg. 1997; 26: 435–439. PubMed Abstract \| Publisher Full Text\n\nAdenoid cystic carcinoma of the head and neck: a review - PubMed. Accessed: February 15, 2023. Reference Source\n\nLiu X, Yang X, Zhan C, et al.: Perineural Invasion in Adenoid Cystic Carcinoma of the Salivary Glands: Where We Are and Where We Need to Go. Front. Oncol. 2020 Aug 18; 10: 1493. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLuna-Ortiz K, Carmona-Luna T, Cano-Valdez AM, et al.: Adenoid cystic carcinoma of the tongue – clinicopathological study and survival analysis. Head Neck Oncol. 2009; 1: 15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHead and neck cancers—major changes in the American Joint Committee on cancer eighth edition cancer staging manual. Accessed: February 28, 2023. Publisher Full Text\n\nKim KH, Sung MW, Chung PS, et al.: Adenoid cystic carcinoma of the head and neck. Arch. Otolaryngol. Head Neck Surg. 1994; 120: 721–726. Publisher Full Text\n\nMin R, Siyi L, Wenjun Y, et al.: Salivary gland adenoid cystic carcinoma with cervical lymph node metastasis: a preliminary study of 62 cases. Int. J. Oral Maxillofac. Surg. 2012; 41: 952–957. PubMed Abstract \| Publisher Full Text\n\nLuna-Ortiz K, Carmona-Luna T, Cano-Valdez AM, et al.: Adenoid cystic carcinoma of the tongue--clinicopathological study and survival analysis. Head Neck Oncol. 2009; 1: 15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNamazie A, Alavi S, Abemayor E, et al.: Adenoid cystic carcinoma of the base of the tongue. Ann. Otol. Rhinol. Laryngol. 2001; 110: 248–253. Publisher Full Text\n\nGarden AS, Weber RS, Morrison WH, et al.: The influence of positive margins and nerve invasion in adenoid cystic carcinoma of the head and neck treated with surgery and radiation. Int. J. Radiat. Oncol. Biol. Phys. 1995; 32: 619–626. PubMed Abstract \| Publisher Full Text\n\nChen AM, Bucci MK, Weinberg V, et al.: Adenoid cystic carcinoma of the head and neck treated by surgery with or without postoperative radiation therapy: prognostic features of recurrence. Int. J. Radiat. Oncol. Biol. Phys. 2006; 66: 152–159. Publisher Full Text\n\nBalamucki CJ, Amdur RJ, Werning JW, et al.: Adenoid cystic carcinoma of the head and neck. Am. J. Otolaryngol. 2012; 33: 510–518. Publisher Full Text\n\nMiglianico L, Eschwege F, Marandas P, et al.: Cervico-facial adenoid cystic carcinoma: study of 102 cases. Influence of radiation therapy. Int. J. Radiat. Oncol. Biol. Phys. 1987; 13: 673–678. PubMed Abstract \| Publisher Full Text\n\nDiaz EM, Kies MS: Chemotherapy for skull base cancers. Otolaryngol. Clin. N. Am. 2001; 34: 1079–85. viii. Publisher Full Text\n\nRodriguez-Russo CA, Junn JC, Yom SS, et al.: Radiation Therapy for Adenoid Cystic Carcinoma of the Head and Neck. Cancers (Basel). 2021 Dec 17; 13(24): 6335. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAdjuvant Therapy for Salivary Gland Carcinomas - PubMed. Accessed: February 27, 2023. Reference Source\n\nSpiro RH, Huvos AG: Stage means more than grade in adenoid cystic carcinoma. Am. J. Surg. 1992; 164: 623–628. PubMed Abstract \| Publisher Full Text" }	[ { "id": "271234", "date": "14 May 2024", "name": "Michał Gontarz", "expertise": [ "Reviewer Expertise maxillofacial surgery", "head and neck oncology", "maxillofacial trauma" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article presents an interesting case of treatment with radiochemotherapy for advanced tongue carcinoma adenoides cysticum (AdCC). The article is well written and contains most of the necessary information about AdCC. However, the short follow-up of the patient does not allow to draw clear conclusions about the patient's treatment. I suggest some corrections to the article.\nIt would be advisable to change the abbreviation ACC to AdCC, since the abbreviation ACC is also found in the literature in relation to acinic cell carcinoma, which can be confusing. In addition, AdCC is the most common histologic type of sublingual salivary gland tumor. Please see the literature review in the article: [Ref-1]\nIn the description of radiotherapy, the term 70Gy/week may be misleading. It is my understanding that the patient received 70Gy in 35 fractions (2Gy/day, 10Gy/week).\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "267668", "date": "17 May 2024", "name": "Damian T. Rieke", "expertise": [], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Authors, I have reviewed your report on a case of ACC of the tongue. Overall, the discussion of available evidence in these rare tumor types is of interest. However, I have a few comments with regards to your work.\n1.\n\nYou describe that ACC account for 10-15% of all tumors in the head and neck region but only 5-10% of all SGC. These numbers do not add up. ACC is considered to be the second most common salivary gland tumor (but might be more common in my experience). Since ACC commonly arise in minor salivary glands, the occurrence in the base of tongue is also not infrequent (you first state that “base of tongue is relatively rare” and later “The occurrence of ACC in the base of the tongue is 8.8%...”) 2.\n\nPlease discuss additional radiation techniques such as proton therapy. 3.\n\nPlease expand the discussion of data for primary radiochemotherapy in comparison to radiotherapy alone 4.\n\nPlease provide additional detail and description of figure 3, ideally also highlighting ACC. 5.\n\nPlease introduce the lymphocytic response score 6.\n\nPlease provide data on identified risk factors (such as perineural invasion) in the patient as identified from biopsy 7.\n\nIn the conclusion you write that standard treatment involves surgery followed by radiation therapy or chemotherapy. However, you earlier describe the lack of data specifically for adjuvant chemotherapy.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-276
https://f1000research.com/articles/13-274/v1	15 Apr 24	{ "type": "Systematic Review", "title": "Influence of deep learning image reconstruction algorithm for reducing radiation dose and image noise compared to iterative reconstruction and filtered back projection for head and chest computed tomography examinations: a systematic review", "authors": [ "Obhuli Chandran M", "Saikiran Pendem", "Priya P S", "Cijo Chacko", "Priyanka .", "Rajagopal Kadavigere", "Obhuli Chandran M", "Saikiran Pendem", "Priya P S", "Cijo Chacko", "Priyanka ." ], "abstract": "Background The most recent advances in Computed Tomography (CT) image reconstruction technology are Deep learning image reconstruction (DLIR) algorithms. Due to drawbacks in Iterative reconstruction (IR) techniques such as negative image texture and nonlinear spatial resolutions, DLIRs are gradually replacing them. However, the potential use of DLIR in Head and Chest CT has to be examined further. Hence, the purpose of the study is to review the influence of DLIR on Radiation dose (RD), Image noise (IN), and outcomes of the studies compared with IR and FBP in Head and Chest CT examinations.\n\nMethods We performed a detailed search in PubMed, Scopus, Web of Science, Cochrane Library, and Embase to find the articles reported using DLIR for Head and Chest CT examinations between 2017 to 2023. Data were retrieved from the short-listed studies using Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines.\n\nResults Out of 196 articles searched, 15 articles were included. A total of 1292 sample size was included. 14 articles were rated as high and 1 article as moderate quality. All studies compared DLIR to IR techniques. 5 studies compared DLIR with IR and FBP. The review showed that DLIR improved IQ, and reduced RD and IN for CT Head and Chest examinations.\n\nConclusions DLIR algorithm have demonstrated a noted enhancement in IQ with reduced IN for CT Head and Chest examinations at lower dose compared with IR and FBP. DLIR showed potential for enhancing patient care by reducing radiation risks and increasing diagnostic accuracy.", "keywords": [ "Low dose", "Computed tomography", "Deep learning image reconstruction", "Iterative reconstruction technique", "Image quality" ], "content": "Introduction\n\nComputed tomography (CT) plays an important role in modern diagnostic radiology and assists in the identification of various complex disorders. Over the past ten years, CT scan utilization has increased significantly globally as new clinical reasons are continually identified. An estimated 375 million CT examinations are continually performed annually worldwide, with a 3-4% annual growth rate. The demands of physicians and other health care providers, as well as technology developments, have had a considerable impact on the world market for CTs. Compared to other traditional imaging modalities, CT scans offer significantly higher radiation doses (RD) despite having significant diagnostic benefits for specific patients. Adult CT scans dramatically raise cancer risk. A positive correlation between RD and cancer risks was found.1–5\n\nA recent study reported seventeen-fold variations in high-dose CT examinations among different countries. There is a four-fold variation in effective dose [ED] for Chest and abdomen examinations with less variation for CT head in adults and suggested optimization of radiation doses.6 The most recommended practice in the CT sector is to reduce CT radiation exposure as low as reasonably achievable while maintaining the Image Quality (IQ). Reducing the exposure factors of tube voltage (kVp) and tube current (mA) reduces RD but increases image noise.7,8 Up until ten years ago, Filtered back projection (FBP) was the only technique used for image reconstruction in CT. Although this method produces high-quality images it has noise issues at low doses and is prone to artifacts. Although an iterative reconstruction (IR) method was proposed in 1970, computational power restrictions prevented its widespread use in clinical settings. The Hybrid Iterative reconstruction (HIR) method was introduced in 2009 which had low computation time and allowed it to be implemented in clinical practice. The HIR combines iteratively reconstructed images in the raw data domain with FBP images to reduce image noise (IN). The first complete model-based iterative reconstruction (MBIR) received FDA approval in 2011. Compared to the HIR technique, this reconstruction minimizes artifacts and noise. However, it requires a greater computational power demand, which results in lengthy reconstruction times. IR techniques, irrespective of type produce lower IN, artifacts, or both at lower doses than FBP.9–15 However, in general, IR at higher levels of reconstruction may result in an artificial, plastic-looking, and blotchy appearance that would eventually lower the IQ and compromise the clinician’s ability to diagnose pathologies, limiting the potential for significant RD reduction.16–18\n\nDeep learning image reconstruction algorithms (DLIR) are the most recent developments in CT image reconstruction technology. DLIRs are increasingly replacing IR techniques due to their disadvantages such as negative image texture and nonlinear spatial resolutions. DLIR is based on deep convolution neural networks (CNN) which learn from the input data sets. It gains the ability to distinguish actual signal and IN through training using pairs of low and high-quality images. In comparison to FBP and IR, the trained CNNs can distinguish between noise and signal much better, allowing for better dose reduction while preserving the image quality. DLIR produces an image texture similar to that of FBP even at low doses and high strengths. DLIR technique may be able to detect the low contrast lesions at low doses without damaging the image texture.19–22 More research is required to determine the potential applications of DLIR in clinical settings. Our literature search showed there is no systematic review performed in head and chest CT examinations using Deep learning reconstruction algorithm for reducing RD and improving IQ in CT. Hence, the purpose of the article is to review the influence of DLIR on RD, IN, and outcomes of the studies compared with IR and FBP in CT Head and Chest examinations.\n\n\nMethods\n\nThis review was carried out as per the “Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA)” guidelines.23\n\nA comprehensive literature search was performed using databases such as “PubMed, Scopus, Web of Science, Cochrane Library, and Embase” to find the relevant original studies (Table 1). The MeSH terms such as “Deep Learning Image Reconstruction” “Radiation dose” “Image quality”, “Head and Chest Computed Tomography” were used (Table 2). The search was limited to the English language including both adult and paediatric populations of Head and Chest CT examinations.\n\nArticles were screened considering the Participant’s Intervention Comparison and Outcome (PICO) methodology. Case studies, case reports, conference abstracts, letters, editorial reviews, meta-analyses, or surveys were not included. The title and abstract of all the articles were independently and blindly screened by the two researchers. The articles that described a comparison of DLIR algorithms with the IR technique or FBP were included in the final review. The exclusion criteria were phantom studies, physics-based performance of DLIR, other language than English, articles with no comparison of DLIR with FBP, HIR/MBIR, and articles with no Hounsfield Unit (HU), Contrast to Noise Ratio (CNR), Signal to Noise Ratio (SNR).\n\nData from each article was assessed independently by two researchers and any differences were solved by the third researcher.\n\nTo evaluate the quality of all the included articles, the custom-made Quality Assessment (QA) scale was used.24 The list of all the questions for the quality assessment (underlying data). A score of 1 was given if the answer to the question was “yes” and each study was assigned a score ranging from 0 to 18. Based on the total scores obtained by each study, the studies were classified into three quality levels: Low- quality studies (score of 6 or lower), Moderate-quality studies (score between 7 and 11), High-quality studies (score of 12 or more).\n\n\nResults\n\nFinally, 15 articles were included (Figure 1).\n\nThe search in PubMed, Scopus, Web of Science, Cochrane Library and Embase resulted in 196 studies. 101 duplicates were removed. The title and abstract of 95 studies were assessed and 76 studies were excluded as they did not meet the inclusion criteria. A total of 19 reports were sought for retrieval. A total of the full text of 19 articles were assessed for eligibility. Among them, 4 articles were excluded (3 studies were excluded due to no comparison of DLIR with FBP and HIR/MBIR, and 1 article were excluded due to lack of HU, CNR, and SNR). Finally, 15 articles were included in the systematic review.\n\nCT imaging has increased recently with the advancement in CT technology. The studies included in the review covered different countries such as China (n = 8), Japan (n = 1), France (n = 1), Korea (n = 3), Netherland (n =1), Sweden (n = 1). The RD data and IQ parameters were collected from different CT vendors such as General Electric (GE) Health care (128, 256, 512-slice, and dual-energy CT), Siemens Healthineers (256-slice), Canon Medical system (320 and 640-slice). A total sample size of 1292 was collected from the included studies. 4 studies used prospective data collection, and 11 studies used retrospective data collection. The characteristics of the study and the outcomes of each study are summarized in Table 3.\n\nThe results of the quality assessment are summarized in Table 4. All studies compared DLR to hybrid iterative reconstruction techniques. 5 studies compared DLIR with IR and FBP algorithms. A total of 14 studies were rated as high and 1 study as moderate quality.\n\nCT head examination: We summarized the percentage IN and RD reduction for various CT examinations in Table 5. A total of five studies in CT brain that used DLIR showed a reduction in IN (18-52%) compared with IR and FBP.25–29 In the brain, a study compared SD with IR (CTDIvol-70.8 mGy & EF-2.8±0.2 mSv) and LD with DLIR (CTDIvol-53.0 mGy & ED-2.1±0.1 mSv) protocol in adult CT brain and noticed a 25% reduction in RD.27 Another study was done with LD DLIR (CTDIvol-18.18 mGy, DLP- 269.43 mGy.cm) protocol of CT brain.29\n\nCT chest examination: A total of nine studies from chest CT that used DLIR showed a reduction in IN (9-50%) compared with IR and FBP.30–39 Four studies compared LD with DLIR and SD with IR for chest CT and observed a reduction (62-97%) in RD.31,37–39 Another 4 studies done with LD chest CT with DLIR [CTDI vol (1.07-2.38 mGy.cm), DLP (79.69-08.7 mGy.cm), SSDE (0.69-1.07 mGy), ED (0.98-1.03 mSv)].30,32,34,35 One study done with Quarter low dose (QLD) CT Chest using DLIR showed 75% reduction in radiation dose compared to IR.33\n\n\nDiscussion\n\nThis systematic review focussed on investigating the influence of DLIR on RD, IN, and outcomes of the studies compared with IR and FBP in Head and Chest CT examinations.\n\nOur review noted that for CT Brain examination, DLIR (Medium and High) showed reduced IN (18-52%), improved IQ (GM-WM differentiation) with better detection of cerebral lesions, and reduced RD (25%). In the Pediatric CT brain, a study by Sun et al. noted that higher strength DLIR reduced image noise and noted better detection of cerebral lesions in 0.625 mm compared to 5 mm slice thickness. The thinner sections of DLIR-H were able to identify micro-hemorrhages of less than 3 mm.29 Nagayama et al. demonstrated a 25% reduction in RD with LD CT-DLIR (120 kVp, 280 mA) compared to SD -IR (120 kVp, 350 mA) and also observed that DLIR had the highest sensitivity in lesion detection (2.9±0.2) compared to MBIR (1.9±0.5) and HIR (1.2±0.4) in adult CT brain.27 Studies by Oostveen et al. and Nagayama et al. showed reduced reconstruction times 44 sec; 24±1 sec compared to MBIR (176 s & 319±17 secs) for Non-contrast CT brain.27–28 Studies by Alagic et al. and Sun et al. reported CTDIvol and DLP of 46.96±0.49 mGy; 847.84±2.25 mGy.cm and 18.18±2.82 mGy; 269.3±57.95 mGy.cm in adult and pediatric CT Head respectively.25,29\n\nOur review noted that LDCT of the chest with DLIR showed higher image contrast and lower IN (9-56%) and reduced RD (62-97%) compared with FBP and IR. Zhao et al. compared LDCT with DLIR (120kvp, 30 mAs) and HRCT with HIR (120kVp, Automatic tube current modulation) for the patients with interstitial lung disease (ILD) and noted that LDCT DLIR showed better visualization of honeycombing and assessment of bronchiectasis.39 Kim et al. noted that DLIR-H yielded higher scores in determining the prominence of the lungs main structures of the lungs.34 Jiang et al. noted that ULD-CT with DLIR under or overestimated the long diameter and sub-solid nodules compared with CECT Thorax. DLIR-H overestimated the solid and calcified nodules while underestimating the long diameter and amount of sub-nodules.31 Wang et al. noted LDCT with DLIR provides higher scores for assessing pulmonary lesions except for sub-solid nodules or ground glass opacity nodules (GGN) compared to SD with HIR, whereas GGN greater than 4 mm can be picked up on LDCT DLIR images.38 Tian et al. reported that DLIR-H appeared to be slightly smoothed and DLIR M provides higher structures on visualization of smoother structures.36 Ferri et al. reported DLIR reconstruction series provided the smallest volume of emphysema compared with Adaptive statistical iterative reconstruction-V (ASIR-V) and FBP and also observed the increase in strength of DLIR led to a decrease in the size of emphysema.30\n\nThe study has a few limitations. Firstly, we did not include phantom studies. Secondly, we did not perform meta-analysis due to heterogeneity in terms of scanners and protocols used for head and chest examinations. The adoption of DLIR algorithms holds promise for improving IQ, reducing RD, and mitigating IN in Head and Chest CT examinations compared to traditional IR and FBP techniques. Healthcare providers may consider incorporating DLIR into their imaging protocols to enhance patient care by reducing radiation risks while maintaining diagnostic accuracy. Furthermore, future research efforts should focus on optimizing DLIR algorithms, investigating their long-term effects on patient outcomes, and evaluating cost-effectiveness compared to conventional reconstruction methods. Additional studies exploring the application of DLIR in other anatomical regions and patient populations could further expand its utility and impact on healthcare delivery.\n\n\nConclusion\n\nIn conclusion, DLIR is a versatile and valuable technology that consistently improves IQ, enhances lesion detection, reduces radiation exposure, and mitigates image artifacts across a wide range of medical imaging applications compared with IR and FBP. A careful selection of strengths of DLIR, slice thickness and radiation dose levels are required for evaluation of tiny lesions, which can overcome with next generation DLIR algorithms. Overall, DLIR holds promise for improving patient care and diagnostic accuracy in various clinical settings.\n\nThe study did not involve any human participants and only systematic review was conducted; hence the written informed consent and Institutional ethical committee approval (IEC) was not required.", "appendix": "Data availability\n\nNo data is associated with this article.\n\nFigshare: F1000 DLIR Systematic Review. https://doi.org/10.6084/m9.figshare.25404226.v3. 40\n\nThis project contains the following underlying data:\n\n• Quality assessment scale\n\n• PRISMA Chart\n\nFigshare: PRISMA_2020_checklist.pdf, https://doi.org/10.6084/m9.figshare.25404226.v3. 40\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nReferences\n\nSmith-Bindman R, Miglioretti DL, Johnson E, et al.: Use of Diagnostic Imaging Studies and Associated Radiation Exposure for Patients Enrolled in Large Integrated Health Care Systems, 1996-2010. JAMA. 2012; 307(22): 2400–2409. PubMed Abstract \| Publisher Full Text\n\nPola A, Corbella D, Righini A, et al.: Computed tomography use in a large Italian region: trend analysis 2004-2014 of emergency and outpatient CT examinations in children and adults. Eur. Radiol. 2018; 28(6): 2308–2318. PubMed Abstract \| Publisher Full Text\n\nMettler FA, Huda W, Yoshizumi TT, et al.: Effective Doses in Radiology and Diagnostic Nuclear Medicine: A Catalog1. Radiology. 2008; 248(1): 254–263. PubMed Abstract \| Publisher Full Text\n\nAgostini A, Borgheresi A, Granata V, et al.: Technological advances in body CT: a primer for beginners. Eur. Rev. Med. Pharmacol. Sci. 2022; 26(21): 7918–7937. PubMed Abstract \| Publisher Full Text\n\nCao CF, Ma KL, Shan H, et al.: CT Scans and Cancer Risks: A Systematic Review and Dose-response Meta-analysis. BMC Cancer. 2022; 22(1): 1238. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSmith-Bindman R, Wang Y, Chu P, et al.: International variation in radiation dose for computed tomography examinations: prospective cohort study. BMJ. 2019; 364: k4931. Publisher Full Text\n\nBaskan O, Erol C, Ozbek H, et al.: Effect of radiation dose reduction on image quality in adult head CT with noise-suppressing reconstruction system with a 256 slice MDCT. J. Appl. Clin. Med. Phys. 2015; 16(3): 285–296. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKubo T, Ohno Y, Kauczor HU, et al.: Radiation dose reduction in chest CT-Review of available options. Eur. J. Radiol. 2014; 83(10): 1953–1961. PubMed Abstract \| Publisher Full Text\n\nWillemink MJ, Noël PB: The evolution of image reconstruction for CT-from filtered back projection to artificial intelligence. Eur. Radiol. 2019; 29(5): 2185–2195. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWillemink MJ, De Jong PA, Leiner T, et al.: Iterative reconstruction techniques for computed tomography Part 1: Technical principles. Eur. Radiol. 2013; 23: 1623–1631. PubMed Abstract \| Publisher Full Text\n\nWillemink MJ, Leiner T, De Jong PA, et al.: Iterative reconstruction techniques for computed tomography part 2: initial results in dose reduction and image quality. Eur. Radiol. 2013; 23: 1632–1642. PubMed Abstract \| Publisher Full Text\n\nHara AK, Paden RG, Silva AC, et al.: Iterative reconstruction technique for reducing body radiation dose at CT: Feasibility study. Am. J. Roentgenol. 2009; 193(3): 764–771. Publisher Full Text\n\nGeyer LL, Schoepf UJ, Meinel FG, et al.: State of the Art: Iterative CT Reconstruction Techniques. Radiology. 2015; 276(2): 339–357. Publisher Full Text\n\nHan WK, Na JC, Park SY: Low-dose CT angiography using ASiR-V for potential living renal donors: a prospective analysis of image quality and diagnostic accuracy. Eur. Radiol. 2020; 30(2): 798–805. PubMed Abstract \| Publisher Full Text\n\nMoloney F, James K, Twomey M, et al.: Low-dose CT imaging of the acute abdomen using model-based iterative reconstruction: a prospective study. Emerg. Radiol. 2019; 26(2): 169–177. PubMed Abstract \| Publisher Full Text\n\nStiller W: Basics of iterative reconstruction methods in computed tomography: A vendor-independent overview. Eur. J. Radiol. 2018; 109: 147–154. PubMed Abstract \| Publisher Full Text\n\nSaiprasad G, Filliben J, Peskin A, et al.: Evaluation of Low-Contrast Detectability of Iterative Reconstruction across Multiple Institutions, CT Scanner Manufacturers, and Radiation Exposure Levels. Radiology. 2015; 277(1): 124–133. PubMed Abstract \| Publisher Full Text\n\nSolomon J, Mileto A, Ramirez-Giraldo JC, et al.: Diagnostic Performance of an Advanced Modeled Iterative Reconstruction Algorithm for Low-Contrast Detectability with a Third-Generation Dual-Source Multidetector CT Scanner: Potential for Radiation Dose Reduction in a Multireader Study. Radiology. 2015; 275(3): 735–745. PubMed Abstract \| Publisher Full Text\n\nZhang Z, Seeram E: The use of artificial intelligence in computed tomography image reconstruction - A literature review. J. Med. Imaging Radiat. Sci. 2020; 51(4): 671–677. Publisher Full Text\n\nKoetzier LR, Mastrodicasa D, Szczykutowicz TP, et al.: Deep Learning Image Reconstruction for CT: Technical Principles and Clinical Prospects. Radiology. 2023; 306(3): e221257. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTimothy P, Szczykutowicz GVT, Dhanantwari A, et al.: A Review of Deep Learning CT Reconstruction: Concepts, Limitations, and Promise in Clinical Practice. Curr. Radiol. Rep. 2022; 10: 101–115.\n\nJensen CT, Liu X, Tamm EP, et al.: Image quality assessment of abdominal CT by use of new deep learning image reconstruction: Initial experience. Am. J. Roentgenol. 2020; 215(1): 50–57. PubMed Abstract \| Publisher Full Text\n\nPage MJ, Mckenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021; 372: n71. Publisher Full Text\n\nAbel van Stiphout J, Driessen J, Koetzier LR, et al.: The effect of deep learning reconstruction on abdominal CT densitometry and image quality: a systematic review and meta-analysis. Eur. Radiol. 2022; 32: 2921–2929. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlagic Z, Diaz Cardenas J, Halldorsson K, et al.: Deep learning versus iterative image reconstruction algorithm for head CT in trauma. Emerg. Radiol. 2022; 29: 339–352. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim I, Kang H, Yoon HJ, et al.: Deep learning-based image reconstruction for brain CT: improved image quality compared with adaptive statistical iterative reconstruction-Veo (ASIR-V). Neuroradiology. 2021; 63(6): 905–912. PubMed Abstract \| Publisher Full Text\n\nNagayama Y, Iwashita K, Maruyama N, et al.: Deep learning-based reconstruction can improve the image quality of low radiation dose head CT. Eur. Radiol. 2023; 33: 3253–3265. PubMed Abstract \| Publisher Full Text\n\nOostveen LJ, Meijer FJA, de Lange F , et al.: Deep learning–based reconstruction may improve non-contrast cerebral CT imaging compared to other current reconstruction algorithms. Eur. Radiol. 2021; 31(8): 5498–5506. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSun J, Li H, Wang B, et al.: Application of a deep learning image reconstruction (DLIR) algorithm in head CT imaging for children to improve image quality and lesion detection. BMC Med. Imaging. 2021; 21(1): 1–9.\n\nFerri F, Bouzerar R, Auquier M, et al.: Pulmonary emphysema quantification at low dose chest CT using Deep Learning image reconstruction. Eur. J. Radiol. 2022; 152: 110338. PubMed Abstract \| Publisher Full Text\n\nJiang B, Li N, Shi X, et al.: Deep Learning Reconstruction Shows Better Lung Nodule Detection for Ultra–Low-Dose Chest CT. Radiology. 2022; 303(1): 202–212. PubMed Abstract \| Publisher Full Text\n\nJiang JM, Miao L, Liang X, et al.: The Value of Deep Learning Image Reconstruction in Improving the Quality of Low-Dose Chest CT Images. Diagnostics (Basel). 2022; 12(10): 2560. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJo GD, Ahn C, Hong JH, et al.: 75% radiation dose reduction using deep learning reconstruction on low-dose chest CT. BMC Med. Imaging. 2023 Sep 11; 23(1): 121. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim JH, Yoon HJ, Lee E, et al.: Validation of deep-learning image reconstruction for low-dose chest computed tomography scan: Emphasis on image quality and noise. Korean J. Radiol. 2021; 22(1): 131–138. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim CH, Chung MJ, Cha YK, et al.: The impact of deep learning reconstruction in low dose computed tomography on the evaluation of interstitial lung disease. PLoS One. 2023; 18: e0291745. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTian Q, Li X, Li J, et al.: Image quality improvement in low-dose chest CT with deep learning image reconstruction. J. Appl. Clin. Med. Phys. 2022; 23(12): e13796. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang H, Li LL, Shang J, et al.: Application of deep learning image reconstruction in low-dose chest CT scan. Br. J. Radiol. 2022; 95(1133). PubMed Abstract \| Publisher Full Text\n\nWang J, Sui X, Zhao R, et al.: Value of deep learning reconstruction of chest low-dose CT for image quality improvement and lung parenchyma assessment on lung window. Eur. Radiol. 2023; 34: 1053–1064. Publisher Full Text\n\nZhao R, Sui X, Qin R, et al.: Can deep learning improve image quality of low-dose CT: a prospective study in interstitial lung disease. Eur. Radiol. 2022; 32(12): 8140–8151. PubMed Abstract \| Publisher Full Text\n\nKadavigere R: F1000 DLIR systematic review. [Dataset]. figshare. 2024. Publisher Full Text" }	[ { "id": "268958", "date": "30 Apr 2024", "name": "Shashi Kumar Shetty", "expertise": [ "Reviewer Expertise Radiation Biology", "Radiation dose related research in CT", "X-rays", "Fluoroscopy etc.. Radiography." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajor comments: The article provides an insightful and comprehensive review of the influence of Deep Learning Image Reconstruction (DLIR) on radiation dose, image noise, and outcomes in head and chest CT examinations compared to traditional Iterative (IR) and Filtered Back Projection (FBP) techniques. The methodology section is meticulously detailed, following PRISMA guidelines. The results section offers a clear summary of the inclusion and exclusion criteria, key outcomes related to DLIR's influence on radiation dose reduction, image noise reduction, and enhancement of image quality in CT head and chest examinations. The inclusion of quality assessment scores adds validation to the review's findings. The discussion and conclusion effectively explain the results, offering potential applications of DLIR in clinical settings.\n\nMinor suggestions: Please proofread for grammatical errors. Additionally, consider including points related to the smaller sample size of pediatric CT cases to provide a more comprehensive overview.\n\nSuggestions to editor: Overall, it is an excellent review article that represents a valuable contribution to the field of CT image reconstruction technology, providing insights into the impact of Deep Learning Image Reconstruction technology on dose reduction and improvement of image quality.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "268955", "date": "08 May 2024", "name": "Dr. Tamijeselvan S", "expertise": [ "Reviewer Expertise Competency based Radiographic Education", "Radiography and Imaging Technology", "Image processing Techniques", "Quality Assurance of Medical Imaging", "Biophysics." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajor comments The review article provides comprehensive review of the Deep Learning Image Reconstruction (DLIR) and its application on radiation dose and image noise. This review particularly concentrating on the application and outcomes in head and chest Computed Tomography examinations compared to traditional Iterative (IR) and Filtered Back Projection (FBP) techniques. In the methodology section the authors follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), which is an evidence-based minimum set of items for reporting in systematic reviews and meta-analyses. It has been clearly explained. In the results the author clearly explains the key outcome in related to the aim and objectives. In particular DLIR's influence on radiation dose reduction, image noise reduction, and enhancement of image quality in CT head and chest examinations were clearly explained. The discussion and conclusion effectively explain the results, Minor comments Some more references may be added to support the review article. The article may include the data of various other anatomical part like thorax. Suggestions to editor: On a whole , it is an excellent review article that represents a valuable contribution for the dose reduction in the CT scan using proper image reconstruction technology. Also this article provides the impact of Deep Learning Image Reconstruction technology on improvement of image quality.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "268965", "date": "15 May 2024", "name": "Thayalan Kuppusamy", "expertise": [ "Reviewer Expertise Radiation physics", "diagnostic radiology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nQuestions/Comments 1.What is the estimated CT examinations number in India, including pediatric?\n2. Why abdomen CT is not taken for the study since it involves larger dose variation .\n3.Why phantom study is excluded, it is basic method and gold standard of dose estimation?\n4.Image noise (IN) depends on type of noise filters used- will all 15 articles used had same noise filter?\n5. Is slice thickness is considered as a parameter in deciding radiation dose?\n6.The RD data and IQ parameter collected from various CT vendors shows variation, means not homogeneous? Comparing the RD with them will result a meaningful data or not? Why Phillips vendor is not included since large number of installation is here in India\n7.CT radiation dose and cancer risk is debatable, it can not be taken as hypothesis. Probability of cancer induction is less if the dose is < 100 mSv. No CT scan offer such magnitude of radiation now a days.\n8.There was no mention about diagnostic reference level (DRL), especially in India. Is the stated DLIR brings the dose below the DRL or not ?\n9. CDDI, focal spot, slice thickness, filtration (bow type filter), tube rotation time, pitch, current modulation, AEC, low dose protocol, kV, mAs, scan area may differ in each CT and influence dose- all the parameter are accounted?\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [] }, { "id": "268959", "date": "29 May 2024", "name": "SENTHIL MANIKANDAN", "expertise": [ "Reviewer Expertise Radiation Imaging and Dosimetry" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajor comments:\nThe objective of this study is to evaluate the impact of the Deep learning image reconstruction (DLIR's) algorithm on Radiation Dose (RD), Image Noise (IN), and Image Quality (IQ) in Head and Chest CT examinations. This study addresses a crucial area of research in image reconstruction technology in CT. The comprehensive approach ensures a thorough understanding of DLIR’s impact on various aspects of CT Head and Chest imaging. The study's methodology is well-structured and follows the PRISMA guidelines, ensuring a systematic and comprehensive approach to data collection and analysis. The inclusion of major databases ensures a comprehensive retrieval of relevant articles, enhancing the study’s credibility and readability. Findings regarding CT head examinations, including the reduction in image noise, improved Image quality with better lesion detection, and reduced radiation dose with DLIR compared to IR and FBP, are well documented and supported by specific studies. Similarly, the observations related to CT chest examinations, such as higher image contrast, lower image noise, and substantial reduction in radiation dose with DLIR, are clearly stated and backed by relevant research. Results mentioned in the study such as a reduction in RD 25% in adult CT brain examinations and 62% to 97% in chest CT examinations add quantitative support to the significant impact of DLIR reducing radiation exposure while maintaining diagnostic accuracy. Acknowledging the limitations of the study, such as the exclusion of phantom studies and heterogeneity provides transparency and enhances the credibility of acknowledging potential biases or gaps in the research process.\nMinor comments:\nEnsure that all abbreviations are clearly defined upon first use. Suggestions to editor The review article adds significant knowledge to the literature about the potential advantages of DLIR techniques to enhance diagnostic accuracy, minimize radiation exposure, and improve image quality in CT brain and Chest examinations. The review provides valuable insights into the advancements of DLIR in CT imaging, its benefits in reducing radiation dose and image noise while improving Image quality, and highlights the potential for further research and application of DLIR in clinical settings.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-274
https://f1000research.com/articles/13-271/v1	15 Apr 24	{ "type": "Research Article", "title": "Using Odih-Score (Modified Klotz Score) for quality of defecation after anorectal malformation following posterior sagittal anorectoplasty (PSARP): Study of validation", "authors": [ "Tubagus Odih Rhomdani Wahid", "Ratu Astuti Dwi Putri", "Ismar Ismar", "Ratu Astuti Dwi Putri", "Ismar Ismar" ], "abstract": "Abstract*\nObjective The diagnostic scale or score is a clinical assessment tool used to determine diagnosis and evaluate further therapy results. The Klotz Score is a previous score modified to create a new instrument, the Odih-score. This new instrument is specifically designed to evaluate the quality of defecation success after operative anorectal malformation and is expected to be simpler and easier to apply in research hospitals. Its primary use is to evaluate the quality of defecation in post-PSARP anorectal malformation patients.\n\nMethod The study conducted between 2016 and 2021, a longitudinal prospective study was conducted at RSUD Arifin Achmad Pekanbaru Riau Indonesia. The study aimed to validate the reliability of the Odih-Score (Modified Klotz Score) research instrument for evaluating defecation quality in post-PSARP anorectal malformation patients. Pearson validation test and Cronbach alpha reliability test were used as parameters for the validation, while the sensitivity and specificity of diagnostic tests were evaluated using research instrument (IBM SPSS Statistics version 25) The research was approved by the Ethical Clearance Board of the Faculty of Medicine, University of Riau, under reference number No.031/UN.19.5.1.1.8/UEPKK/2019.\n\nResults The analysis of the validation test results indicates that the Odih-Score is statistically significant (Sig.<0.05) and has a greater r-count value (0.573-0.790) than the r-table value (0.202). The research reliability test also shows a high level of reliability (Cronbach alpha 0.814) for all five items of the Odih-Score instrument. Further, the sensitivity and specificity test as a diagnostic test resulted in an AUC value of 0.798, with an Odih-Score cut-off point of 11.\n\nConclusion Odih-Score (Modified Klotz’s score) is considered valid and reliable and can be used as a diagnostic test instrument to evaluate the quality of post-anorectal Malformation defecation with PSARP.", "keywords": [ "Odih-Score", "Klotz Score", "Anorectal Malformation", "PSARP" ], "content": "Introduction\n\nAnorectal malformation is a congenital disorder in the form of an imperfect anus or without an anus.1–3 The incidence of anorectal malformations is about 1 per 4000 population annually.1–3 The prevalence of anorectal malformations in Riau, Indonesia is estimated at 34 cases annually.4–6 The management of anorectal malformations depends on the classification and severity of the disorder.7,8 The definitive surgical that is widely used up to this point is the method introduced by De Vries and Pena the Posterosagittal Anorectoplasy (PSARP) approach.7,8 This surgical method is widely used because it is considered more dynamic and obtains better surgical results in bowel function and fecal continence. The success of the PSARP Technique can be measured by the Klotz Score.4,9\n\nThe Klotz score is one of the parameters that can be used for the evaluation of bowel function or defecation. Klotz scores are classified into excellent, good, sufficient, and insufficient to assess the quality of postoperative defecation.9 Previous studies have shown that Klotz scores have good predictive values for the evaluation of postoperative defecation quality function.6 This assessment and classification of score results has several assessment items that are sometimes difficult to apply to communicate to patients, so researchers aim to modify the Klotz score to make it easier for researchers and other practicing doctors, especially in Indonesia.\n\n\nMethods\n\nThis study was designed with a prospective longitudinal study approach to validate and reliability of the research instrument named Odih-Score (Modified Klotz Score) (Table 1) in the form of 5 questions which were then used as a scale or score to assess the quality of postoperative defecation of PSARP anorectal malformations.\n\nThe participants of this study included all patients after anorectal malformation who had undergone surgery with the PSARP technique. The study sample is a pediatric patient accompanied by a parent or guardian of the patient who is willing to provide informed written consent, willing to participate in the research and able to understand the questions prepared. Pediatric patients after Anorectal Malformation PSARP Technique with a minimum age of 6 years who can be communicated with in conducting directed history are included in the inclusion criteria. The exclusion criteria are pediatric patients who cannot be communicated with in conducting directed history or the age of <6 years old.\n\nScoring system: Odih-Score, also known as Modified Klotz’s score as shown in Table 1, is a scoring system used to assess the quality of defecation in patients with post-PSARP anorectal malformations. This score was developed or modified from previous studies, particularly Klotz scores. The questionnaire item underwent validation and reliability tests to create new research instruments that are easier to use and can be applied by doctors to evaluate the quality of defecation in anorectal malformation patients after PSARP. This system is especially useful at Arifin Achmad Pekabaru Hospital. The Odih-Score system comprises of 5 variables that evaluate the quality of defecation after PSARP. These variables are the frequency of defecation, the ability to hold stool, the consistency of stool, pain experienced during defecation, and the feeling of wanting to defecate. Four of these variables are based on internationally recognized Klotz criteria, while the fifth is a new addition by the researcher. The fifth variable is considered easier to assess objectively in the evaluation of post-PSARP defecation. Each variable is rated on a 3-point Likert scale, ranging from 1 (mild complaints) to 3 (severe complaints). These ratings are then classified into good, sufficient, and poor defecation qualities.\n\nContent validity method: Two pediatric surgeons and one pediatric digestive surgeon consultant reviewed the Odih-Score questionnaire to ensure inclusion of all valid and reliable assessment variables.\n\nFeasibility method: Although most items have been pre-validated, Odih-Skor is retrialed iteratively with a sample of registered patients to gather their input on the clarity of each item.\n\nConcurrent validity method: During the initial visit, patients who met the inclusion criteria were asked to complete the Odih-Score questionnaire through a structured and directed history by a research expert. The researcher then evaluated the final criteria based on the total points obtained from the Odih-Score.\n\nReproducibility and internal consistency method: To ensure reproducibility, patients are asked to complete the Odih-Score at least twice: during their first outpatient visit and later during hospitalization or follow-up, with a minimum interval of 3 months.\n\nConstruct validity method: During the initial visit, every participant in the study was given an Odih-Score questionnaire to complete. The assumption was that patients with higher Odih-Scores would have a lower quality of life. To assess the constructive validity of Odih-Scores, correlations between the quality-of-life domain outcomes and Odih-Score are evaluated.\n\nDiscriminant validity method: In a subgroup of post-PSARP anorectal malformation patients, the validity of the discriminant questionnaire was assessed. This was done by comparing the Odih-Score scores reported by the participants before and 3-6 months after the first scoring, to evaluate the improvement in symptoms. Those who reported improvement in symptoms were expected to have lower symptom severity scores, while those who complained of no change or worsening of symptoms were expected to have higher scores.\n\nReliability: after the item is declared valid, proceed with reality analysis using consistency using a reliability test with Cronbach alpha, declared a reliable item if the value of Cronbach alpha >0.6.\n\nThe statistical analysis was carried out using version 25 of the statistical software suite developed by IBM SPSS software.\n\nFirstly, a variable normality test was performed using Skewness and Kurtosis, followed by a validation analysis of five items using the Pearson validation test. Next, a reliability test was conducted using consistency measured by Cronbach alpha. The Spearman test correlation coefficient was used to evaluate the construct and validity of the discriminant. Finally, Receiver Operating Characteristic (ROC) and Area Under the Curve (AUC) tests were conducted to measure sensitivity and specificity as diagnostic test parameters.\n\nThis research has been declared to have passed the ethical review by the Ethical Clearance Board of the Faculty of Medicine, University of Riau with number 031/UN.19.5.1.1.8/UEPKK/2019 on 25th January 2019.\n\n\nResults\n\nThe study collected data on 95 post-PSARP anorectal malformation patients who met the inclusion criteria out of 282 patients listed in the medical records. The researchers analyzed the participants in a structured manner with five items, and the participants felt that their clinical condition represented well all the symptoms included in the Odih-Score questionnaire. The data was then analyzed for reproducibility, internal consistency, concurrent, construct, and clinical validity in 95 patients. The study reported that 52.63% of the participants were male (with a male-female ratio of 1.2:1), 64.51% had a high lesion type, and 66.31% underwent the full-PSARP technique (as shown in Table 2).\n\nTable 3 presents the results of both the validation and reproducibility tests. The validation test is conducted using the Pearson test and measures the correlation between two sets of data. In our case, the correlation coefficient (r) is calculated, and the value ranges from 0.573 to 0.790. To determine if this is a valid correlation, we compare the calculated r value to the r-table value at a 5% significance level in a static r-table distribution (n=95). The table r value for this distribution is 0.202. If the r-count value is greater than the table r value, then we can consider the correlation coefficient as valid.10–12 To ensure the validity of the study, we analyzed five items and found that their significance value was less than 0.05, indicating valid results. After that, we conducted a reliability test using the Cronbach alpha test. The results of the validation and reliability tests help us ensure the accuracy and credibility of our findings.13 Cronbach’s alpha coefficient of internal consistency for 5 items was 0.814 in 95 patients, indicating excellent reliability (Table 4).\n\nThe Odih-Score research data will be analyzed for sensitivity and specificity using Receiver Operating Characteristic (ROC) and Area Under the Curve (AUC) as a diagnostic tool.14,15 The ROC curve analysis in this study (shown in Figure 1) resulted in an AUC Odih-Score value of 0.798 (95%CI 0.544–0.882) (as shown in Table 5). The optimal value of sensitivity and specificity cut off between the Odih-Score and post-Anorectal Malformation defecation quality with PSARP was found to be 10.89 (rounded to 11). This means that a total Odih-score of at least 11 indicates poor defecation quality in patients after Anorectal Malformation with PSARP (as depicted in Figure 2).\n\n\nDiscussion\n\nAnorectal malformation is a congenital disorder where the anus is either absent or imperfect, and surgery is required for definitive management.1–3 De Vries and Pena introduced the Posterosagittal Anorectoplasty (PSARP) technique which is widely used to improve bowel function and postoperative fecal continence for patients with anorectal malformations.6–8 Defecation quality evaluation scoring is still commonly used today. The Klotz score is a widely used scale based on previous studies.16,17 Odih-Score is a modified version of the Klotz score, which is known for its ease of use among clinicians, particularly at Arifin Achmad Hospital. The Odih-Score consists of 5 items, 4 of which are borrowed from the Klotz score, and 1 new item added. Each of these grades is scored using a modified 3-point Likert scale with answer point choices.18 The results of data analysis using the Pearson validation test showed that Odih-Score has a significance value of Sig.<0.05, with r-count value being greater than the r-table value.\n\nDeveloping instruments for assessment requires the use of reliable methods, such as questionnaires designed with scoring or scaling systems. It is crucial to ensure that the chosen measurement model is consistent with the assessment methods used. Scoring tools are a vital element of instrument validity.19 Messick defines validity as a characteristic not of the test, but of the meaning, interpretation, and consequences of its scores.20 Researchers developing measurement tools should consider different perspectives on measurement models and their impact on assessment systems to determine which approach is most appropriate for their research objectives.21,22\n\nWhen researchers use a questionnaire to collect data, it is important that the questionnaire is of high quality. A questionnaire is considered to be of high quality if it has been validated and proven to be reliable. The validation test is conducted to determine if the questionnaire is suitable for measuring and obtaining research data from respondents. To conduct the validation test, researchers use the Pearson correlation coefficient to determine the correlation between each item on the questionnaire and the total answers provided by the respondent.10,11 The research instrument is said to be valid if the value of the r-count coefficient is greater than the value of the r-table or the significance value (Sig.) <0.05.\n\nThe reliability test aims to determine if a research instrument produces consistent results when the questionnaire is administered repeatedly.13 Before conducting reliability tests, it is important to confirm the validity of the research instrument. In this study, the reliability test analysis indicates that the Odih-Score research instrument is reliable, as the Cronbach alpha value for its five items is 0.814, which is above the accepted threshold of 0.6.13\n\nThe sensitivity and specificity of Odih-Score as a diagnostic test was tested, and it obtained an AUC value of 0.798. A good test ability is declared if AUC is greater than or equal to 0.7. This shows that Odih-Score has a high diagnostic parameter value strength when evaluating the quality of defecation. The optimal cut-off value for Odih-Score sensitivity and specificity is 11. These analysis results can be used as a diagnostic assessment parameter to determine the quality of post-Anorectal Malformation defecation with PSARP.\n\n\nConclusion\n\nOdih-Score (Modified Klotz’s score) can be used as a diagnostic test to evaluate postoperative defecation quality in anorectal malformation patients treated with PSARP. The score is reliable and valid.\n\nThis research has been declared to have passed the ethical review by the Ethical Clearance Board of the Faculty of Medicine, University of Riau with number 031/UN.19.5.1.1.8/UEPKK/2019 on 25th January 2019.\n\nThe study sample is a pediatric patient accompanied by a parent or guardian of the patient who is willing to provide informed written consent, willing to participate in the research and able to understand the questions prepared.\n\nStatement template for SRQR checklists:\n\n• Repository name: Figshare\n\n• ‘SRQR guidelines’ checklist https://doi.org/10.6084/m9.figshare.24416644.v3\n\n• data are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0).", "appendix": "Data availability\n\nFigshare: Odih Score for Quality of Defecation after Anorectal Malformation following Posterior Sagittal Anorectoplasty (PSARP): Study of Validation, https://doi.org/10.6084/m9.figshare.24416644.v4.\n\nThis project contains the following underlying data:\n\n• Table containing the raw data of the study\n\nFigshare: Odih Score for Quality of Defecation after Anorectal Malformation following Posterior Sagittal Anorectoplasty (PSARP): Study of Validation, https://doi.org/10.6084/m9.figshare.25414966.v1.\n\nThis project contains the following underlying data:\n\n• Table containing questionnaires, interview guides, example consent forms\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to thank all of the medical professionals and associates who contributed to this study.\n\n\nReferences\n\nCaldamone AA: Operative Pediatric Surgery 7th ed. J. Pediatr. Urol. 2014; 10(1): 204. Publisher Full Text\n\nBhatnagar S: Anorectal Malformations (Part 2). J. Neonatal Surg. 2015; 4(2). Publisher Full Text\n\nPelizzo G, et al.: Anorectal Malformations: Ideal Surgery Timing to Reduce Incontinence and Optimize QoL. Children. 2023; 10(2): 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWahid TOR, et al.: Prognosis of Hirschsprung’s disease after pull through surgery in Arifin Achmad general hospital of Riau Province. Malaysian J. Med. Heal. Sci. 2020; 16(June): 6–9.\n\nPutri GY, Wahid TOR, Masdar H: Angka Keberhasilan Posterosagittal Anorectoplasty (PSARP) yang Dinilai dari Skor KLOTZ pada Pasien Malformasi Anorektal di Bangsal Bedah RSUD Arifin Achmad Provinsi Riau Periode Januari 2009-Desember 2014. Jom Fk. 2014; 1(2): 1–8.\n\nWahid TOR, Putri RAD: Quality of defecation in patients with anorectal malformation following posterior sagittal anorectoplasty (PSARP) in Arifin Achmad General Hospital of Riau Province, Indonesia. Indones. J. Biomed. Sci. 2022; 16(1): 34–36. Publisher Full Text\n\nAbatanga FA, Lakhoo K: Paediatric Surgery: A Comprehensive Text- Volume 2.2011; pp. 358–365.\n\nChavan RN, Chikkala B, Das C, et al.: Anorectal Malformation: Paediatric Problem Presenting in Adult. Case Rep. Surg. 2015; 2015: 1–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWong CWY, Chung PHY, Tam PKH, et al.: Quality of life and defecative function 10 years or longer after posterior sagittal anorectoplasty and laparoscopic-assisted anorectal pull-through for anorectal malformation. Pediatr. Surg. Int. 2020; 36(3): 289–293. PubMed Abstract \| Publisher Full Text\n\nSullivan GM: A Primer on the Validity of Assessment Instruments. J. Grad. Med. Educ. 2011; 3(2): 119–120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMiot HA: Correlation analysis in clinical and experimental studies. J. Vasc. Bras. 2018; 17(4): 275–279. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSanchez MM, Binkowitz BS: Guidelines for measurement validation in clinical trial design. J. Biopharm. Stat. 1999; 9(3): 417–438. Publisher Full Text\n\nTaber KS: The Use of Cronbach’s Alpha When Developing and Reporting Research Instruments in Science Education. Res. Sci. Educ. 2018; 48(6): 1273–1296. Publisher Full Text\n\nHajian-Tilaki K: Receiver operating characteristic (ROC) curve analysis for medical diagnostic test evaluation. Caspian J. Intern. Med. 2013; 4(2): 627–635. PubMed Abstract\n\nMandrekar JN: Receiver operating characteristic curve in diagnostic test assessment. J. Thorac. Oncol. 2010; 5(9): 1315–1316. Publisher Full Text\n\nGhorbanpoor M, Dehvan B, Rahimi S, et al.: Fecal Incontinence after Posterior Sagittal Anorectoplasty for Anorectal Malformation: A Single-Center Study. Scientifica (Cairo). 2018; 2018: 1–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nvan Ling JA , Bökkerink GMJ, de Blaauw I , et al.: Development of a posterior sagittal anorectal surgical teaching model. BMC Pediatr. 2021; 21(1): 57–59. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBernstein IH: Likert Scale Analysis. Encycl. Soc. Meas. 2004; 2: 497–504. Publisher Full Text\n\nAvila ML, Stinson J, Kiss A, et al.: A critical review of scoring options for clinical measurement tools. BMC. Res. Notes. 2015; 8(1): 611–612. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMessick S: Standards of Validity and the Validity of Standards in Performance Asessment. Educ. Meas. Issues Pract. 1995; 14(4): 5–8. Publisher Full Text\n\nReise SP, Bonifay WE, Haviland MG: Scoring and modeling psychological measures in the presence of multidimensionality. J. Pers. Assess. 2013; 95(2): 129–140. PubMed Abstract \| Publisher Full Text\n\nTrikalinos TA, et al.: Chapter 8: Meta-analysis of test performance when there is a ‘gold standard. J. Gen. Intern. Med. 2012; 27 Suppl 1(SUPPL.1): S56–S66. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "268157", "date": "06 May 2024", "name": "Parveen Kumar", "expertise": [ "Reviewer Expertise Rehabilitation", "Osteopathy", "Chiropractice", "Outcome measures", "Psychometric properties" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. Is the work clearly and accurately presented and does it cite the current literature? - 7 References cited are more than 10 years old and 2 references are more than 25 years old. 2. Is the study design appropriate and is the work technically sound? - Study design is appropriate but technically authors require to go through the process of Validity and Reliability testing methods. 3. Are sufficient details of methods and analysis provided to allow replication by others? - In any research articles, methods section requires to be replicable and reproducible, but the present manuscript lacks these qualities totally. Explanation is lacking regarding no. of patients recruited, sample size determination, complete process of validation and reliability. 4. If applicable, is the statistical analysis and its interpretation appropriate? - For content validity, Delphi method or any other scientific method. - For concurrent validity, correlation with an existing valid and reliable scale must be carried out. - For reliability, how many readings were obtained? What type of reliability was determined - Relative/ Absolute/ Inter-rater/ test-retest reliability? 5. Are all the source data underlying the results available to ensure full reproducibility? - Results must be explained in line with proper data analysis.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-271
https://f1000research.com/articles/13-268/v1	15 Apr 24	{ "type": "Case Report", "title": "Case Report: Holistic dental care for a child with Hunter syndrome: Addressing dental ramifications, overcoming challenges, and enhancing quality of life", "authors": [ "Swagata Saha", "Krishna Priya", "Kavita Rai", "Manju R", "Krithika Shetty", "Amitha M Hegde", "Ananya Rao K", "Dhvani Abhijit Tanna", "Mohanaram S", "Shreya S", "Swagata Saha", "Krishna Priya", "Kavita Rai", "Krithika Shetty", "Amitha M Hegde", "Ananya Rao K", "Dhvani Abhijit Tanna", "Mohanaram S", "Shreya S" ], "abstract": "Abstract: Hunter syndrome (MPS II), an X-linked recessive lysosomal storage disorder, is a result of deficiency of the iduronate 2-sulfatase enzyme (IDS), leading to cognitive impairment, systemic organ involvement, and increased dental problems. This case report describes the management of a child with Hunter syndrome who was referred to the Department of Paediatric and Preventive Dentistry for pain in the upper front teeth. Intraoral examination revealed severe early childhood caries, prompting planning for full-mouth rehabilitation under general anaesthesia due to the child’s uncooperative behaviour. In response to recommendations from the Department of Otolaryngology and the Department of Paediatric Surgery, a comprehensive treatment plan consolidated full-mouth rehabilitation in addition to adenoidectomy and inguinal and umbilical herniotomy procedures during a single session of general anaesthesia. Successful interventions were reflected in the uneventful one-month follow-up of the patient, highlighting the efficacy of the interdisciplinary approach. The key takeaway underscores the importance of collaborative interventions, emphasising singular intubation for patients requiring recurrent hospitalisations, providing both monetary relief and reducing post operative healing time. Designed to address global developmental delay in the child, a personalised home care plan was also implemented. Evaluation of plaque and gingival indices before and after the home care regimen demonstrated a notable improvement, indicating an enhanced oral quality of life.", "keywords": [ "Hunter Syndrome", "Dental Rehabilitation", "General Anaesthesia", "Multidisciplinary Approach", "Oral Intubation", "Dental Pain", "Dental caries" ], "content": "Introduction\n\nHunter syndrome, an X-linked recessive mucopolysaccharide disorder, is characterised by a deficiency in the enzyme iduronate sulfatase, resulting in the accumulation of dermatan and heparan sulphates in various tissues. This disorder, which exhibits both mild and severe forms, is distinguished as an X-linked recessive condition from other autosomal recessive mucopolysaccharide disorders. The clinical manifestations of Hunter syndrome include macrocephaly, developmental delay, dysmorphic facies, skeletal abnormalities, joint contractures, hepatosplenomegaly, cardiac valvular disease, hirsutism, hyperkinesis, and rough behaviour. Inguinal hernias are reported in 60% of male patients, highlighting a characteristic feature of this syndrome. In addition, people with Hunter syndrome often experience umbilical hernias. Frequent otitis media and hearing problems are common secondary systemic manifestations, further illustrating the extensive impact of this disorder on various aspects of health.1\n\nThe oral manifestations are prominent and involve a shortened and broad mandible, radiolucent jaw lesions, flattened temporomandibular joints, macroglossia, peg-shaped teeth with wide spacing, highly arched palate with flattened alveolar ridges, and hyperplastic gingiva. Charles Hunter’s early observations of this disease in children, dating to 1915, highlighted features such as a slowed learning process, tonsil and adenoid issues, severe respiratory infections, and numerous physical abnormalities, often increasing with age.2\n\nHunter syndrome is extremely rare, affecting less than 20 cases per million births, and stands out as the rarest form of mucopolysaccharide disorder. It is important to note that the disorder can appear in successive births even without a family history of mucopolysaccharide disorders, making genetic counseling essential.3\n\nChildren with Hunter syndrome often experience severe dental problems, including high dental caries, due to various factors such as malformed teeth, poor oral hygiene, and limited access to dental care. This case report illustrates the challenging but essential task of full-mouth rehabilitation for a child with Hunter syndrome, addressing these dental issues to improve their oral health and overall quality of life.\n\n\nCase report\n\nA 4-year-old male patient presented to the Department of Paediatric and Preventive Dentistry at the AB Shetty Memorial Institute of Dental Sciences, Deralakatte, Mangaluru, with the chief complaint of decay in the region of the upper front tooth for the past month. The referral originated from the Department of Pediatrics at Justice KS Hegde Charitable Hospital, with a thorough family history analysis that revealed no hereditary patterns of the disease and parents involved in a non-consanguineous marriage (Figure 1).\n\nDuring the 32nd week of intrauterine development, ultrasound revealed oligohydramnios, resulting in intrauterine growth restriction (IUGR). The subsequent timeline showing the major events is shown in Figure 2. The patient was diagnosed with Hunter syndrome through biochemical genetic testing at the Centre for DNA Fingerprinting at Kasturba Medical College, Mangalore. The assay using 4-methylumbelliferone confirmed the deficient activity of Iduronate 2-sulfatase (4.95 nmol/4 h/ml vs control), while the enzyme assay of Arylsulfatase indicated normal results. The diagnosis was confirmed by whole genome sequencing.\n\nAfter a year, the patient presented with complaints of pain in the upper front teeth, mouth breathing, and swelling over the right inguinal hernia (measuring 2 × 2 cm over the umbilicus and the right inguinal region, spontaneously reducible, and expanding on the cough impulse). On physical examination, the child presented with a clumsy gait, thick coarse hair and skin, generalised facial puffiness (Figure 3) and brittle unkempt nails. On dental examination, severe early childhood caries was identified. Despite initial attempts to guide behaviour in the dental operating room, the child, who exhibited a Frankel rating of (--), displayed high apprehension and global developmental delay. Subsequently, a collaborative approach involving multiple departments was implemented to provide treatment under general anaesthesia. The Department of Otolaryngology performed endoscopic adenoidectomy to address grade IV adenoid hypertrophy, while the Department of Paediatric Surgery performed a umbilical and right inguinal herniotomy. Oral rehabilitation (Oral prophylaxis; Pulpectomy (Metapex) with respect to FDI Tooth Number 63, 64, Glass Ionomer Cement Type IX restoration with respect to FDI Tooth Number 65, 75, 55; Indirect Pulp therapy with respect to FDI Tooth Number 51, 53, 54, 74, 84, 85 (Biodentine); Composite Restoration with respect to FDI Tooth Number 63, 51; Extraction with respect to FDI Tooth Number 61, 62; Topical Fluoride application (APF gel)), was undertaken by the Department of Pediatric and Preventive Dentistry (Figure 4). This comprehensive interdisciplinary effort aimed to address the diverse health concerns of the child efficiently and with due consideration of their overall well-being. After the procedure, the child received a comprehensive medication regimen and was reviewed after one week. One month after the procedure, the patient reported an uneventful follow-up, with no new dental complaints.\n\nA holistic approach to subsequent oral care was diligently implemented. The personalised home oral care routine introduced a wide range of activities, including gum massage, blowing exercises, and oral motor drills, designed not only to stimulate oral sensory muscles but also to prevent potentially harmful coping mechanisms that arise from regression in daily activities.4 Recognising the delicate nature of the oral epithelium, the integration of topical vitamin E into twice daily oral massage was intended to promote epithelization and overall oral health.5 Confronting the challenge posed by the child’s inability to spit, a suite of recommendations was proposed, including the use of fluoride-free toothpaste that was safe to consume in minimal amounts, soft bristled or electric toothbrushes, routine tongue scraping, and post-meal mouth rinse facilitated by an irrigation syringe. Dietary modification, a critical aspect of this holistic care plan, advocates limiting the consumption of sweet and sticky foods6,7 and incorporating probiotics.8,9 The importance of regular mealtimes and family meals10,11 further enriched the comprehensive care approach. During recall visits, the application of topical 5% sodium fluoride with casein phosphopeptide – amorphous calcium phosphate complexes (CCP-ACP) remineralisation paste was recommended every three to six months. This strategic intervention aimed to improve oral health over time. Assessment of plaque and gingival indices before and after implementation of the home care regimen revealed a significant improvement after 6 months of follow-up, underscoring improved oral quality of life.\n\n\nDiscussion\n\nThis case report underscores the effectiveness of employing a multidisciplinary approach to address the various challenges encountered during a singular intubation procedure performed under general anaesthesia for a child. The decision to adopt this approach was rooted in the goal of mitigating possible side effects related to multiple intubations, a consideration that became important given the intricacies of managing a difficult airway. This approach not only led to a shorter hospital stay, thus reducing the risk of nosocomial infections and promoting cost effectiveness, but also proved to be notably advantageous for the child, especially considering that individuals with Hunter syndrome often require frequent hospital visits due to compromised general health.12 However, it is crucial to recognise that this strategy poses a challenge due to the extended intubation hours, which can complicate extubation and postoperative recovery. Fortunately, this concern was effectively addressed in the present case through meticulous time management. In particular, the entire procedure was completed successfully in a time frame of four hours. The primary objective of our multidisciplinary approach was to effectively manage pain, improve oral hygiene, and mitigate degenerative potential.\n\nThe collaborative procedure, conducted in coordination with the Department of Otolaryngology and involving adenoidectomy, required oral intubation due to the impracticality of nasal intubation. Unfortunately, this choice compromised the field of vision and accessibility for comprehensive dental rehabilitation. After adenoidectomy, a continuous suction process became imperative to address blood aggregation in the oral cavity and maintain a blood-free field for treatment. Inherent in individuals with Hunter syndrome is the characteristic of macroglossia. After intubation, there was significant tongue enlargement, which exacerbated the challenges related to our field of vision and presented a potential risk of airway obstruction. This situation required vigilant supervision. Additionally, an increased fragility of oral tissues was observed, which further added to the complexity of the procedure.13\n\nThe decision to administer general anaesthesia for dental treatment to this child came from the challenging behaviour exhibited on the dental chair. However, the successful completion of full-mouth rehabilitation helped us to focus on implementing preventive strategies. Given the diagnosis of global developmental delay, conventional oral hygiene practices were not feasible, which required the adoption of an innovative and modified preventive regimen. Structural and skeletal deformities associated with these conditions also affect the overall health and well-being of children with Hunter syndrome.\n\nCrucially, ongoing follow-up for such cases is imperative due to reported cases of associated jaw lesions, reminiscent of dentigerous cysts.14,15 Monitoring, particularly during the second to fourth decades of life, is essential. Recognising these lesions, particularly those associated with unerupted first permanent molars containing pools of chondroitin sulphate B, is significant. Their tendency to worsen with age underscores the need for vigilance and early interventions. The key takeaway is that as paediatric dentists, a comprehensive approach is crucial, particularly for children with syndromes such as Hunter syndrome. Recognising and addressing unique challenges and collaborating across disciplines improve dental care and contribute to overall well-being.\n\n\nConsent\n\nEthical approval was waived for this case report as it does not involve experimental interventions. Patient consent for publication, including written consent for clinical details and images, was obtained from the patient’s father, with confidentiality preserved.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nWe express our appreciation to the entire team involved in this operation, including the general anaesthesia team, the Department of ENT, the Department of Paediatric Surgery, and dental assistants, for their exceptional dedication. We are also grateful to the patient and his parents for their cooperation.\n\n\nReferences\n\nBurton BK, Giugliani R: Diagnosing Hunter syndrome in pediatric practice: practical considerations and common pitfalls. Eur. J. Pediatr. 2012; 171: 631–639. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDowns AT, Crisp T, Ferretti G: Hunter’s syndrome and oral manifestations: a review. Pediatr. Dent. 1995; 17: 98–100. PubMed Abstract\n\nMartin R, Beck M, Eng C, et al.: Recognition and Diagnosis of Mucopolysaccharidosis II (Hunter Syndrome). Pediatrics. 2008; 121: e377–e386. PubMed Abstract \| Publisher Full Text\n\nEisengart JB, King KE, Shapiro EG, et al.: The nature and impact of neurobehavioral symptoms in neuronopathic Hunter syndrome. Mol. Genet. Metab. Rep. 2020; 22: 100549. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKonuk Sener D, Aydin M, Cangur S, et al.: The Effect of Oral Care with Chlorhexidine, Vitamin E and Honey on Mucositis in Pediatric Intensive Care Patients: A Randomized Controlled Trial. J. Pediatr. Nurs. 2019; 45: e95–e101. PubMed Abstract \| Publisher Full Text\n\nFarsad-Naeimi A, Asjodi F, Omidian M, et al.: Sugar consumption, sugar sweetened beverages and Attention Deficit Hyperactivity Disorder: A systematic review and meta-analysis. Complement. Ther. Med. 2020; 53: 102512. PubMed Abstract \| Publisher Full Text\n\nVossoughi M, Eskandari R, Bakhtiar M: Oral health behaviours and cariogenic food consumption in children with attention-deficit/hyperactivity disorder: a cross-sectional study. Can. J. Dent. Hyg. 2023; 57: 109–116. PubMed Abstract\n\nHaukioja A: Probiotics and Oral Health. Eur. J. Dent. 2010; 4: 348–355. PubMed Abstract \| Publisher Full Text\n\nAnsari F, Neshat M, Pourjafar H, et al.: The role of probiotics and prebiotics in modulating of the gut-brain axis. Front. Nutr. 2023; 10: 1173660. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNishide S, Yoshihara T, Hongou H, et al.: Daily life habits associated with eveningness lead to a higher prevalence of dental caries in children. J. Dent. Sci. 2019; 14: 302–308. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCoulthard JD, Pot GK: The timing of the evening meal: how is this associated with weight status in UK children? Br. J. Nutr. 2016; 115: 1616–1622. PubMed Abstract \| Publisher Full Text\n\nBradley LA, Haddow HRM, Palomaki GE: Treatment of mucopolysaccharidosis type II (Hunter syndrome): results from a systematic evidence review. Genet. Med. 2017; 19: 1187–1201. PubMed Abstract \| Publisher Full Text\n\nDivatia JV, Bhowmick K: Complications of endotracheal intubation and other airway management procedures.2005.\n\nDowns AT, Crisp T, Ferretti G: Literature Review Hunter’s syndrome and oral manifestations: a review.\n\nZhang LL, Yang R, Zhang L, et al.: Dentigerous cyst: a retrospective clinicopathological analysis of 2082 dentigerous cysts in British Columbia, Canada. Int. J. Oral Maxillofac. Surg. 2010; 39: 878–882. PubMed Abstract \| Publisher Full Text" }	[ { "id": "271448", "date": "21 May 2024", "name": "Vivek Padmanabhan", "expertise": [ "Reviewer Expertise Pediatric Dentistry" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article provides a comprehensive overview of Hunter syndrome, emphasizing its clinical manifestations, diagnostic challenges, and the interdisciplinary approach required for effective management, with a focus on dental care. Here's a constructive review of the article:\nClarity and Depth of Information: The article effectively communicates complex medical concepts in a clear and understandable manner. It provides detailed information about the clinical manifestations of Hunter syndrome, including both systemic and oral manifestations, which enhances the reader's understanding of the disorder.\nRelevance and Significance: The article highlights the importance of recognizing Hunter syndrome as a rare genetic disorder with significant implications for both systemic health and oral health. It emphasizes the need for genetic counselling and interdisciplinary collaboration in managing the condition, which adds value to the medical literature.\nCase Presentation and Analysis: The case report presented in the article offers valuable insights into the challenges encountered in providing dental care to a child with Hunter syndrome. It effectively illustrates the diagnostic process, treatment interventions, and outcomes, providing practical information for healthcare professionals involved in similar cases.\nMultidisciplinary Approach: The article appropriately emphasizes the importance of a multidisciplinary approach in managing Hunter syndrome, particularly in cases requiring dental rehabilitation under general anaesthesia. It discusses the collaboration between departments such as Pediatrics, Otolaryngology, and Pediatric Surgery, underscoring the holistic care provided to the patient.\nClinical Insights and Recommendations: The article provides valuable clinical insights into the challenges and considerations specific to dental care in patients with Hunter syndrome. It offers practical recommendations for dental interventions, home care routines, and long-term follow-up, which are useful for healthcare professionals involved in the care of such patients.\nLimitations and Future Directions: While the article provides a comprehensive overview of Hunter syndrome and its management, it could benefit from discussing potential limitations of the presented case report, such as the generalizability of the findings to other patients with Hunter syndrome. Additionally, suggestions for future research directions or areas for further investigation would enhance the article's contribution to the field.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "271443", "date": "28 May 2024", "name": "Raghavendra Shetty", "expertise": [ "Reviewer Expertise Pediatric dentistry", "AI in pediatric dentistry" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case report describes the successful management of a child with Hunter syndrome (MPS II) who suffered from severe dental problems and is very well written. The article gives holistic dental care for a child with Hunter syndrome. It involves the collaborative approach involving multiple departments including the Department of Otolaryngology, which performed endoscopic adenoidectomy, and the Department of Paediatric Surgery, which performed an umbilical and right inguinal herniotomy. The holistic approach to dental care is illustrated very well. Strengths:\nDescribes the importance of dental care for children with Hunter syndrome. Provides a detailed account of the challenges associated with dental treatment in such patients, including behavioural issues and underlying physiological factors. Emphasizes the benefits of holistic dental care, potentially including full-mouth rehabilitation under general anaesthesia in severe cases. Showcases the positive impact of successful treatment on the child's oral health and potentially, their overall quality of life. Highlights The report highlights the need for collaboration between pediatric dentists and other healthcare professionals, such as pediatricians, pediatric surgeons and otolaryngologists, to ensure comprehensive care for children with Hunter syndrome. Future research could explore effective behaviour management strategies specifically tailored to children with Hunter syndrome undergoing dental treatment.\nOverall, this case report offers a valuable contribution by underlining the crucial role of dental care in managing Hunter syndrome and improving the well-being of affected children.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-268
https://f1000research.com/articles/13-267/v1	15 Apr 24	{ "type": "Case Report", "title": "Case Report: Impression Making for Flabby Ridge: An Innovative Approach", "authors": [ "Padmashini Gnanam", "Siddharthan Selvaraj", "Patmeni Kumarasan", "Satish Vasanth Dhandapani", "Padmashini Gnanam", "Patmeni Kumarasan" ], "abstract": "A flabby ridge is an area of mobile soft tissue found superficially, which affects both maxillary and mandibular alveolar ridges. It is a common finding in long term denture wearers, where the rate of bone resorption is very fast leading to development of hyperplastic soft tissue over the alveolar bone. Fabricating a denture over the flabby ridge poses a problem to the dentist because masticatory forces can displace this mobile denture-bearing tissue, leading to altered denture positioning and loss of peripheral seal. Forces exerted during the act of impression making can result in distortion of the mobile tissue leading to ill-fitting dentures. All these factors compromise the retention, stability, and support of the complete denture. This paper presents a case report for a patient with Kelly’s Combination Syndrome, wherein, an innovative impression technique was used to record the flabby ridges during the process of denture construction. The resultant denture was more comfortable for the patient and did not exert undue pressure over the hypermobile tissues.", "keywords": [ "Flabby Ridge", "Edentulous Patients", "Prosthodontics", "Rehabilitation" ], "content": "Introduction\n\nThe main aim of complete denture prosthodontics is to rehabilitate the patient’s missing teeth and adjacent bone by providing a stable prosthesis, which in turn restores function, esthetics and comfort in the patient. Jacobson and Krol have clearly stated that retention, stability, and support are the paramount factors which determine the success of complete denture prosthesis.1\n\nThe restoration of the dento-maxillary system functions by complete denture prosthesis depends on the correct evaluation of the balance between the positive and negative elements of the support areas, the suction areas and the neutral ones in the edentulous prosthetic fields.2\n\nIdeally, the alveolar ridge should be covered by masticatory mucosa of 1.5 – 2 mm thickness for adequate soft tissue support for the denture.3,4\n\nThe Glossary of Prosthodontic Terms defines flabby ridge as excessive movable tissue.5 In everyday language, flabby ridge can be described as the mobile soft tissue present over the remaining residual alveolar ridge.6\n\nMassad and Lobel have classified flabby tissues based on their displaceability7\n\n1. Low displaceability\n\n2. Average clinically acceptable displaceability\n\n3. High displaceability\n\nAmong the three classes, highly displaceable tissues are difficult to treat.7 Among the various etiological factors proposed by Desjardin and Tolman,4 bone resorption, excessive atrophy of alveolar bone, nutritional deficiencies, improper forces were considered detrimental for flabby ridge development. Lynch and Allen in 20048 and Kelly in 19729 reported that flabby ridges mainly result from clinical situations where the edentulous ridge is opposed by remaining natural teeth. Many studies indicate that the prevalence of flabby ridges occurs up to 24% of edentulous maxilla and in 5% of edentulous mandible.10\n\nEllsworth Kelly in 19729 reported a peculiar condition where flabby ridge was present in the anterior maxilla due to presence of mandibular anterior teeth. He explained that the remaining teeth generated excessive trauma to maxillary anterior ridge as all the forces of mastication are directed on to this area.\n\nLammie explained the mechanism behind this by showing that the compressive and rotational forces generated by the remaining mandibular teeth are transmitted to the maxilla causing resorption of underlying alveolar bone.11\n\nKelly showed that this specific pattern of bone resorption in the anterior maxilla is then followed by hyperplasia of the fibrous tissue overlying the bone.9\n\nKelly named this condition as Combination Syndrome, as it was associated with other typical features such as extrusion of remaining mandibular anterior teeth, palatal papillary hyperplasia, down growth of maxillary tuberosity and bone loss in the mandibular posterior region.9\n\nLammie iterated that in clinical conditions of complete maxillary edentulousness opposing mandibular Kennedy Class 1 or 2 situations, combination syndrome is more likely to occur when rehabilitation is done only by a single maxillary complete denture.11\n\nRetention, stability, and support is compromised in complete dentures when flabby tissues are present.3 Constant movement of tissues under the denture causes loss of peripheral seal which results in compromised denture retention.1,6\n\nSupport for the complete dentures is jeopardized if the flabby ridge shows more than 2 mm displaceability under stress.12\n\nIn the past 45 years, there have not been many advancements and innovations in the materials and techniques used for fabricating acrylic dentures for completely edentulous patients.2\n\nWith the current knowledge, materials and techniques available, fabrication of a retentive maxillary acrylic denture for such patients is an onerous challenge. Many techniques have been proposed for management of flabby ridges.8\n\nThe commonly used techniques can be divided into:\n\n1. Surgical method – removal of flabby ridge through scalpel surgery or by injecting a sclerosing agent6\n\n2. Surgical ridge augmentation – bone grafts are placed to augment the residual alveolar ridge.1,4,6,9,8\n\n3. Implant-prosthetic management – making of overdentures after bone augmentation and implant placement.2\n\n4. Prosthetic methods such as modifications in impression techniques, balancing the occlusal load are frequently done to manage flabby tissues.6,13,14\n\n5. CAD-CAM technology – with the advent of computerized technique for fabricating complete dentures, the dentist can virtually check the occlusal contacts, select the type of occlusion and also choose the direction of force distribution, making the difficulties faced with flabby mucosa a thing of the past.2\n\nAmong the methods described modifications in impression making have captivated the minds of prosthodontists since the 1900s. Two schools of thought have been proposed for recording flabby tissues. Most of the clinicians advocated the compressive technique of impression making. However, after the 1930s, the scenario slowly began to change with many clinicians favoring the static philosophy of impression recording.1\n\nThere have been various static methods discussed in literature over the years. These include use of spacers or perforations in the impression trays, use of detachable impression trays, scraping of impression trays.15\n\nThe principles of making a good impression which are sought after by prosthodontists include recording the complete area of the maxilla/mandible, recording of peripheries, achieving valve seal without interfering with function, accurate adaptation without causing injurious displacement of underlying tissue.16\n\nThere are three philosophies of impression making. They include mucocompressive (displacive, entire denture bearing tissues are displaced), mucostatic (non-displacive, denture bearing tissues are not displaced) and selective pressure impression (denture bearing tissues are selectively displaced).8,17,18\n\nFor recording flabby tissues, considerations must be taken for the difference in displaceability shown by the flabby tissue and the rest of the arch. Several modifications have been reported in literature which includes double spacers, multiple relief holes, or a window where the flabby tissue is located.12,19–23\n\nWatson in 1970 proposed a window impression technique. In this technique, a window was created in the custom tray over the flabby tissues. The flabby tissues were recorded using a mucostatic material (impression plaster) and zinc-oxide eugenol impression paste was used for the rest of the healthy denture bearing area.24\n\nIn our case report, we wish to demonstrate a modification in the technique of impression making for a patient with flabby ridge in the anterior maxillary region.\n\n\nCase report\n\nA 65-year-old female patient reported to our clinic at the Faculty of Dentistry, AIMST University with a complaint of ill-fitting maxillary complete denture from a year.\n\nOn intra-oral examination, an edentulous maxillary arch with severely displaceable anterior flabby ridge was observed. This was opposed by teeth in anterior region of the mandible. A few posterior teeth were missing. There was a down growth of both maxillary tuberosities. The mandible in the posterior region showed resorption of bone. By the presence of the following factors, it was diagnosed as the starting stage of Kelly’s combination syndrome. A treatment plan was formulated for this patient (Figure 1).\n\nA treatment plan was formulated to provide the patient with a new maxillary conventional complete denture and a mandibular partial denture.\n\nTo record the flabby tissues at rest position, a special window impression technique for the definitive impression was designed.\n\nOn the first appointment, primary impressions of the maxilla and mandible were made using alginate (Zelgan, Dentsply) material and edentulous stock trays.\n\nFollowing this, the impressions were poured with dental stone (Dental stone, Type III, Kulzer). In the maxillary cast, the flabby ridge area was marked, followed by fabrication of a specialized custom tray (Figure 2).\n\nSteps for fabrication of custom tray:\n\n1. A wax spacer (Metrowax, England) was adapted over the maxillary cast. Extra layer of spacer was added over the flabby ridge portion. This will ensure relief over the area.\n\n2. Light cure polymethyl methacrylate sheet (Shandong Huge Dental Material Corp., China) was adapted over the spacer. The extent of the flabby ridge was marked on the cast.\n\n3. Corresponding to that marking, an anterior window was outlined on the tray material using a sharp knife. This was done before curing to facilitate removal of the window at a later stage.\n\n4. Two posterior handles were fabricated over the premolar region on both sides.\n\n5. The light cure resin sheet was cured\n\n6. A thermoplastic vacuum resin sheet of 0.5 mm thickness was adapted over the tray. The excess was cut off with sharp scissors to fit the tray exactly.\n\n5- The light cure anterior window was removed. The resultant tray had only thermoplastic resin sheet covering the anterior flabby region with space in between for passive placement of impression material.\n\nOn the secondary impression appointment, the tray was tried in the patient’s mouth. The borders were trimmed to be 2 mm shorter than the depth of sulcus. The extent of the anterior window to the extent of the flabby ridge was confirmed (Figure 3).\n\nBorder molding was performed using green stick compound (Tracing Sticks, Kemdent, England) by the conventional technique. Following the border molding, a secondary impression of the maxilla was made using light body PVS impression material (Panasil Initial Contact Light, Kettenbach GmbH, Germany). The outline of the flabby ridge was marked in the patient’s mouth using an indelible marker. After careful inspection of the impression, the impression was reseated in the mouth to transfer the markings onto the impression surface. This facilitated easy removal of the light body from the area of flabby ridge using a scalpel blade (Figure 4).\n\nThree holes were made over the anterior region on the thermoplastic resin sheet. The impression was re-seated in the patient mouth. Alginate (Chroma 1, Dentapex, Italy) was mixed in a fluid consistency and loaded into a wide bore syringe. Alginate material was injected through one of the side holes until the entire space was filled with the material and some excess material overflowed through the other holes. Once the material was set, the tray was carefully removed and disinfected (Figure 5).\n\nFor the mandibular arch, conventional border molding was done by open tray technique and impression was made using Zinc oxide eugenol impression paste (Impression Paste, SS White, The Netherlands) and a pickup impression was made using a stock tray and alginate impression material.\n\nMaster casts were poured from the upper and lower impressions. Denture bases and occlusal rims were fabricated for jaw relation procedure. Vertical dimension and centric jaw relation was recorded. The teeth setting was done after articulation of the casts. Following try-in, a maxillary conventional complete denture and a mandibular partial denture was issued to the patient. That patient was comfortable with the denture and satisfied with the esthetics and function (Figure 6).\n\n\nDiscussion\n\nThe key to a successful denture treatment lies in making an accurate impression of the edentulous ridge and functional sulcus. The presence of flabby tissues compromises the retention and stability of the denture. This occurs due to the elastic recoil of the fibrous soft tissues of the flabby ridge during function.6,25 In selective pressure technique, the tissues are compressed during impression making. Using the conventional technique for flabby ridges will lead to compression of the flabby portion also. Fabricating a denture over compressed flabby tissue will lead to compromised retention and stability causing frequent dislodgement of the denture.\n\nSeveral impression techniques and methods have been described in the literature for recording flabby tissue during impression making. However, there is no evidence to support that one impression technique will provide a stable and retentive denture on flabby ridges as compared to others.17 This report presents an innovative window technique for the impression of anterior maxillary flabby ridge using PVS impression material and alginate.\n\nThere have been various studies in literature to make the impression of the entire arch along with the peripheral seal followed by preparation of window and recording the displaceable tissues with a low viscosity impression material.17 On the other side of the coin, some authors have suggested that a custom tray with a window must be made prior to border molding to allow for accurate peripheral tracing of the functional sulcus and improved final impression. The displaceable tissues should be recorded in a static position through the window after final impression.8\n\nThe main disadvantage of these techniques is the inability to control the uniform application of the low viscosity impression material. This mainly arises due to difference in the chair positions and the fact that gravity can cause the impression material to flow downwards (maxillary arch).\n\nThe various materials that can be used to record the flabby tissues are impression plaster, light body PVS, impression waxes and alginate. These materials provide a mucostatic impression of the displaceable tissue. For the rest of the arch, a multitude of impression materials are available, namely zinc oxide eugenol, heavy body PVS, light body PVS etc. These materials record the tissues in a mucocompressive state.\n\nIn the technique described in the article, the use of clear polyethylene sheet helped the clinician to see the flow of the impression material and the adaptation of the impression to the flabby ridge. The clear sheet also acted as a scaffold to hold and prevent the impression material from drooping down, away from the tissue. Furthermore, in this technique, the operator was able to control the amount of material flowing on to the flabby ridge. No pressure was exerted over the thermoplastic resin sheet. Presence of extra vents caused overflow of the excess material, hence there was no shortage of material in the impression.\n\nThe initial cutting of the anterior window prior to curing allowed for easy removal of the window. Therefore, the authors recommend clinical application of this window technique for final impression of flabby maxillary ridge in the fabrication of complete dentures.\n\n\nSummary\n\nThe modified window technique described in this report demonstrates an easy and effective way to control the amount of pressure applied on the flabby tissues. The tray is easy to fabricate, and the procedure is not cumbersome. This method can also be used with other materials such as impression plaster, which can be poured through the venting holes. Impressions can also be made using a combination of heavy body PVS for the secondary impression and light body PVS to record the flabby tissues.\n\nEthical approval was waived for this case report.\n\nWritten consent was obtained from the study participant, consent to publish the details has been obtained and anonymization done.", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\n\nReferences\n\nBindhoo YA, Thirumurthy VR, Kurien A: Complete mucostatic impression: a new attempt. J. Prosthodont. 2012 Apr; 21(3): 209–214. PubMed Abstract \| Publisher Full Text\n\nŞtefănescu CL, Zaharia A, Murineanu RM, et al.: Flabby Ridge, a Challenge for Making Complete Dentures. Appl. Sci. 2021 Aug 11; 11(16): 7386. Publisher Full Text\n\nLabban N: Management of the flabby ridge using a modified window technique and polyvinylsiloxane impression material. Saudi Dent. J. 2018 Jan 1; 30(1): 89–93. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPark SY, Yun Y, Park C, et al.: Integration of an intraoral scan and a conventional impression for fabricating complete dentures for a patient with flabby tissues. J. Prosthet. Dent. 2023 Jan 5. PubMed Abstract \| Publisher Full Text\n\nGlossary of Prosthodontic Terms. J. Prosthet. Dent. 2005; 94: 10–92. Publisher Full Text\n\nPai UY, Reddy VS, Hosi RN: A single step impression technique of flabby ridges using monophase polyvinylsiloxane material: a case report. Case Rep. Dent. 2014 Apr 27; 2014: 1–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAntonelli J, Guerrero M, Georgescu M, et al.: Quantifying flabby ridge tissue displacement during impression-making for patients with combination syndrome. Compend. Contin. Educ. Dent. 2019 Sep; 40(8).\n\nShin JO, Ko KH, Huh YH, et al.: Displacement of simulated flabby tissue by different tray designs and impression materials. J. Prosthodont. 2019 Apr; 28(4): 444–451. PubMed Abstract \| Publisher Full Text\n\nBagga R, Robb ND, Fenlon MR: An investigation into the prevalence of combination syndrome. J. Dent. 2019 Mar 1; 82: 66–70. Publisher Full Text\n\nIkbal M, Dammar I, Mude AH, et al.: Window impression technique for a single denture with maxillary anterior flabby ridge. J. Case Rep. Dent. Med. 2019 May 1; 1(2): 40–42. Publisher Full Text\n\nLammie GA: The reduction of the edentulous ridges. J. Prosthet. Dent. 1960; 10: 605–611. Publisher Full Text\n\nLi J, Sommer C, Wang HL, et al.: Creating a virtual patient for completely edentulous computer-aided implant surgery: A dental technique. J. Prosthet. Dent. 2021 Apr 1; 125(4): 564–568. PubMed Abstract \| Publisher Full Text\n\nSrivastava S, Mishra S, Chopra D: Modified Tray with Mesh Design for the Management of Flabby Ridge: A Case Report. Front. Dent. 2019 Mar; 16(2): 149–152. PubMed Abstract \| Publisher Full Text\n\nLiddelow KP: The prosthetic treatment of the elderly. B. Dent. J. 1964; 117: 9.\n\nMattoo KA, Kumar L, Rehman SU: Flabby Ridge Management Using Paint on Technique - Meticulous Review. JMSCR. 2019; 7(10): 518–521. Publisher Full Text\n\nMattoo KA, Goswami R, Yunus N, et al.: Prosthetic Management of Flabby Hyperplastic Edentulous Ridge Tissue Using Different Clinical Impression Techniques–A Critique Case Series.\n\nZarone F, Ruggiero G, Di Mauro MI, et al.: Accuracy of three impression materials on the totally edentulous maxilla: in vitro/in silico comparative analysis. Materials. 2020 Jan 22; 13(3): 515. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHakeem AA, Shah SA, Shazana Q, et al.: Management of the flabby ridge using a window technique with monophase polyvinyl siloxane elastomeric impression material.\n\nDadarwal A, Paliwal J, Sharma V, et al.: Microstrain Analysis of Selective Pressure Techniques for Mandibular Complete Denture Impression: An in vivo Study. Cureus. 2022 Mar 31; 14(3). Publisher Full Text\n\nHong SJ, Lee H, Paek J, et al.: Combining conventional impressions and intraoral scans: a technique for the treatment of complete denture patients with flabby tissue. J. Prosthodont. 2019 Jun; 28(5): 592–595. PubMed Abstract \| Publisher Full Text\n\nMostafa AZ, Alanazi SM, Almarshedy SM: Custom double tray for a special impression technique for flabby maxillary residual ridge: Case report. Clin. Case Reports. 2022 Mar; 10(3): e05593. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBhochhibhoya A, Rana SB, Sharma R, et al.: Impact of sociodemographic factors, duration of edentulism, and medical comorbidities on the mental attitudes of individuals with complete edentulism. J. Prosthet. Dent. 2021 May 19; 128: 1283–1288. Publisher Full Text\n\nYamazaki F, Mihara Y, Maeda Y, et al.: Determination of the lingual border of lower complete dentures: How to use a silicone impression material? J. Oral Rehabil. 2020 May; 47(5): 613–619. PubMed Abstract \| Publisher Full Text\n\nAbdelbagi NF: Comprehensive Prosthodontic Treatment of an Elderly Patient with Compromised Ridges: A Clinical Case Report. J. Oral Res. 2021 Oct 31; 10(5): 1–1, 11. Publisher Full Text\n\nYadav M, Sardar C, Mistry G, et al.: Flabby tissue-revisited: case report. Int. J. Appl. Dent. Sci. 2021; 7: 82–85. Publisher Full Text" }	[ { "id": "273608", "date": "31 May 2024", "name": "Mohamed Zahoor Ul Huq", "expertise": [ "Reviewer Expertise Dental Prosthesis", "Bio-Materials", "application of new methods and Dentofacial orthopedics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe case report is well-written and needs some minor corrections.\n1. The discussion needs to elaborate. Please provide a few more studies about Flabby Ridge in the discussion section.\n2. The reference no.18 is not in the format as per the reference format guidelines. Kindly correct the reference format.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "278854", "date": "08 Jun 2024", "name": "Ricca Chairunnisa", "expertise": [ "Reviewer Expertise Prosthodontics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPlease add:\nIn the case history/ examination: - Medical history - Radiographic examination (showing severe resorption in the anterior part of maxillary alveolar ridge) - How long have the maxillary dentures been worn? - How long have the lower jaw posterior teeth been missing? - Examination of existing dentures (retention, adaptation, occlusion and articulation, cleanliness, artificial teeth, Occlusal scheme) - Patient's chewing habits\nIn treatment planning/ procedure: - Details in impression technique, how to achieve good final impression using alginate material without tray support and adhesive material. - Denture base design (flabby ridge is relieved or not) - Occlusal scheme choosen for this case to minimize occlusal force in the maxillary anterior alveolar ridge - Selection and arrangement of artificial teeth according to the occlusal scheme choosen - Type of lower partial denture\nIn the discussion: - The reason to choose non surgically treatment - The reason to those that mention in treatment planning (impression technique, denture base design, occlusal scheme, selection and arrangement of artificial teeth to overcome the problems) - It is mentioned that the impression technique was selective pressure which is combination of mucostatic (for flabby ridge) and mucocompressive (for other part of denture bearing area) technique. But the impression materials used (alginate and light body) are both mucostatic materials. Need more explanation how to get the selective pressure.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-267
https://f1000research.com/articles/13-264/v1	15 Apr 24	{ "type": "Software Tool Article", "title": "FAST a Digital Sales Transformation Software for the Real Estate Industry", "authors": [ "Victor Acosta", "Luis Garcia", "Alex Pacheco", "Luis Garcia", "Alex Pacheco" ], "abstract": "Nowadays, organisations are encountering ever-more challenging demands, and those that do not adapt risk closure. This trend is particularly notable in small and medium-sized enterprises, where deficits in technology adoption are often particularly conspicuous. Companies that succeed in streamlining their sales process are more likely to enjoy better outcomes, underlining the crucial requirement of implementing technical solutions to tackle these problems with optimal efficiency. Therefore, the aim of this investigation is to deploy a web-based system for the purpose of enhancing sales management in a company operating in the field of real estate and construction. The system was constructed utilising Extreme Programming XP methodology, consisting of four phases: planning (user stories), design (system outline), coding (system programming) and testing (testing). The introduction of a web-based system highly streamlined the company’s sales process, reducing information search times by 64% and decreasing time spent on recording sales data by 62%. The system enabled greater sales activity during the day, resulting in a 72% increase in task performance. It also aided the accounting department in streamlining revenue reporting. This demonstrates that the system is an efficient tool for enhancing the sales process, reducing yearly tasks, and minimizing recording time.", "keywords": [ "Systematization", "web systems", "sales management", "time", "agile methodologies" ], "content": "1. Introduction\n\nThe rapidly increasing production of data across a variety of social domains has created an pressing need for efficient tools that can precisely analyze and manage this information in a clear and understandable manner.1,2 At present, the manual handling of these operations has become intricate and prone to errors, necessitating a technological solution for centralised and real-time data control and visualisation.3 One solution is to develop a web-based system that enhances the efficiency of the sales process to a significant degree.4\n\nThis technology for business intelligence can integrate all data and intelige records of business transactions in a unified manner.5,6 It also offers a thorough and current overview of sales behaviour.7,8 Furthermore, the implementation of a system enables customised customer follow-up, resulting in heightened levels of customer satisfaction and loyalty.9 On the contrary, the provision of real-time reports and statistics will enhance managers’ capability to evaluate sales performance and boost customer contentment.10\n\nIn this context, web-based tools or systems present an appealing option for enhancing sales management.11 The approach aims to automate business processes, centralise information, and optimise customer service, with the goal of achieving substantial growth and success for the organisation.12 Furthermore, the implementation of integrated automation has the potential to notably diminish the burden of manual labour, leading to a heightened optimisation of accessible resources and a decrease in errors.13\n\nThe adoption of a web-based system using Open Source distribution tools facilitates comprehensive information management for corporations.14,15 It can offer swift, effortless, and gratifying services to enhance organizational sales.16 Furthermore, the company implemented a web-based system which enhanced the product registration process and subsequently boosted sales figures.5\n\nSeveral case studies indicate that incorporating a web-based system for sales management within a company enhances sales process efficiency and decision-making.17,18 Furthermore, there is robust, contemporary evidence concerning the particular correlation between this tool and its ability to enhance data visualisation and sales management within commercial projects.19–21\n\nThe purpose of this article is to evaluate the web-based sales management system’s effectiveness upon implementation in Titanio SAC. This will lead to the optimization of commercial processes and contribute to the company’s sustainable growth within the market. Moreover, the article aims to examine the system’s efficiency, taking into account factors such as information search times and sales process duration.\n\nThis study enhances the construction and real estate sector’s knowledge and development by presenting crucial insights into the implementation of a web-based sales management system, and its impact on construction businesses. The study’s results and conclusions, which promote efficiency, productivity, and informed decision-making, could potentially expedite and enhance company growth.\n\nThis article is divided into five sections, with the first section serving as the Introduction, where issues encountered by companies regarding sales and systematisation are presented. Section 2, known as the Method, provides a detailed account of the hardware and step-by-step procedure employed in developing the web system, using the project methodology. Section 3, named Results, involves the production of infographics to illustrate the working of the system and its interfaces. Section 4 of this study compares and analyses the findings with existing research and relevant theoretical frameworks. Subsequently, in Section 5, the author presents their conclusions on the benefits of their research and their recommendations for future studies.\n\n\n2. Methods\n\nIn this section, we describe the methods used in the development and operation of our software,22 a programme designed to improve decision making for micro and small enterprises in the real estate sector.\n\nA laptop equipped with an AMD Ryzen 9 5900HX processor, Radeon Graphics, Windows 11 Pro 64-bit OS (10.0, build 22621), and 16384MB of RAM was utilised. The website structure was constructed using the PHP 8 programming language whilst adhering to the MVC (Model View - Controller) design pattern and incorporating REST APIs for database communication.\n\nExtreme Programming (XP) was employed following 4 fundamental activities, which are carried out in accordance with the guidelines or stages (Figure 1).23–25\n\nThis figure has been reproduced with permission from Ref. 26.\n\n2.2.1 Planning phase: The system requirements were extracted by detailing all user stories according to the customer’s demands. The first requirement allows for the login and registration of users, including both administrators and salespeople. The second requirement facilitated the projects and the lots assigned to them, while the third requirement enabled the allocation of sales to the lots assigned to the said projects. The fourth requirement facilitated the assignment of payments to the sold lots, and the fifth requirement generated a report of the sold lots and the accounts receivable. It is crucial to note that in this phase, the participants were assigned certain roles showing in Figure 2.\n\n2.2.2 Design phase: The most relevant user stories have been selected and simplified for convenience. Furthermore, CRC (Class-Responsibility-Collaboration) cards will be created to enhance the system analysis effectively. Refer to the Figure 3 for an illustration:\n\n2.2.3 Coding phase: Technical abbreviations will be explained when first used. The website structure was developed using HTML tags, CSS for style, color, and box layout, and JavaScript for HTML object manipulation as shown in Figure 4. Additionally, the site incorporates various technologies such as Materialize CSS, which is a design framework based on Google’s Material Design, DataTables for managing data in tables, Select2 for adding search functionality in combo-boxes, and PDFMake for exporting reports. The language will remain objective and value-neutral, with a passive and impersonal tone. The text will adhere to correct grammar, spelling, and punctuation. Regular author and institution formatting will be maintained, using clear and concise language with precise technical terms. The text will avoid colloquial language and unnecessary jargon. Sentences and paragraphs will have a logical flow of information with causal connections between statements. Common academic sections will be included, with factual and unambiguous titles and hedging to maintain a balanced view. The web system operates using PHP 8 programming language, with the implementation of the MVC (Model View - Controller) design pattern. Additionally, MySQL version 10.0 is utilized as the database management system and the eschema is on Figure 5, and REST APIs are employed to transfer data between the view and controller.\n\n2.2.4 Testing phase: The system underwent unit-level testing to identify any code faults and improve its quality, and these tests were incorporated into the development process, which can be seen in Figure 6. Following this, supervised acceptance testing was conducted with the client to grant final approval to the application.\n\nDifferent features have been incorporated into this software compared to existing solutions available on the market:\n\n• Tailored to meet the requirements of small and medium enterprises in the real estate industry, our software is precisely tailored for micro and small firms in the sector to enhance management decision-making, conforming to their workflows and specific demands.\n\n• Customised options are available to users who can access reports to make queries on sales, outstanding targets, percentage progress of the sales project, and more.\n\nBy outlining the methodology and distinctive features, our software provides a comprehensive manual for the creation and adoption of the technology in small and micro real estate businesses, thus encouraging its ability to be replicated and emphasising its practicality.\n\n\n3. Use cases\n\nPreface: Data Initialization Process\n\nThe system’s data initialization process is executed automatically, in accordance with the installation procedures outlined in the “Readme.md” file, which can be found in the relevant repository.27\n\nUse case 1: Sales Report\n\nThe developed user interface has the ability to create project-specific reports on lots sold which include graphical representations of both sold and unsold lots, along with sales dates (Figure 7).\n\nInput:\n\n- Access to the “Reports” view.\n\n- Select the report batches per project.\n\nOutput:\n\n- Batch report by project.\n\nUse case 2: Dues receivable report\n\nThe interface presents a comprehensive list of lots with outstanding fees. The information displayed includes the due date, amount payable, as well as the contact details and name of the owner (Figure 8).\n\nInput:\n\n- Access to the “Report” view.\n\n- Select payments per Project.\n\nOutput:\n\n- Accounts receivable report.\n\nUse case 3: Sales register\n\nFor the sales process there is a list of sales in which the information of the sale is indicated, likewise the sellers can register the sales, where the buyer, the location, the project, lot and price are indicated; which can take about 2 minutes to complete (Figure 9).\n\nInput:\n\n- Access to sales.\n\n- Enter lot amount, owner and form of payment.\n\nOutput:\n\n- Register of Sales.\n\n- Payment schedule.\n\nUse case 4: Dashboard\n\nAfter the application has been developed, the user logs in and the main interface displays their dashboard. The dashboard includes a graph of projects with remaining lots to be sold, sorted from highest to lowest, and another graph displaying owners and their respective accumulated balances, sorted from highest to lowest, as depicted in Figure 10.\n\nInput:\n\n- Access to the “Dashboard” view.\n\nOutput:\n\n- Report of unsold lots by project.\n\n- Report of accumulated balances by owner.\n\n\n4. Discussion\n\nBased on the system’s evaluation, there has been a substantial decrease of around 64% in the duration spent exploring details in the sales process. This decline showcases a distinctive effectiveness in sales proceedings, which is an exceptional advantage for real estate enterprises. Additionally, previous research has demonstrated that streamlining the information search process enables organisations to provide a responsive, uncomplicated and fulfilling service, ultimately leading to increased sales.16 It is noted that a web-based enterprise sales management system not only improves the efficiency of sales processes, but also contributes to more effective decision making.17,18\n\nThe system design has been found to be extremely efficient in streamlining the process and considerably decreasing manual operations. Consequently, transaction recording time has been reduced by 62%. These findings are consistent with previous research,3,5,6,13 which observes that the introduction of a sales system streamlines customer service. Additionally, the findings align with previous research,4,9 indicating that utilizing the system results in enhanced processing times and an augmentation of sales.\n\nOne of the noteworthy features of our system is its sales interface, which allows for precise customer tracking and simplifies the recording and analysis of customer behaviour. This approach is in line with,14,15 who affirmed that analogous systems aid in personalised tracking of consumers. What’s more, the systems automate business records19–21 and ensure efficient control of information.10\n\nThe use of a dashboard has yielded dependable outcomes and enhanced supervision of process metrics and objectives, ensuring prompt delivery and efficient handling of tasks, transactions and documentation. Additionally, this tool features graphical interfaces to interact with databases, making it a vital component of business intelligence.28,29 Furthermore, it streamlines the decision-making process by enabling companies to efficiently visualise sales, time and product data.30–32\n\nTherefore, a web-based system proves to be a dependable approach for real estate companies that seek enhanced efficiency in their sales process. The system has shown high adherence to the established objectives by optimising the process and improving usability via the Dashboard, thereby promoting informed decision-making in the company.\n\n\n5. Conclusions\n\nThe implemented system has demonstrated its effectiveness in enhancing the sales process, reducing yearly tasks, and minimizing registration times.\n\nConsistent with previous research, these findings provide evidence of the significance of sales systems in optimising customer service and diminishing processing delays, resulting in augmented sales.\n\nThe execution of the sales interface has facilitated precise customer tracking and enhanced information administration, aligning with research emphasising the value of systems in personalised customer tracking and automation of business records.\n\nIt is advisable that future researchers employ alternative methodologies to determine whether equivalent outcomes can be achieved. Such methodologies may include Waterfall, Scrum or V Methodology.", "appendix": "Data availability\n\nZenodo: luisgarciaheredia. (2023). luisgarciaheredia/database: FAST a digital sales transformation software for the real estate industry (v1.0). Zenodo. https://doi.org/10.5281/zenodo.10071938. 27\n\nData are available under the terms of the Creative Commons Attribution 4.0 International (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe thank the Constructora e Inmobiliaria Titanio SAC for their strong support and help with this study. The authors would like to thank Alex Pacheco of the Faculty of Engineering and Architecture of Universidad Cesar Vallejo for his methodological advice on this study.\n\n\nReferences\n\nOchoa NE, Aparicio NI, García WH: Análisis de la Integración de las TIC en el sector empresarial de Santander a través de un Big Data. Alpha Centauri. mar. 2023; 4(1): 12–24. Publisher Full Text\n\nTownsend Valencia J, Figueroa Filián J: Digital transformation models in the management of commercial companies. COODES. 2022; 10(2): 407–429.\n\nSoledispa X, Álvares I, Baque A, et al.: Tecnologías de información y comunicación en la gestión empresarial de las pymes. Polo del Conocimiento. 2023; 4(1): 12–24.\n\nWengler S, Hildmann G, Vossebein U: Digital transformation in sales as an evolving process. J. Bus. Ind. Mark. may 2021; 36(4): 599–614. Publisher Full Text\n\nGarcía DDL, Hernández JS, Barral OP, et al.: Procedimiento para el cálculo y la mejora de la capacidad tecnológica en organizaciones empresariales. Revista Universidad y Sociedad. may 2021; 13(3): 382–390.\n\nIvonne Balanzategui-García RI, Elizabeth Ramírez-Salas AI, Susana Soto-Benítez V III, et al.: Procesos de sistematización de la gestión de contabilidad en las empresas industriales. Dominio de las Ciencias. sep. 2021; 7(5): 524–544. Publisher Full Text\n\nVanegas DA, Tarazona-Bermúdez GM, Rodríguez-Rojas LA: Mejora de la toma de decisiones en ciclo de ventas del subsistema comercial de servicios en una empresa de IT. Revista científica. may 2020; 38: 174–183. Publisher Full Text\n\nSantistevan-Villacreses KL, Sánchez-Chávez SB, Arias-Haro JL: Las plataformas digitales y su impacto en las ventas de las pequeñas empresa del cantón Pajón. Dominio de las Ciencias. feb. 2022; 8(1): 204–218. Publisher Full Text\n\nViteri-Cevallos CJ, Murillo-Párraga DY: Inteligencia de Negocios para las Organizaciones. Revista Arbitrada Interdisciplinaria Koinonía. jul. 2021; 6(12): 304–333. Publisher Full Text\n\nGuitarra Romero R: Prospectiva e Inteligencia Estratégica Aplicada a la Micro, Pequeña y Mediana Empresa. Tendencias. 2019; 20(1): 107–129. Publisher Full Text\n\nAlbarracín-Zambrano L, Ponce-Bravo JF, Hidalgo-Fernández MA, et al.: Sistema web adaptativo para mejorar la gestión de ventas en empresas. Cienciametria. dic. 2021; 7(2): 948–952. Publisher Full Text\n\nDuque Vaca MÁ, Rosero Miranda RH, Piñas Bonilla SP: Aplicación web para la gestión de pedidos e inventario de una empresa artesanal utilizando servicios web restful. Polo del Conocimiento. 2022; 7(8): 971–992. Publisher Full Text\n\nMejía-Neira Á, Jabba D, Carrillo-Caballero G, et al.: Influencia de la Ingeniería de Software en los Procesos de Automatización Industrial. Información Tecnológica. 2019; 30(5): 221–230. Publisher Full Text\n\nRivera Ramírez JG, Gonzabay de la A EE, Morán BMM, et al.: El uso del software de código abierto en el IoT. Ciencia Latina Revista Científica Multidisciplinar. nov. 2022; 6(6): 1704–1867. Publisher Full Text\n\nAdriano WG, Cuji DAG: Influencia del código abierto y su simplicidad en el desarrollo de sistemas web académicos. Revista Científica y Tecnológica UPSE. jun. 2023; 10(1): 10–18. Publisher Full Text\n\nLiu C: Development and Application of Sales System Software Based on Computer Network. Wirel. Commun. Mob. Comput. 2022; 2022: 1–7. Publisher Full Text\n\nMorelos Gómez J, Cardona Arbeláez D, Lora Guzmán H: Aproximación conceptual y teórica sobre las herramientas que permiten mejorar las prácticas y proceso de calidad en las empresas. Conocimiento global; Accedido: 21 de febrero de 2024. Reference Source\n\nMedina Chicaiza RP, Chango Guanoluisa M, Corella Cobos M, et al.: Transformación digital en las empresas: una revisión conceptual. J. Sci. Res. 2022; 7(1): 756–770. Publisher Full Text\n\nAcuña NC, Medina PAA: Características de la integración de las TIC en la gestión administrativa de las medianas empresas comerciales de la ciudad de Pilar, año 2022. Ciencia Latina Revista Científica Multidisciplinar. nov. 2022; 6(6): 1066–1083. Publisher Full Text\n\nAlmaguer Almaguer A, Malleuve Martínez A: El proceso de digitalización como una transformación organizacional: Clave de eficiencia y competitividad. Revista Cubana de Transformación Digital; Accedido: 21 de febrero de 2024. Reference Source\n\nDudin MN, Afanasyev VV, Voropaev MV, et al.: Estado y problemas de digitalización de la gestión de universidades en Rusia y en tres países latinoamericanos (Argentina, Chile y Brasil). Formación Universitaria. 2020 dic; 13(6): 61–76. Publisher Full Text\n\nGarcia L, Acosta V, Pacheco A: FAST a digital sales transformation software for the real estate industry. Universidad Cesar Vallejo; [Software]. Publisher Full Text\n\nMolina-Ríos JR, Honores-Tapia JA, Pedreira-Souto N, et al.: Comparativa de metodologías de desarrollo de aplicaciones móviles. 3C Tecnología. Glosas de innovación aplicadas a la pyme. 2021; 10(2): 73–93. Accedido: 21 de febrero de 2024. Reference Source\n\nBautista-Villegas E: Metodologías agiles XP y Scrum, empleadas para el desarrollo de páginas web, bajo MVC, con lenguaje PHP y framework Laravel. Revista Amazonía Digital. 2022; 1(1): e168. ene. Publisher Full Text\n\nHuayta Meza FT, Pachecho Moscoso LE, Aquino Sinche N: Sistema de seguimiento de egresados de la Facultad de Ingeniería Electrónica - Sistemas de la Universidad Nacional de Huancavelica, sede Pampas. GnosisWisdom. may 2021; 1(2): 02–12. Publisher Full Text\n\nCarrasco Gonzaga MK, Ocampo Pazos WJ, Ulloa Meneses LJ, et al.: Metodología híbrida de desarrollo de software combinando XP y SCRUM. Mikarimin. Revista Científica Multidisciplinaria. 2019; 5(2).\n\nAcosta V, Garcia L, Pacheco A; FAST a digital sales transformation software for the real estate industry. [Dataset]. Universidad Cesar Vallejo. Publisher Full Text\n\nPaz IIC, Coral MAV: Dashboard digital para el monitoreo de indicadores y metas de los proyectos de consultores San Martín E.I.R.L. Revista Científica de Sistemas e Informática. 2021; 1(1). ene. Publisher Full Text\n\nTherón Sánchez R: «Data visualization: pathways between art and science in the production and consumption of images. Fonseca. J. Commun. nov. 2021; 23(1): 39–60. Publisher Full Text\n\nCoaboy EG, Jumbo JC: Plataformas de visualización de datos tolerantes a fallos por medio de MongoDB. Revista Científica Ecociencia. abr. 2021; 8(2): 45–70. Publisher Full Text\n\nPérez Quintero J, Alonso Ramírez L, Montané Jiménez LG, et al.: VisCFDI: Aplicación web interactiva para visualización y análisis de datos de facturas electrónicas en México. Revista de Investigación en Tecnologías de la Información. jun. 2023; 11(23): 82–97. Publisher Full Text\n\nCajas JM, Chicaiza DK, Álvarez ML, et al.: Desarrollo de un sistema BI Inteligencia de Negocios para la toma de decisiones gerenciales: Caso práctico empresa CTLSPORTS. Revista Académica y Científica VICTEC. 2023; 4(6). Accedido: 21 de febrero de 2024. Reference Source" }	[ { "id": "268541", "date": "23 May 2024", "name": "Jansen Wiratama", "expertise": [ "Reviewer Expertise Information Systems Analysis and Design", "User Experience", "Human and Computer Interaction", "Software Engineering." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. According to the UML basic theory (ref: Systems Analysis and Design, Alan Dennis, Barbara, 2020), XP is one of the models from Agile Methodology, yet this paper calls it a Methodology. I recommend revising the words XP as Methodology into a Model.\n2. Please provide the Use Case Diagrams and Activity Diagrams.\n3. There is no testing based on the FAST app/software, yet in the abstract, there's a claim to reduce information search times by 64% and decrease time spent recording sales data by 62%. The system enabled more excellent sales activity during the day, resulting in a 72% increase in task performance. Please provide the testing table in the discussion section. I want to recommend usability testing for this FAST app/software.\n5. The advice for future research is that including waterfall is not wise because the waterfall model is unsuitable for the kind of application that is developed quickly (Just like FAST). Additionally, once again, Waterfall, Scrum, and V Models are not at Methodology, but Models from SDLC Methodology.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [] }, { "id": "285959", "date": "22 Jul 2024", "name": "Anggraini Sukmawati", "expertise": [ "Reviewer Expertise strategic human resource management", "talent management", "organizational transformation", "leadership" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nA manuscript with an interesting idea and the potential to provide valuable benefits to SMEs, especially those in the real estate sector. The authors should explain how the sales business process in the small and medium scale real estate industry currently exists, and at which stages simplification or savings can be made with the FAST software built by the authors. The authors should develop a robust argument why the performance indicators of the FAST software are chosen: information search times and decreasing time spent on recording sales data for increase in task performance. It is necessary to add an explanation of the calculation methods to prove that there is a reduction in information search times by 64% and decreasing time spent on recording sales data by 62% so as to obtain an increase in task performance of 72% as claimed by the authors.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [] }, { "id": "285962", "date": "29 Jul 2024", "name": "Ari Apriani", "expertise": [ "Reviewer Expertise Marketing management and digital business" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article in question explores developing and implementing a new application to improve task performance within the real estate industry. This research is highly relevant given the rapid technological advancements and the increasing reliance on digital solutions in various industries. It addresses the need for more efficient tools in the real estate sector, which can significantly enhance operational performance and customer satisfaction.\n\n1. In the background, it is necessary to explain the real estate industry data (quantitatively) that serves as a reference for why this application needs to be developed, so that the problems become clear and this application becomes the right solution. It is essential to provide quantitative data about the real estate industry to establish a strong foundation for the development of the application. This will help readers understand the existing challenges in the industry and how the application can serve as a viable solution. Detailed statistics and trends can highlight the urgency and importance of this technological intervention.\n\n2. Please add a use case diagram of the system to this application, so that readers can see how the application being developed will be used. Including a use case diagram would greatly enhance the reader's understanding of how the application functions and is utilized within the industry. This visual representation can illustrate user interactions and system processes, making the application’s practical implications clearer. 3. The achievements resulting from the implementation of this application should be explained by comparing the data before and after using the application. For instance, if it is stated that task performance increased by 72%, what was the performance percentage before? The article mentions an improvement in task performance by 72%. It is crucial to provide comparative data showing performance metrics before the implementation of the application. This comparison will substantiate the claims of improvement and offer a clearer picture of the application's impact. 4. In the suggestions, it is necessary to reconsider the appropriate methods for future research. In the suggestions for future research, it would be beneficial to reconsider and possibly expand on the methodological approaches. This could involve exploring alternative research methods or additional data collection techniques to strengthen the validity and reliability of the findings.\nOverall, the article presents a promising solution to a relevant problem in the real estate industry. By incorporating the suggested quantitative data, use case diagrams, and comparative performance metrics, the authors can provide a more robust and convincing argument for their application. Additionally, refining the methodological considerations and ensuring clarity in presentation will further strengthen the article.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-264

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.